Split (3)

train · 24.8k rows

headings list	keywords list	title stringlengths 20 281	id stringlengths 20 20	toc stringlengths 57 522 ⌀	sections list	abstract list	summary list	year stringclasses 13 values
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "mechanisms of signal transduction", "applied mathematics", "membrane potential", "brain electrophysiology", "electrophysiology", "random variables", "neuroscience", "covariance", "epileptic seizures", "algorithms", "simulation and modeling", "clinical medicin...	Seizure pathways: A model-based investigation	journal.pcbi.1006403	null	[ [ "Understanding how and why the brain generates spontaneous seizures is an unsolved problem in neuroscience .", "The medical implications of seizures are profound , with over 50 million people affected by epilepsy , and at least 30% not adequately controlled by available therapies [1] .", "Surgical tre...	[ "We present the results of a model inversion algorithm for electrocorticography ( ECoG ) data recorded during epileptic seizures .", "The states and parameters of neural mass models were tracked during a total of over 3000 seizures from twelve patients with focal epilepsy .", "These models provide an estimate o...	[ "A fundamental question in clinical neuroscience is how and why the brain generates epileptic seizures .", "To address this problem it is important to unify theoretical models of seizure mechanisms with clinical data .", "This study investigated a large database of human epileptic seizure recordings .", "Mode...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Synaptic Homeostasis and Restructuring across the Sleep-Wake Cycle	journal.pcbi.1004241	null	[ [ "In the hippocampus , slow-wave sleep ( SWS ) is characterized by large amplitude , low-frequency oscillations of the local field potential ( LFP ) , concomitant with a phasic regime of neuronal firing , with relatively low mean firing rates and intermittent synchronization [1–4] .", "In contrast , rapid-...	[ "Sleep is critical for hippocampus-dependent memory consolidation .", "However , the underlying mechanisms of synaptic plasticity are poorly understood .", "The central controversy is on whether long-term potentiation ( LTP ) takes a role during sleep and which would be its specific effect on memory .", "To a...	[ "Sleep is important for long lasting memories .", "There exists , however , a controversy regarding the mechanisms by which sleep modifies synapses to consolidate enduring memories .", "One theory posits that sleep weakens synapses , leading to the forgetting of all but the strongest memories .", "The alterna...	2015
[ "Introduction", "Results", "Discussion" ]	[ "flow cytometry", "medicine and health sciences", "vesicles", "pathology and laboratory medicine", "molecular probe techniques", "gene regulation", "pathogens", "microbiology", "immunoblotting", "dna transcription", "retroviruses", "viruses", "immunodeficiency viruses", "non-coding rna", ...	Nuclear RNA surveillance complexes silence HIV-1 transcription	journal.ppat.1006950	null	[ [ "The human immunodeficiency virus-1 ( HIV-1 ) remains one of the world’s leading health threats with over 36 million people infected worldwide ( UNAIDS , Global Report , 2016 ) .", "Despite significant advances in antiretroviral therapy , it is not currently possible to eradicate HIV-1 infection due to th...	[ "Expression from the HIV-1 LTR can be repressed in a small population of cells , which contributes to the latent reservoir .", "The factors mediating this repression have not been clearly elucidated .", "We have identified a network of nuclear RNA surveillance factors that act as effectors of HIV-1 silencing ."...	[ "Following integration into the host genome , HIV-1 expression is silenced in a small population of cells , largely via epigenetic mechanisms that repress LTR-mediated transcription .", "This repression creates a reservoir of cells that prevent an effective cure .", "It is unclear how and why integrated HIV-1 b...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "musculoskeletal system", "bone", "birth defects", "molecular development", "gene regulation", "genetics", "gene expression", "molecular genetics", "musculoskeletal anatomy", "biology", "anatomy and physiology", "cartilage", "morphogenesis", "pattern formation", ...	Tbx2 Terminates Shh/Fgf Signaling in the Developing Mouse Limb Bud by Direct Repression of Gremlin1	journal.pgen.1003467	null	[ [ "Polydactyly , the condition of having more than the normal number of toes and/or fingers is the most frequent form of limb malformation in humans with an incidence of 1∶500 .", "It most commonly occurs as post-axial polydactyly ( extra digit ( s ) towards 5th finger in limb ) , less common is pre-axial p...	[ "Vertebrate limb outgrowth is driven by a positive feedback loop that involves Sonic hedgehog ( Shh ) and Gremlin1 ( Grem1 ) in the posterior limb bud mesenchyme and Fibroblast growth factors ( Fgfs ) in the overlying epithelium .", "Proper spatio-temporal control of these signaling activities is required to avoi...	[ "Developmental defects of the limb skeleton , such as variations from the normal number of digits , can result from an abnormal size of the early limb bud .", "The mechanisms that restrict limb bud growth to avoid polydactyly , i . e . the formation of extra digits , are unclear .", "Gremlin 1 ( Grem1 ) has bee...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "genomics", "genome evolution", "heredity", "genetics", "molecular genetics", "biology", "gene flow", "microbiology", "bacterial evolution", "genetics and genomics" ]	The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation	journal.pgen.1002222	null	[ [ "Prokaryotes , both bacteria and archaea , have remarkably plastic genomes because they can acquire genetic information at high rates by horizontal transfer from other prokaryotes .", "This allows them to adapt rapidly to specific niches and results in large differences in gene repertoires among closely r...	[ "Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions .", "Conjugation allows the broadest range and the highest gene transfer input per transfer event .", "While conjugative plasmids have been studied for decades , the number and diversity of inte...	[ "Some mobile genetic elements spread genetic information horizontally between prokaryotes by conjugation , a mechanism by which DNA is transferred directly from one cell to the other .", "Among the processes allowing genetic transfer between cells , conjugation is the one allowing the simultaneous transfer of lar...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "genetics and genomics/genetics of disease", "oncology/breast cancer" ]	Heterogeneity of Breast Cancer Associations with Five Susceptibility Loci by Clinical and Pathological Characteristics	journal.pgen.1000054	null	[ [ "Breast cancers vary greatly in clinical behavior , morphological appearance , and molecular alterations .", "Accumulating epidemiologic data also suggest that different types of breast cancers have different risk factor profiles and thus might result from different etiologic pathways ( which might be sha...	[ "A three-stage genome-wide association study recently identified single nucleotide polymorphisms ( SNPs ) in five loci ( fibroblast growth receptor 2 ( FGFR2 ) , trinucleotide repeat containing 9 ( TNRC9 ) , mitogen-activated protein kinase 3 K1 ( MAP3K1 ) , 8q24 , and lymphocyte-specific protein 1 ( LSP1 ) ) assoc...	[ "This report from the Breast Cancer Association Consortium evaluates whether common variants in five recently identified breast cancer susceptibility loci ( FGFR2 , TNRC9 , MAP3K1 , 8q24 , and LSP1 ) influence the clinical presentation of breast cancer and survival after diagnosis .", "We studied these susceptibi...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "schoolchildren", "medicine and health sciences", "pathology and laboratory medicine", "education", "pathogens", "sociology", "tropical diseases", "microbiology", "social sciences", "geographical locations", "treponematoses", "bacterial diseases", "signs and symptoms", "neglected tropical ...	Community-based mass treatment with azithromycin for the elimination of yaws in Ghana—Results of a pilot study	journal.pntd.0006303	null	[ [ "Yaws is a chronic , relapsing , neglected tropical disease caused by Treponema pallidum spp .", "pertenue , a spirochaete closely related to that which causes syphilis [1] .", "The disease is currently reported from 13 of the 85 countries previously considered endemic in the 1950s , with an estimated...	[ "The WHO yaws eradication strategy consists of one round of total community treatment ( TCT ) of single-dose azithromycin with coverage of > 90% .", "The efficacy of the strategy to reduce the levels on infection has been demonstrated previously in isolated island communities in the Pacific region .", "We aimed...	[ "In this study , we provided a single round of total community treatment ( TCT ) with azithromycin to the population of a sub-district in Ghana ( 16 , 287 people ) that is endemic for yaws and surrounded by other yaws-endemic communities to determine whether a sustained decrease in yaws prevalence could be achieved...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "animal types", "medicine and health sciences", "domestic animals", "tropical diseases", "diet", "social sciences", "ebola hemorrhagic fever", "neuroscience", "animals", "habits", "animal products", "physiological processes", "research design", "academic skills", "cognitive psychology", ...	The socio-economic drivers of bushmeat consumption during the West African Ebola crisis	journal.pntd.0005450	null	[ [ "The recent Ebola virus disease ( EVD , [1] ) epidemic that emerged in March 2014 in West Africa [2 , 3] was the largest recorded , resulting in over 28 , 600 cases and 11 , 300 deaths in Guinea , Liberia and Sierra Leone [4] .", "EVD is a deadly zoonotic disease that is transmitted to humans through cont...	[ "Bushmeat represents an important source of animal protein for humans in tropical Africa .", "Unsustainable bushmeat hunting is a major threat to wildlife and its consumption is associated with an increased risk of acquiring zoonotic diseases , such as Ebola virus disease ( EVD ) .", "During the recent EVD outb...	[ "The consumption of wild animal meat , commonly known as bushmeat , is widespread throughout tropical regions .", "Bushmeat provides an essential source of protein and income for human livelihoods .", "However , its consumption is linked to the transmission of zoonotic diseases , such as Ebola , and its over-ha...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "nucleic acid synthesis", "non-coding rna sequences", "messenger rna", "rna extraction", "green fluorescent protein", "membrane proteins", "developmental biology", "luminescent proteins", "rna synthesis", "embryos", "cellular structures and organelles", "extraction techniques", "chemical syn...	Slam protein dictates subcellular localization and translation of its own mRNA	journal.pbio.2003315	null	[ [ "Subcellular RNA localization is a widespread phenomenon [1–4] .", "A large-scale survey of RNA localization in Drosophila embryos by RNA in situ hybridization with fluorescent probes revealed that about 70% of all tested transcripts were distributed in a specific subcellular pattern , such as apical or b...	[ "Many mRNAs specifically localize within the cytoplasm and are present in RNA-protein complexes .", "It is generally assumed that localization and complex formation of these RNAs are controlled by trans-acting proteins encoded by genes different than the RNAs themselves .", "Here , we analyze slow as molasses (...	[ "While proteins and their encoding messenger RNAs share the same intracellular space during the translation process , thereafter they are usually spatially and biochemically separated .", "RNA localization follows a specific subcellular pattern—such as apical or basal—and is thought to have important physiologica...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	Helminthic Infections Rates and Malaria in HIV-Infected Pregnant Women on Anti-Retroviral Therapy in Rwanda	journal.pntd.0002380	null	[ [ "Globally , the most common nematode species that cause soil-transmitted helminthic diseases are Ascaris lumbricoides , Trichuris trichiura , and the hookworm species Necator americanus and Ancylostoma duodenale [1] , [2] , [3] .", "Although morbidity due to helminths can be controlled by delivering preve...	[ "Within sub-Saharan Africa , helminth and malaria infections cause considerable morbidity in HIV-positive pregnant women and their offspring .", "Helminth infections are also associated with a higher risk of mother-to-child HIV transmission .", "The aim of this study was to determine the prevalence of , and the...	[ "There is an overlap in the worldwide distribution of intestinal worms ( helminths ) , malaria and HIV .", "Co-infections with helminth and malaria parasites cause a significant problem in the host , particularly in the presence of HIV infection .", "The aim of this study was to assess the prevalence of intesti...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "flow cytometry", "innate immune system", "medicine and health sciences", "immune physiology", "cytokines", "immunology", "cell differentiation", "developmental biology", "systems science", "mathematics", "stem cells", "genome analysis", "molecular development", "research and analysis meth...	Cell Fate Decision as High-Dimensional Critical State Transition	journal.pbio.2000640	null	[ [ "A multipotent stem cell or a progenitor cell is in a state that poises it to be able to commit to one of multiple available options of predestined cell lineages and to differentiate .", "However , its state-characteristic gene expression profile is stably maintained because the cell is in a stable ( or m...	[ "Cell fate choice and commitment of multipotent progenitor cells to a differentiated lineage requires broad changes of their gene expression profile .", "But how progenitor cells overcome the stability of their gene expression configuration ( attractor ) to exit the attractor in one direction remains elusive .", ...	[ "A certain type of multipotent progenitor cell of the blood can commit to either the white ( myeloid ) or the red ( erythroid ) blood cell lineage , thus making a discrete binary cell fate decision .", "To test a theory on fundamental principles of cell fate dynamics ( as opposed to the usually studied molecular ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "computer science", "computer modeling", "biology", "neuroscience", "physiotherapy and rehabilitation" ]	Use It and Improve It or Lose It: Interactions between Arm Function and Use in Humans Post-stroke	journal.pcbi.1002343	null	[ [ "Stroke often leaves patients with predominantly unilateral motor impairments .", "Although the affected upper extremity is often not completely paralyzed , the recovery of upper extremity function is often achieved solely by compensatory use , i . e . , choice of the less-affected arm [1] .", "Improv...	[ "“Use it and improve it , or lose it” is one of the axioms of motor therapy after stroke .", "There is , however , little understanding of the interactions between arm function and use in humans post-stroke .", "Here , we explored putative non-linear interactions between upper extremity function and use by deve...	[ "Although , there is now definitive evidence that intensive task-specific practice is effective for improving upper extremity function and use after stroke , it is unclear how individual patients recover from stroke , and how they respond to therapy .", "Here , we propose a novel computational model of stroke rec...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "luciferase", "protein interactions", "pathology and laboratory medicine", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "dna transcription", "viruses", "dna viruses", "molecular biology techniques", "stat proteins", "herpesviruses", ...	Human cytomegalovirus UL23 inhibits transcription of interferon-γ stimulated genes and blocks antiviral interferon-γ responses by interacting with human N-myc interactor protein	journal.ppat.1006867	null	[ [ "Human cytomegalovirus ( CMV ) , a member of the human herpesvirus family , is a common opportunistic virus causing severe ailments and deaths in people with immature or compromised immune systems [1–4] .", "HCMV ability to evade the host immune system can significantly impact the course of illness .", ...	[ "Interferon-γ ( IFN-γ ) represents one of the most important innate immunity responses in a host to combat infections of many human viruses including human herpesviruses .", "Human N-myc interactor ( Nmi ) protein , which has been shown to interact with signal transducer and activator of transcription ( STAT ) pr...	[ "Interferon-γ ( IFN-γ ) responses are vital for a host to combat infections of many human viruses including human herpesviruses .", "Upon treatment of IFN-γ , transcription of many genes responsible for IFN-γ immune responses is activated primarily by the signal transducer and activator of transcription ( STAT ) ...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Arabidopsis BREVIPEDICELLUS Interacts with the SWI2/SNF2 Chromatin Remodeling ATPase BRAHMA to Regulate KNAT2 and KNAT6 Expression in Control of Inflorescence Architecture	journal.pgen.1005125	null	[ [ "In flowering plants , internode patterning and pedicel characteristics are two important determinants of inflorescence architecture , which is highly diversified among flowering plant species [1 , 2] .", "Inflorescence architecture results from the activity of the shoot apical meristem ( SAM ) , a cluste...	[ "BREVIPEDICELLUS ( BP or KNAT1 ) , a class-I KNOTTED1-like homeobox ( KNOX ) transcription factor in Arabidopsis thaliana , contributes to shaping the normal inflorescence architecture through negatively regulating other two class-I KNOX genes , KNAT2 and KNAT6 .", "However , the molecular mechanism of BP-mediate...	[ "BP is a class-I KNOX transcription factor that controls normal inflorescence architecture development by repressing the expression of two KNOX genes , KNAT2 and KNAT6 .", "In this study , we showed that Arabidopsis BP directly interacts with the SWI2/SNF2 chromatin remodeling ATPase BRM .", "brm and bp mutants...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology/cell signaling", "developmental biology/plant growth and development", "cell biology/developmental molecular mechanisms", "plant biology/plant-environment interactions", "cell biology/plant cell biology", "genetics and genomics/plant genetics and gene expression" ]	FHY1 Mediates Nuclear Import of the Light-Activated Phytochrome A Photoreceptor	journal.pgen.1000143	null	[ [ "Plants are sessile organisms and therefore have to adapt growth and development to the environmental conditions at their site of germination .", "Light is one of the most important factors directing such adaptive responses and it is involved in many developmental steps throughout the life of plants [1] ,...	[ "The phytochrome ( phy ) family of photoreceptors is of crucial importance throughout the life cycle of higher plants .", "Light-induced nuclear import is required for most phytochrome responses .", "Nuclear accumulation of phyA is dependent on two related proteins called FHY1 ( Far-red elongated HYpocotyl 1 ) ...	[ "In response to changes in the environment , animals can take shelter while the sessile plants must adapt to the prevalent conditions .", "Great plasticity in growth and development are striking examples of how plants cope with a changing environment .", "In plants , light is both a source of energy and an esse...	2008
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "medicine and health sciences", "tropical diseases", "social sciences", "sand flies", "parasitic diseases", "neuroscience", "psychological and psychosocial issues", "health care", "neglected tropical diseases", "insect vectors", "infectious diseases", "scars", "zoonoses", ...	Psychological and Psychosocial Consequences of Zoonotic Cutaneous Leishmaniasis among Women in Tunisia: Preliminary Findings from an Exploratory Study	journal.pntd.0005090	null	[ [ "Cutaneous leishmaniasis is the most common form of leishmaniasis .", "It is a skin infection caused by a unicellular parasite transmitted by infected sandflies that feed on the blood of rodents bred in caves or burrows in degraded environments .", "It is known also as Oriental Sore , Biskra Button , ...	[ "The incidence of zoonotic cutaneous leishmaniasis ( ZCL ) makes it the most widespread parasitic disease in Tunisia and the Arab world .", "Yet , few studies have addressed its psychological and psychosocial effects .", "The purpose of this study was to examine the psychosocial impact of ZCL scars among Tunisi...	[ "Zoonotic cutaneous leishmaniasis ( ZCL ) is the most common form of leishmaniasis in Tunisia .", "The disease is not severe and heal spontaneously with a definitive scar causing a social impact mainly when the lesion occurs in the face .", "Yet , few studies have addressed these psychological and psychosocial ...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant anatomy", "gene regulation", "ovules", "brassica", "plant science", "model organisms", "experimental organism systems", "plants", "flowering plants", "research and analysis methods", "arabidopsis thaliana", "genome complexity", "gene expression", "leaves", "flowers", "eukaryota"...	Ovule identity mediated by pre-mRNA processing in Arabidopsis	journal.pgen.1007182	null	[ [ "Ovules are fundamental for plant reproductive success and food production .", "Ovule development predetermines the female gametophyte , proper fertilization , and ultimately fruit growth , as well as embryo and seed development [1] .", "Importantly , seeds constitute the primary basis for human suste...	[ "Ovules are fundamental for plant reproduction and crop yield as they are the precursors of seeds .", "Therefore , ovule specification is a critical developmental program .", "In Arabidopsis thaliana , ovule identity is redundantly conferred by the homeotic D-class genes SHATTERPROOF1 ( SHP1 ) , SHP2 and SEEDST...	[ "Plant ovules are crucial reproductive structures in which the female gametophyte develops , giving rise to seeds after fertilization .", "Global food supply depends mainly on seed production , thus understanding the underlying regulatory mechanisms that orchestrate ovule development is vitally important .", "T...	2018
[ "Introduction", "Results", "Methods", "Discussion" ]	[ "synthetic genetic systems", "genetic networks", "engineering and technology", "synthetic biology", "cell differentiation", "dna transcription", "developmental biology", "protein expression", "network analysis", "molecular biology techniques", "synthetic gene oscillators", "research and analys...	Multi-modality in gene regulatory networks with slow promoter kinetics	journal.pcbi.1006784	null	[ [ "In this paper , a GRN is formally defined as a set of nodes ( genes ) that are connected with each other through regulatory interactions via the proteins that the genes express .", "The regulatory proteins are called transcription factors ( TFs ) .", "A TF regulates the expression of a gene by revers...	[ "Phenotypical variability in the absence of genetic variation often reflects complex energetic landscapes associated with underlying gene regulatory networks ( GRNs ) .", "In this view , different phenotypes are associated with alternative states of complex nonlinear systems: stable attractors in deterministic mo...	[ "Regulatory mechanisms of slow gene activation and deactivation play a role in triggering and sustaining phenotypically heterogeneous , yet genetically identical ( clonal ) , cellular populations in a wide variety of biological processes .", "These range from embryonic development and hematopoietic cell different...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular neuroscience", "animal genetics", "nervous system", "neuronal differentiation", "neuroscience", "cell differentiation", "gene function", "developmental biology", "behavioral neuroscience", "genetic predisposition", "animal cells", "gene expression", "gene disruption", "cellular ...	A Conserved Role for p48 Homologs in Protecting Dopaminergic Neurons from Oxidative Stress	journal.pgen.1004718	null	[ [ "Dopaminergic ( DA ) neurons play critical roles in motor control , cognition and motivation and are affected in many neurological and psychiatric disorders [1] , [2] , [3] , [4] .", "The progressive degeneration of DA neurons in the substantia nigra pars compacta ( SNc ) is a principal pathological featu...	[ "Parkinson's disease ( PD ) is the most common neurodegenerative movement disorder characterized by the progressive loss of dopaminergic ( DA ) neurons .", "Both environmental and genetic factors are thought to contribute to the pathogenesis of PD .", "Although several genes linked to rare familial PD have been...	[ "Parkinson's disease is a common movement disorder with no known cure .", "Its characteristic motor symptoms are primarily caused by the progressive loss of midbrain dopaminergic neurons .", "Although studies have shown that various environmental and genetic factors both contribute to the development of the dis...	2014
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "taxonomy", "plant anatomy", "medicine and health sciences", "applied mathematics", "epidemiological methods and statistics", "simulation and modeling", "algorithms", "phylogenetics", "data management", "plant science", "mathematics", "phylogenetic analysis", "research and analysis methods",...	Inferring epidemiological parameters from phylogenies using regression-ABC: A comparative study	journal.pcbi.1005416	null	[ [ "To control epidemics , we must understand their dynamics .", "Classical analyses typically rely on prevalence or incidence data [1 , 2] , which correspond to the total number of reported cases , and the number of newly reported cases through time , respectively .", "By combining such data with epidem...	[ "Inferring epidemiological parameters such as the R0 from time-scaled phylogenies is a timely challenge .", "Most current approaches rely on likelihood functions , which raise specific issues that range from computing these functions to finding their maxima numerically .", "Here , we present a new regression-ba...	[ "Given the rapid evolution of many pathogens , analysing their genomes by means of phylogenies can inform us about how they spread .", "This is the focus of the field known as “phylodynamics” .", "Most existing methods inferring epidemiological parameters from virus phylogenies are limited by the difficulty of ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genome expression analysis", "x chromosome inactivation", "genome evolution", "gene regulation", "dna transcription", "gene function", "animal models", "caenorhabditis elegans", "model organisms", "molecular genetics", "chromosome biology", "gene expression", "biology", "molecular biology...	Chromosome-Biased Binding and Gene Regulation by the Caenorhabditis elegans DRM Complex	journal.pgen.1002074	null	[ [ "The development of multi-cellular organisms is orchestrated by transcription factors", "that coordinate the spatiotemporal expression of sets of target genes .", "Transcription", "factors often act together in the context of multi-protein complexes .", "For instance ,", "DREAM is a multi-...	[ "DRM is a conserved transcription factor complex that includes E2F/DP and pRB", "family proteins and plays important roles in development and cancer .", "Here we", "describe new aspects of DRM binding and function revealed through genome-wide", "analyses of the Caenorhabditis elegans DRM subunit LIN-54 .", ...	[ "X chromosomes differ in number between the sexes and differ from autosomes in", "their associated proteins and gene regulatory properties .", "In C .", "elegans both X chromosomes are partially silenced in hermaphrodite", "germlines .", "Germline-expressed and essential genes are autosome-enriched and ar...	2011
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "microbiology", "viral structure", "retroviruses", "viruses", "immunodeficiency viruses", "rna viruses", "materials science", "materials physics", "protein structure", "sequence motif...	Structure of a Spumaretrovirus Gag Central Domain Reveals an Ancient Retroviral Capsid	journal.ppat.1005981	null	[ [ "Spuma- or foamy viruses ( FVs ) are complex retroviruses that constitute the only members of the Spumaretrovirinae subfamily within the Retroviridae family [1] .", "They have been isolated from a variety of primate hosts [2–5] as well as from cats [6–8] , cattle [9] , horses [10] and sheep [11] .", "...	[ "The Spumaretrovirinae , or foamy viruses ( FVs ) are complex retroviruses that infect many species of monkey and ape .", "Despite little sequence homology , FV and orthoretroviral Gag proteins perform equivalent functions , including genome packaging , virion assembly , trafficking and membrane targeting .", "...	[ "Foamyviruses ( FVs ) or Spuma-retroviruses derive their name from the cytopathic effects they cause in cell culture .", "However , infection in humans is benign and FVs have entered the human population through zoonosis from apes resulting in the emergence of Prototype FV ( PFV ) .", "Like all retroviruses , F...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "cell biology", "neuroscience" ]	Cell Lineages and the Logic of Proliferative Control	journal.pbio.1000015	Are common, generic strategies used in the quantitative control of tissue growth and regeneration? An investigation of feedback effects in multistage lineages suggests they are.	[ [ "In biology , “control” is often used interchangeably with “regulation , ” but in engineering , control has a precise meaning: It refers to the strategies that enable a system to achieve desired ends , usually in a robust manner .", "To begin talking about the control needs of growing tissues and organs ,...	[ "It is widely accepted that the growth and regeneration of tissues and organs is tightly controlled .", "Although experimental studies are beginning to reveal molecular mechanisms underlying such control , there is still very little known about the control strategies themselves .", "Here , we consider how secre...	[ "Many tissues and organs grow to precise sizes and , when injured , regenerate accurately and rapidly .", "Here , we ask whether the organization of cells into lineages , and the feedback interactions that occur within lineages , are necessary elements of control strategies that make such behavior possible .", ...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "cell death", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "pathogens", "immunology", "cell processes", "microbiology", "toxicology", "retroviruses", "viruses", "immunodeficiency viruses", "toxicity", "rna viruses", "white blood ce...	Latency reversal agents affect differently the latent reservoir present in distinct CD4+ T subpopulations	journal.ppat.1007991	null	[ [ "Current antiretroviral therapy ( ART ) is extremely effective at suppressing HIV viremia below the limit of detection of standard clinical assays and substantially reduces the morbidity and mortality associated with the HIV-1 infection .", "However , ART is unable to fully eliminate and eradicate HIV fro...	[ "Latency reversal agents ( LRAs ) have proven to induce HIV-1 transcription in vivo but are ineffective at decreasing the size of the latent reservoir in antiretroviral treated patients .", "The capacity of the LRAs to perturb the viral reservoir present in distinct subpopulations of cells is currently unknown ."...	[ "HIV infection is an incurable disease .", "Despite antiretroviral therapy , a pool of cells with HIV in a latent state persists and precludes fully eradication of the viral infection .", "The cells that contain this latent viral reservoir are very diverse , and therefore different therapeutic strategies would ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	A Dynamical Model of Oocyte Maturation Unveils Precisely Orchestrated Meiotic Decisions	journal.pcbi.1002329	null	[ [ "The mitotic division cycle is the sequence of events by which a growing cell replicates all its components , including DNA , and divides them , after mitosis , into two nearly identical daughter cells [1] .", "Meiosis is an alternative mode of cell division in which a diploid cell undergoes two successiv...	[ "Maturation of vertebrate oocytes into haploid gametes relies on two consecutive meioses without intervening DNA replication .", "The temporal sequence of cellular transitions driving eggs from G2 arrest to meiosis I ( MI ) and then to meiosis II ( MII ) is controlled by the interplay between cyclin-dependent and...	[ "In the life cycle of sexual organisms , a specialized cell division -meiosis- reduces the number of chromosomes in gametes or spores while fertilization or mating restores the original number .", "The essential feature that distinguishes meiosis from mitosis ( the usual division ) is the succession of two rounds...	2012
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "acoustics", "medicine and health sciences", "resonance frequency", "classical mechanics", "vibration", "larynx", "vertebrates", "animals", "mammals", "throat", "respiratory system", "sound pressure", "amniotes", "trachea", "birds", "resonance", "physics", "eukaryota", "anatomy",...	The evolution of the syrinx: An acoustic theory	journal.pbio.2006507	null	[ [ "Direct visualization of the sound-producing larynx [23] and syrinx [12] and experiments with an excised larynx [24–27] and syrinx [11 , 13 , 15] confirm that both organs function as self-oscillating valves driven by airflow .", "The primary sound then travels along the respiratory tract above the source ...	[ "The unique avian vocal organ , the syrinx , is located at the caudal end of the trachea .", "Although a larynx is also present at the opposite end , birds phonate only with the syrinx .", "Why only birds evolved a novel sound source at this location remains unknown , and hypotheses about its origin are largely...	[ "The larynx is an important valve in the respiratory system of all air-breathing vertebrates that is located at the upper end of the trachea .", "In some amphibians , in nonavian reptiles , and in mammals , it has also assumed the function of a vocal organ .", "In contrast , birds have evolved a new and unique ...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "velocity", "learning", "medicine and health sciences", "classical mechanics", "education", "adaptive training", "sociology", "experimental design", "social sciences", "neuroscience", "learning and memory", "training (education)", "research design", "cognitive psychology", "research and ...	Temporal specificity of the initial adaptive response in motor adaptation	journal.pcbi.1005438	null	[ [ "When voluntary movement encounters a physical perturbation , the motor system generates an adaptive response that counteracts the perturbation’s effects during subsequent movements .", "Several studies have suggested that this adaptive response is motion-state-dependent in the sense that it’s time course...	[ "Repeated exposure to a novel physical environment eventually leads to a mature adaptive response whereby feedforward changes in motor output mirror both the amplitude and temporal structure of the environmental perturbations .", "However , adaptive responses at the earliest stages of learning have been found to ...	[ "With repeated exposure to a perturbation , the sensorimotor system learns to develop an adaptive response that is highly specific to both the amplitude and temporal structure of that perturbation in order to effectively counteract it .", "It is widely known that the amplitude of the adaptive response starts smal...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "antimicrobials", "invertebrates", "medicine and health sciences", "nuclear staining", "parasitic cell cycles", "cell cycle and cell division", "drugs", "cell processes", "microbiology", "cloning", "parasitic diseases", "animals", "parasitology", "glossina", "developmental biology", "t...	A quorum sensing-independent path to stumpy development in Trypanosoma brucei	journal.ppat.1006324	null	[ [ "Pathogenic bacteria and protozoan parasites often employ a coat of surface molecules to protect themselves from host immune attack .", "These surface coats are sometimes variable and hence , not only act as a physical shield but have evolved as an efficient camouflage strategy .", "The surface-expose...	[ "For persistent infections of the mammalian host , African trypanosomes limit their population size by quorum sensing of the parasite-excreted stumpy induction factor ( SIF ) , which induces development to the tsetse-infective stumpy stage .", "We found that besides this cell density-dependent mechanism , there e...	[ "African trypanosomes escape the mammalian host’s immune system by antigenic variation of their variant surface glycoprotein ( VSG ) coat .", "VSGs are expressed from a specialized region in the genome , the expression site ( ES ) , that contains essential expression site associated genes ( ESAGs ) .", "So far ...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "liver", "enzyme-linked immunoassays", "pathology and laboratory medicine", "in vivo imaging", "epithelial cells", "bone marrow cells", "signs and symptoms", "immunologic techniques", "research and analysis methods", "imaging techniques", "animal cells", "hepa...	Interferon-beta expression and type I interferon receptor signaling of hepatocytes prevent hepatic necrosis and virus dissemination in Coxsackievirus B3-infected mice	journal.ppat.1007235	null	[ [ "Coxsackievirus B3 ( CVB3 ) is a single-stranded RNA virus that belongs to the genus of human Enterovirus [1] .", "CVB3 infections are very common , especially in children and neonates , and mostly cause only mild disease .", "However , occasionally also severe disease with fatal outcome , such as myo...	[ "During Coxsackievirus B3 ( CVB3 ) infection hepatitis is a potentially life threatening complication , particularly in newborns .", "Studies with type I interferon ( IFN-I ) receptor ( IFNAR ) -deficient mice revealed a key role of the IFN-I axis in the protection against CVB3 infection , whereas the source of I...	[ "CVB3 belongs to human enteroviruses and is transmitted through the fecal-oral route .", "Infections with CVB3 are mostly unnoticed or cause flu-like symptoms , however , they can also cause severe disease , such as myocarditis , pancreatitis , and hepatitis .", "Although CVB3 does not efficiently trigger plasm...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "motor systems", "computational neuroscience", "biology", "computational biology", "neuroscience", "learning and memory" ]	Estimating the Relevance of World Disturbances to Explain Savings, Interference and Long-Term Motor Adaptation Effects	journal.pcbi.1002210	null	[ [ "There is a large body of evidence to suggest that the nervous system maintains internal representations of variables that are relevant to the production of movement [1] , [2] , [3] .", "Internal models allow us to make repeatable and reliable movements despite a highly variable world and body , and our n...	[ "Recent studies suggest that motor adaptation is the result of multiple , perhaps linear processes each with distinct time scales .", "While these models are consistent with some motor phenomena , they can neither explain the relatively fast re-adaptation after a long washout period , nor savings on a subsequent ...	[ "Trying to explain how humans adapt to new motor behaviors and retain them over time is a central focus in motor control .", "Many aspects of adaptation , including savings and interference , have proven difficult to explain in a coherent manner .", "Linear dynamical models have been successful at describing th...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biomacromolecule-ligand interactions", "protein interactions", "animal models", "model organisms", "membrane receptor signaling", "proteins", "muscle fibers", "biology", "molecular biology", "biochemistry", "zebrafish", "signal transduction", "transmembrane proteins", "cell biology", "c...	Jamb and Jamc Are Essential for Vertebrate Myocyte Fusion	journal.pbio.1001216	Jamb and Jamc are an essential cell surface receptor pair that interact to drive fusion between muscle precursor cells during zebrafish development.	[ [ "Cell–cell fusion is crucial for several biological processes , including placental development [1] , bone remodelling [2] , fertilisation [3] , and formation of skeletal muscle fibres [4] , but surprisingly remains poorly understood .", "Skeletal muscle forms the bulk of tissue in vertebrates and is comp...	[ "Cellular fusion is required in the development of several tissues , including skeletal muscle .", "In vertebrates , this process is poorly understood and lacks an in vivo-validated cell surface heterophilic receptor pair that is necessary for fusion .", "Identification of essential cell surface interactions be...	[ "The fusion of precursor cells is a crucial step in many biological processes , one of which is the development of skeletal muscle .", "The molecular and cell biology of fusion of muscle precursors has been well described in Drosophila melanogaster larvae , leading to insights into the process in vertebrates .", ...	2011
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "yeast and fungi", "infectious diseases", "genetics and genomics", "eukaryotes" ]	Haplotype Mapping of a Diploid Non-Meiotic Organism Using Existing and Induced Aneuploidies	journal.pgen.0040001	null	[ [ "Researchers are using Haplotype Maps ( HapMaps ) with increasing frequency , due to their utility in revealing underlying sequence variation [1] .", "HapMaps facilitate the study of factors influencing recombination and genetic diversity , as the three primary activities that alter haplotype structure ar...	[ "Haplotype maps ( HapMaps ) reveal underlying sequence variation and facilitate the study of recombination and genetic diversity .", "In general , HapMaps are produced by analysis of Single-Nucleotide Polymorphism ( SNP ) segregation in large numbers of meiotic progeny .", "Candida albicans , the most common hu...	[ "Candida albicans , a heterozygous diploid yeast , is the most prevalent fungal pathogen .", "It often acquires resistance to anti-fungal drugs via genome-altering recombination events .", "In many organisms , recombination events are analyzed using Haplotype Maps ( HapMaps ) , which show the location of differ...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "viral envelope", "virology", "biology and life sciences", "microbiology", "viral structure" ]	Well-Ordered Trimeric HIV-1 Subtype B and C Soluble Spike Mimetics Generated by Negative Selection Display Native-like Properties	journal.ppat.1004570	null	[ [ "The HIV-1 envelope glycoprotein ( Env ) is a trimer of heterodimers composed of two non-covalently associated subunits: the receptor-binding gp120 and the fusion machinery-containing gp41 .", "Each subunit is derived from a gp160 precursor glycoprotein following cleavage by cellular furins [1] .", "H...	[ "The structure of BG505 gp140 SOSIP , a soluble mimic of the native HIV-1 envelope glycoprotein ( Env ) , marks the beginning of new era in Env structure-based immunogen design .", "Displaying a well-ordered quaternary structure , these subtype A-derived trimers display an excellent antigenic profile , discrimina...	[ "The HIV envelope glycoprotein ( Env ) is the sole virally encoded gene product on the surface of the virus and , as such , is the only target of neutralizing antibodies .", "A broadly efficacious HIV vaccine will likely need to generate a robust neutralizing antibody response directed at conserved elements of th...	2015
[ "Introduction", "Methods and Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "medicine and health sciences", "enzyme-linked immunoassays", "immune physiology", "pathology and laboratory medicine", "pathogens", "immunology", "tropical diseases", "microbiology", "geographical locations", "ebola hemorrhagic fever", "virus...	Minimally Symptomatic Infection in an Ebola ‘Hotspot’: A Cross-Sectional Serosurvey	journal.pntd.0005087	null	[ [ "Despite over 28 , 000 reported cases of Ebola virus disease ( EVD ) in the 2013–16 pandemic as of March 27 , 2016 [1] , we are only beginning to trace the complex biosocial processes that have promoted spread of the virus [2 , 3] .", "Important questions remain , including how to best use tools such as n...	[ "Evidence for minimally symptomatic Ebola virus ( EBOV ) infection is limited .", "During the 2013–16 outbreak in West Africa , it was not considered epidemiologically relevant to published models or projections of intervention effects .", "In order to improve our understanding of the transmission dynamics of E...	[ "With over 28 , 000 reported cases , the 2013–16 West African Ebola virus disease epidemic is the largest and longest on record .", "This study provides further evidence that Ebola , like other viruses , causes a spectrum of clinical manifestations that may include minimally symptomatic infection .", "The findi...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "gene regulation", "regulatory proteins", "dna-binding proteins", "notch signaling", "dna transcription", "endocrine physiology", "developmental biology", "organism development", "gland development", "transcription factors", "growth factors", "fibroblast growt...	FGF-induced Pea3 transcription factors program the genetic landscape for cell fate determination	journal.pgen.1007660	null	[ [ "During development of a complex multicellular organism , organ identity is determined by the combination of lineage-specific and signal-induced transcription factors .", "In mammalian lacrimal gland development , the extracellular signals include Fibroblast Growth Factor ( FGF ) , Bone Morphogenetic Prot...	[ "FGF signaling is a potent inducer of lacrimal gland development in the eye , capable of transforming the corneal epithelium into glandular tissues .", "Here , we show that genetic ablation of the Pea3 family of transcription factors not only disrupted the ductal elongation and branching of the lacrimal gland , b...	[ "FGF signaling regulates cell fate decision by inducing genome-wide changes in gene expression .", "We identified Pea3 family transcription factors as the key effectors of FGF signaling in reprograming the epithelia transcriptome .", "Pea3 factors control both the feedback and feedforward circuities of FGF sign...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "model organisms", "genetics", "biology", "genetics and genomics" ]	Disruption of Chtf18 Causes Defective Meiotic Recombination in Male Mice	journal.pgen.1002996	null	[ [ "Precise chromosome segregation is crucial to ensure that germ cell development proceeds normally during meiosis , and that genetic information is accurately transmitted to the gametes .", "For chromosome segregation to proceed flawlessly during meiosis , homologous chromosomes must undergo several proces...	[ "CHTF18 ( chromosome transmission fidelity factor 18 ) is an evolutionarily conserved subunit of the Replication Factor C-like complex , CTF18-RLC .", "CHTF18 is necessary for the faithful passage of chromosomes from one daughter cell to the next during mitosis in yeast , and it is crucial for germline developmen...	[ "Meiosis is the specialized process of cell division during germ cell development that results in formation of eggs and sperm .", "Genetic exchange between maternal and paternal chromosomes occurs during meiosis in a process called homologous recombination , in which DNA double- strand breaks are made and then re...	2012
[ "Introduction", "Materials, subjects and methods", "Results", "Discussion" ]	[ "mycobacterium leprae", "medicine and health sciences", "body fluids", "fibrinogen", "tropical diseases", "neutral lipids", "fibrin", "bacterial diseases", "neglected tropical diseases", "glycoproteins", "bacteria", "infectious diseases", "lipids", "proteins", "actinobacteria", "blood ...	Blood coagulation abnormalities in multibacillary leprosy patients	journal.pntd.0006214	null	[ [ "Leprosy remains an important public health problem worldwide .", "Damage to peripheral nerves and bone absorption [1] results in the deformities and disability that are hallmarks of the disease .", "There are two separate aspects to the disease .", "The first aspect involves direct infection of S...	[ "Leprosy is a chronic dermato-neurological disease caused by Mycobacterium leprae infection .", "In 2016 , more than 200 , 000 new cases of leprosy were detected around the world , representing the most frequent cause of infectious irreversible deformities and disabilities .", "In the present work , we demonstr...	[ "Hemostatic illnesses are frequently associated with acute and chronic infections .", "In the present work we demonstrated that leprosy patients developed hemostatic abnormalities , like the formation of an atypical lipid clot mass during sera harvesting , a phenomenon previously observed and never unraveled .", ...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "markov models", "chromosomal inversions", "invertebrate genomics", "chromosome mapping", "mathematics", "dna recombination", "molecular biology techniques", "dna", "genotyping", "research and analysis methods", "gene mapping", "chromosome biology", "chromosomal aberrations", "hidden marko...	GOOGA: A platform to synthesize mapping experiments and identify genomic structural diversity	journal.pcbi.1006949	null	[ [ "Over the last decade , genetic research has been revolutionized by the availability of whole genome sequences for many of the world’s medically , ecologically , and agriculturally important species .", "It has also become clear that a single reference genome sequence is insufficient for many species .", ...	[ "Understanding genomic structural variation such as inversions and translocations is a key challenge in evolutionary genetics .", "We develop a novel statistical approach to comparative genetic mapping to detect large-scale structural mutations from low-level sequencing data .", "The procedure , called Genome O...	[ "Genome sequences are an essential resource for genetic research in many species .", "However , most species exhibit considerable variation in genomic organization , making a single reference sequence inadequate .", "This variation complicates quantitative trait mapping and population genomics .", "We introdu...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "biology" ]	Signal Peptidase Complex Subunit 1 Participates in the Assembly of Hepatitis C Virus through an Interaction with E2 and NS2	journal.ppat.1003589	null	[ [ "Over 170 million people worldwide are chronically-infected with hepatitis C virus ( HCV ) , and are at risk of developing chronic hepatitis , cirrhosis , and hepatocellular carcinoma [1] .", "HCV is an enveloped virus of the family Flaviviridae , and its genome is an uncapped 9 . 6-kb positive-strand RNA...	[ "Hepatitis C virus ( HCV ) nonstructural protein 2 ( NS2 ) is a hydrophobic , transmembrane protein that is required not only for NS2-NS3 cleavage , but also for infectious virus production .", "To identify cellular factors that interact with NS2 and are important for HCV propagation , we screened a human liver c...	[ "Viruses hijack host cells and utilize host-derived proteins for viral propagation .", "In the case of hepatitis C virus ( HCV ) , many host factors have been identified that are required for genome replication; however , only a little is known about cellular proteins that interact with HCV proteins and are impor...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience" ]	Receptive Fields in Primate Retina Are Coordinated to Sample Visual Space More Uniformly	journal.pbio.1000063	Receptive fields in primate retina have irregular shapes, but they interlock like puzzle pieces to provide highly uniform coverage of visual space.	[ [ "In primates , high-resolution visual information is encoded by the magnocellular and parvocellular pathways , which respectively originate in the retina as populations of parasol and midget retinal ganglion cells ( RGCs ) [1] .", "These populations are expected to represent the visual scene efficiently a...	[ "In the visual system , large ensembles of neurons collectively sample visual space with receptive fields ( RFs ) .", "A puzzling problem is how neural ensembles provide a uniform , high-resolution visual representation in spite of irregularities in the RFs of individual cells .", "This problem was approached b...	[ "All visual information reaching the brain is transmitted by retinal ganglion cells , each of which is sensitive to a small region of space known as its receptive field .", "Each of the 20 or so distinct ganglion cell types is thought to transmit a complete visual image to the brain , because the receptive fields...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Mechanisms of Stage-Transcending Protection Following Immunization of Mice with Late Liver Stage-Arresting Genetically Attenuated Malaria Parasites	journal.ppat.1004855	null	[ [ "Unlike other infectious diseases , malaria parasites continue to defy the development of a protective vaccine .", "One main difference between pathogens currently amenable to vaccination and malaria parasites is the degree of complexity of the parasites causing malaria , Plasmodium spp .", "These euk...	[ "Malaria , caused by Plasmodium parasite infection , continues to be one of the leading causes of worldwide morbidity and mortality .", "Development of an effective vaccine has been encumbered by the complex life cycle of the parasite that has distinct pre-erythrocytic and erythrocytic stages of infection in the ...	[ "Malaria is arguably one of the deadliest infectious diseases in human history .", "Today , it infects nearly 300 million people each year and kills up to 1 million of those—mostly women and children under the age of 5—and no effective malaria vaccine has been developed .", "Traditional subunit vaccines for pat...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "biochemistry", "cytoskeletal proteins", "cell motility", "actin filaments", "cell biology", "proteins", "protein structure", "structural proteins", "biology and life sciences", "dynamic actin filaments" ]	EhCoactosin Stabilizes Actin Filaments in the Protist Parasite Entamoeba histolytica	journal.ppat.1004362	null	[ [ "Human amoebiasis is caused by the protist parasite E . histolytica .", "The parasite is highly motile and displays high level of phagocytic activity in the trophozoite stage .", "Motility and phagocytosis are essential processes for the survival and invasion of host tissues by the parasite , and larg...	[ "Entamoeba histolytica is a protist parasite that is the causative agent of amoebiasis , and is a highly motile organism .", "The motility is essential for its survival and pathogenesis , and a dynamic actin cytoskeleton is required for this process .", "EhCoactosin , an actin-binding protein of the ADF/cofilin...	[ "E . histolytica is an important pathogen and a major cause of morbidity and mortality in developing nations .", "High level of motility and phagocytosis is responsible for the parasite invading different tissues of the host .", "Phagocytosis and motility depend on highly dynamic actin cytoskeleton of this orga...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "public health and epidemiology", "epidemiology", "neglected tropical diseases", "leprosy" ]	Leprosy among Patient Contacts: A Multilevel Study of Risk Factors	journal.pntd.0001013	null	[ [ "The primary aim of all disease control measures is to reduce the incidence , prevalence , morbidity and/or mortality rates to the lowest level possible in a given population .", "However , once control program objectives have been met , continuous interventions are necessary to maintain these minimal rat...	[ "This study aimed to evaluate the risk factors associated with developing leprosy among the contacts of newly-diagnosed leprosy patients .", "A total of 6 , 158 contacts and 1 , 201 leprosy patients of the cohort who were diagnosed and treated at the Leprosy Laboratory of Fiocruz from 1987 to 2007 were included ....	[ "Leprosy is an infectious disease that can lead to physical disabilities , social stigma , and great hardship .", "Transmitted from person to person , it is still endemic in developing countries , like Brazil and India .", "Effective treatment has been available since 1960 , but early diagnosis of the disease r...	2011
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "dengue virus", "medicine and health sciences", "pathology and laboratory medicine", "togaviruses", "chikungunya infection", "influenza", "pathogens", "tropical diseases", "microbiology", "geographical locations", "orthomyxoviruses", "alphaviruses", "viruses", "north america", "age group...	Clinical and epidemiologic characteristics of dengue and other etiologic agents among patients with acute febrile illness, Puerto Rico, 2012–2015	journal.pntd.0005859	null	[ [ "As malaria incidence continues to decrease throughout the tropics , a new area of research has focused on identifying etiologies of non-malaria , acute febrile illness ( AFI ) [1 , 2] .", "Knowledge is limited in this area , in large part because AFIs often have similar non-specific clinical presentation...	[ "Identifying etiologies of acute febrile illnesses ( AFI ) is challenging due to non-specific presentation and limited availability of diagnostics .", "Prospective AFI studies provide a methodology to describe the syndrome by age and etiology , findings that can be used to develop case definitions and multiplexed...	[ "We conducted a prospective study of acute febrile illness ( AFI ) in Puerto Rico to better understand the etiology of AFI among all age groups in the tropics .", "Such findings could assist clinicians to identify disease-specific characteristics , which can then be used to initiate proper patient management .", ...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "gene regulation", "dna-binding proteins", "cloning", "plant physiology", "habits", "plant science", "crops", "molecular biology techniques", "dna", "plants", "flowering plants", "promoter regions", "research and analysis methods", "crop science", "artificial gene amplification and exten...	Innovation of a Regulatory Mechanism Modulating Semi-determinate Stem Growth through Artificial Selection in Soybean	journal.pgen.1005818	null	[ [ "Stem growth habit is an important morphological and adaptation trait in flowering plants , which is primarily shaped by regulatory processes converting the vegetative shoot apical meristems ( SAMs ) that form leaves to the inflorescence meristems ( IMs ) and then floral meristems ( FMs ) that form flowers [1...	[ "It has been demonstrated that Terminal Flowering 1 ( TFL1 ) in Arabidopsis and its functional orthologs in other plants specify indeterminate stem growth through their specific expression that represses floral identity genes in shoot apical meristems ( SAMs ) , and that the loss-of-function mutations at these func...	[ "Similar to the “green revolution” semi-dwarf cereals , semi-determinate soybean varieties are lodging-resistant and particularly suitable for planting in high fertility and irrigated environments .", "Nevertheless , molecular mechanisms underlying semi-determinate stem growth have not been deciphered in any flow...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/neglected tropical diseases", "immunology/innate immunity", "cell biology/microbial growth and development", "biochemistry/biomacromolecule-ligand interactions", "microbiology/parasitology", "infectious diseases/protozoal infections", "immunology/immunity to infections" ]	Trypanosome Lytic Factor, an Antimicrobial High-Density Lipoprotein, Ameliorates Leishmania Infection	journal.ppat.1000276	null	[ [ "Human blood is a potentially hostile environment to colonizing pathogens due in part to effectors of innate immunity .", "Trypanosome Lytic Factors ( TLFs ) are a subset of high-density lipoproteins ( HDLs ) that protect against infection by many but not all species of the African trypanosome .", "Tw...	[ "Innate immunity is the first line of defense against invading microorganisms .", "Trypanosome Lytic Factor ( TLF ) is a minor sub-fraction of human high-density lipoprotein that provides innate immunity by completely protecting humans from infection by most species of African trypanosomes , which belong to the K...	[ "Innate immunity ( present from birth ) is the first line of defense against microorganisms and provides an initial barrier against disease .", "Here we show that a minor sub-fraction of human high-density lipoprotein ( the good cholesterol ) , known as Trypanosome Lytic Factor ( TLF ) , not only kills the parasi...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology/epidemiology", "infectious diseases/neglected tropical diseases", "ophthalmology/eye infections" ]	What Will Happen If We Do Nothing To Control Trachoma: Health Expectancies for Blinding Trachoma in Southern Sudan	journal.pntd.0000396	null	[ [ "Trachoma is one of the oldest infectious diseases known to mankind and is the leading infectious cause of blindness , estimated to be responsible for 2 . 9% of blindness worldwide [1] .", "Recurrent infection with ocular Chlamydia trachomatis results in chronic inflammation , scarring , trichiasis , corn...	[ "Uncontrolled trachoma is a leading cause of blindness .", "Current global trachoma burden summary measures are presented as disability adjusted life years but have limitations due to inconsistent methods and inadequate population-based data on trachomatous low vision and blindness .", "We aimed to describe mor...	[ "Summary measures of population health attempt to express disease burden in terms of a common “currency” and are useful in establishing public health priorities .", "Disability adjusted life years ( DALYs ) , a health gap measure , have previously been used to estimate burden due to trachoma; however , their meth...	2009
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "pharmacologic analysis", "knees", "action potentials", "medicine and health sciences", "legs", "membrane potential", "limbs (anatomy)", "electrophysiology", "neuroscience", "simulation and modeling", "compartment models", "one-compartment models", "mathematics", "pharmacology", "neurona...	Gain control with A-type potassium current: IA as a switch between divisive and subtractive inhibition	journal.pcbi.1006292	null	[ [ "The activity of a neuron is driven by barrages of synaptic inputs .", "Synaptic inputs are classified as either excitatory ( those that promote spike generation ) and inhibitory ( those that impede spike generation ) .", "The interplay between these two “opposing” inputs influences how neurons proces...	[ "Neurons process and convey information by transforming barrages of synaptic inputs into spiking activity .", "Synaptic inhibition typically suppresses the output firing activity of a neuron , and is commonly classified as having a subtractive or divisive effect on a neuron’s output firing activity .", "Subtrac...	[ "Neurons process information by generating spikes in response to two types of synaptic inputs .", "Excitatory inputs increase spike rates and inhibitory inputs decrease spike rates ( typically ) .", "The interaction between these two input types and the transformation of these inputs into spike outputs is not ,...	2018
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "carbohydrate metabolism", "neurochemistry", "chemical compounds", "astrocytes", "carbohydrates", "neuroscience", "organic compounds", "macroglial cells", "glucose", "glucose metabolism", "camp signaling cascade", "cell signaling", "protein kinase signaling cascade", "animal cells", "che...	Norepinephrine stimulates glycogenolysis in astrocytes to fuel neurons with lactate	journal.pcbi.1006392	null	[ [ "The management of energy in the brain is organized by an oligocellular cooperative called the neural-glial-vasculature ensemble ( NGV ) .", "Each component is assigned distinct tasks during the chain of events that extract reducing equivalents from glucose to support every brain function .", "While t...	[ "The mechanism of rapid energy supply to the brain , especially to accommodate the heightened metabolic activity of excited states , is not well-understood .", "We explored the role of glycogen as a fuel source for neuromodulation using the noradrenergic stimulation of glia in a computational model of the neural-...	[ "Although efficient compared to computers , the human brain utilizes energy at 10-fold the rate of other organs by mass .", "How the brain is supplied with sufficient on-demand energy to support its activity in the absence of neuronal storage capacity remains unknown .", "Neurons are not capable of meeting thei...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "gene regulation", "regulatory proteins", "ocular anatomy", "dna-binding proteins", "vertebrates", "reporter genes", "animals", "animal models", "osteichthyes", "developmental biology", "model organisms", "transcription factors", "gene types", "embryos", ...	The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6	journal.pgen.1006441	null	[ [ "Cellular and molecular mechanisms of vertebrate lens development are objects of intense studies for many decades , reviewed in [1] .", "In particular , lens induction represents a classical developmental model allowing investigation of cell specification , spatiotemporal control of gene expression , as w...	[ "Lens induction is a classical developmental model allowing investigation of cell specification , spatiotemporal control of gene expression , as well as how transcription factors are integrated into highly complex gene regulatory networks ( GRNs ) .", "Pax6 represents a key node in the gene regulatory network gov...	[ "While significant insights into the functional role of some transcription factors during lens formation have been accomplished , much less is known about the intricate wiring of the gene regulatory network ( GRN ) that controls the earliest stages of lens development .", "Our genetic experiments presented here d...	2016
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "infectious diseases/viral infections", "ecology/population ecology", "public health and epidemiology" ]	Predicting the Timing and Magnitude of Tropical Mosquito Population Peaks for Maximizing Control Efficiency	journal.pntd.0000385	null	[ [ "Only a few of the approximately 3000 mosquito species known worldwide feed on human blood [1] .", "Unfortunately , these human pest species are responsible for the deaths of millions of people each year by transmitting some of the deadliest-known diseases , such as malaria , yellow fever , dengue , and R...	[ "The transmission of mosquito-borne diseases is strongly linked to the abundance of the host vector .", "Identifying the environmental and biological precursors which herald the onset of peaks in mosquito abundance would give health and land-use managers the capacity to predict the timing and distribution of the ...	[ "Mosquitoes carry several diseases that are potentially fatal to people .", "The risk of disease transmission is high when mosquitoes are abundant in an area , and it is therefore the job of health professionals to control or prevent mosquito outbreaks in certain areas , especially those close to human habitation...	2009
[ "Introduction", "Results", "Discussion", "Models" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "mitochondrial dna", "dose prediction methods", "toxicology", "dna damage", "toxicity", "pharmaceutics", "forms of dna", "mitochondria", "dna", "bioenergetics", "pharmacology", "cellular structures and organelles", "oxi...	A Biophysical Systems Approach to Identifying the Pathways of Acute and Chronic Doxorubicin Mitochondrial Cardiotoxicity	journal.pcbi.1005214	null	[ [ "Doxorubicin ( DOX ) is an anthracycline antibiotic with potent antineoplastic properties [1] .", "It has a broad-spectrum and is widely prescribed in the treatment of many types of cancers , including solid tumors and leukemias [2] .", "Yet , the clinical use of this drug is restricted by its severe ...	[ "The clinical use of the anthracycline doxorubicin is limited by its cardiotoxicity which is associated with mitochondrial dysfunction .", "Redox cycling , mitochondrial DNA damage and electron transport chain inhibition have been identified as potential mechanisms of toxicity .", "However , the relative roles ...	[ "Doxorubicin is a potent anticancer drug , but its efficacy is limited by a cumulative dose-dependent cardiotoxicity .", "Multiple pathways are involved in the drug cardiotoxicity , however , the underlying mechanisms are still not fully elucidated .", "Here we developed a computational model to study doxorubic...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "rna processing", "biophysic al simulations", "gene expression", "genetics", "molecular genetics", "biology", "computational biology", "genetics and genomics" ]	Modelling Reveals Kinetic Advantages of Co-Transcriptional Splicing	journal.pcbi.1002215	null	[ [ "The splicing of precursor messenger RNA ( pre-mRNA ) is an essential process in the expression of most eukaryotic genes .", "The five small nuclear ribonucleoproteins ( snRNPs ) and the many non-snRNP-associated proteins that constitute the splicing machinery , assemble anew on each precursor RNA to form...	[ "Messenger RNA splicing is an essential and complex process for the removal of intron sequences .", "Whereas the composition of the splicing machinery is mostly known , the kinetics of splicing , the catalytic activity of splicing factors and the interdependency of transcription , splicing and mRNA 3′ end formati...	[ "The coding information for the synthesis of proteins in mammalian cells is first transcribed from DNA to messenger RNA ( mRNA ) , before being translated from mRNA to protein .", "Each step is complex , and subject to regulation .", "Certain sequences of DNA must be skipped in order to generate a functional pr...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/disease models", "neurological disorders/movement disorders" ]	Transgenic Rat Model of Neurodegeneration Caused by Mutation in the TDP Gene	journal.pgen.1000887	null	[ [ "TAR DNA-binding protein ( TDP-43 ) is a highly conserved ribonucleoprotein that is encoded by the TDP gene and can bind to RNA , DNA , and proteins [1]-[3] .", "In mammals , the primary transcript of the TDP gene can be alternatively spliced to generate 11 mRNA molecules .", "The major splice variant...	[ "TDP-43 proteinopathies have been observed in a wide range of neurodegenerative diseases .", "Mutations in the gene encoding TDP-43 ( i . e . , TDP ) have been identified in amyotrophic lateral sclerosis ( ALS ) and in frontotemporal lobe degeneration associated with motor neuron disease .", "To study the conse...	[ "Amyotrophic lateral sclerosis , a condition also known as Lou Gehrig's disease , is characterized by progressive degeneration of motor neurons , denervation atrophy of skeletal muscles , and eventual paralysis of affected limbs .", "The signature pathology of Lou Gehrig's disease is the formation of intracellula...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "connectomics", "calcium imaging", "visual system", "cellular neuroscience", "neuroanatomy", "anatomy", "neuronal morphology", "neural networks", "nervous system", "biology and life sciences", "sensory systems", "neuroscience", "neuroimaging" ]	Pyramidal Cells Make Specific Connections onto Smooth (GABAergic) Neurons in Mouse Visual Cortex	journal.pbio.1001932	Light and electron microscopy of the primary visual cortex of mice indicates that pyramidal neurons connect preferentially to inhibitory neurons.	[ [ "The concept of the cortical “column” is one of the few organising principles for cortical circuits that we have , yet the characteristic orientation columns in the primary visual cortex ( V1 ) of the cat and monkey appear to be completely absent in rodent V1 .", "In place of the ordered maps of orientati...	[ "One of the hallmarks of neocortical circuits is the predominance of recurrent excitation between pyramidal neurons , which is balanced by recurrent inhibition from smooth GABAergic neurons .", "It has been previously described that in layer 2/3 of primary visual cortex ( V1 ) of cat and monkey , pyramidal cells ...	[ "The mammalian visual cortex , which is part of the cerebral cortex , contains 50 to 100 thousands of neurons per cubic millimetre , most of which are excitatory ( 85% ) and the minority , inhibitory ( 15% ) .", "Unlike neurons in the retina , neurons in the visual cortex are preferentially activated by lines or ...	2014
[ "Introduction", "Results", "Discussion", "Methods" ]	[]	The Essential Complexity of Auditory Receptive Fields	journal.pcbi.1004628	null	[ [ "Encoding models provide a powerful , objective means to evaluate our understanding of how sensory neural systems represent complex natural stimuli [1 , 2] .", "An encoding model describes any time-varying neural signal ( single- or multiunit activity [3 , 4] , local field potential [5] , hemodynamic acti...	[ "Encoding properties of sensory neurons are commonly modeled using linear finite impulse response ( FIR ) filters .", "For the auditory system , the FIR filter is instantiated in the spectro-temporal receptive field ( STRF ) , often in the framework of the generalized linear model .", "Despite widespread use of...	[ "Understanding how the brain solves sensory problems can provide useful insight for the development of automated systems such as speech recognizers and image classifiers .", "Recent developments in nonlinear regression and machine learning have produced powerful algorithms for characterizing the input-output rela...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "messenger rna", "microbiology", "operons", "bacterial diseases", "mutation", "enterobacteriaceae", "dna", "cellular structures and organelles", "bacteria", "bacterial pathogens", "infectious diseases", "me...	Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme	journal.pgen.1007615	null	[ [ "Synonymous mutations have traditionally been considered to be silent with respect to fitness because they do not change the encoded amino acid .", "However , synonymous mutations can alter mRNA structures in ways that alter translation initiation , mRNA stability , or even protein folding due to changes ...	[ "Synonymous mutations do not alter the specified amino acid but may alter the structure or function of an mRNA in ways that impact fitness .", "There are few examples in the literature , however , in which the effects of synonymous mutations on microbial growth rates have been measured , and even fewer for which ...	[ "When a new enzyme is needed , microbes often recruit a pre-existing enzyme with a promiscuous activity corresponding to the newly needed activity .", "Such enzymes are often the “weak-link” in metabolism because they have not evolved to efficiently catalyze the new reaction .", "Under these circumstances , inc...	2018
[ "Introduction", "Methods", "Discussion" ]	[ "dermatology", "infectious diseases", "veterinary diseases", "zoonoses", "medicine and health sciences", "skin infections", "travel-associated diseases", "leishmaniasis", "neglected tropical diseases", "biology and life sciences", "tropical diseases", "parasitic diseases", "veterinary scienc...	Species-Directed Therapy for Leishmaniasis in Returning Travellers: A Comprehensive Guide	journal.pntd.0002832	null	[ [ "Leishmaniasis , infection by Leishmania parasites , is increasingly reported among travellers , especially in adventurous and eco-tourists [1]–[6] and military personnel [7]–[11] .", "Three syndromes are distinguished: visceral ( VL ) , cutaneous ( CL ) and mucocutaneous leishmaniasis ( MCL ) .", "VL...	[ "Leishmaniasis is increasingly reported among travellers .", "Leishmania species vary in sensitivity to available therapies .", "Fast and reliable molecular techniques have made species-directed treatment feasible .", "Many treatment trials have been designed poorly , thus developing evidence-based guidelines...	[ "Human leishmaniasis is caused by unicellular parasites that are injected into the skin by sand-flies , small , flying insects .", "Many different Leishmania species cause various manifestations of disease , both of the skin and internal organs .", "Leishmaniasis is a curable disease but clear guidelines on the...	2014
[ "Introduction", "Model", "Results", "Discussion" ]	[ "theoretical biology", "physiology", "biology", "anatomy and physiology", "molecular cell biology" ]	Osteoprotegerin in Bone Metastases: Mathematical Solution to the Puzzle	journal.pcbi.1002703	null	[ [ "Based on the model described above , the presence of osteoprotegerin in bone metastases should lead to reduced bone destruction and tumor growth .", "In agreement with this prediction , the systemic application of OPG leads to a decrease in tumor burden [8] , and Corey and colleagues [9] demonstrated tha...	[ "Bone is a common site for cancer metastasis .", "To create space for their growth , cancer cells stimulate bone resorbing osteoclasts .", "Cytokine RANKL is a key osteoclast activator , while osteoprotegerin ( OPG ) is a RANKL decoy receptor and an inhibitor of osteoclastogenesis .", "Consistently , systemic...	[ "Breast and prostate cancers commonly metastasize to bone .", "To create more space for their expansion , metastatic tumors activate osteoclasts , the only cells capable of bone destruction .", "The main osteoclast stimulator is the cytokine RANKL , while osteoprotegerin ( OPG ) acts as a RANKL inhibitor .", ...	2012
[ "Introduction", "Results", "Discussion", "Material and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "immune physiology", "spleen", "immunology", "microbiology", "parasitic diseases", "parasitic protozoans", "protozoan life cycles", "bone marrow cells", "developmental biology", "protozoans", "leishmania", "neutrophils", "w...	HIF-1α is a key regulator in potentiating suppressor activity and limiting the microbicidal capacity of MDSC-like cells during visceral leishmaniasis	journal.ppat.1006616	null	[ [ "Elimination of intracellular pathogens requires the induction of pro-inflammatory cytokines and cytotoxic molecules secretion .", "Unfortunately , this process also leads to local tissue disruption and inflammation .", "Inflamed tissues represent a challenging microenvironment , characterized by hypo...	[ "Leishmania donovani is known to induce myelopoiesis and to dramatically increase extramedullary myelopoiesis .", "This results in splenomegaly , which is then accompanied by disruption of the splenic microarchitecture , a chronic inflammatory environment , and immunosuppression .", "Chronically inflamed tissue...	[ "The protozoan parasite Leishmania donovani causes chronic infection in the spleen , which is accompanied by a chronic inflammatory environment , an enlargement of the organ , and immunosuppression .", "The environment of chronically inflamed tissues is characterized by low oxygen levels and tissue disruption , w...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "cell biology/cellular death and stress responses" ]	Cdk2 Is Required for p53-Independent G2/M Checkpoint Control	journal.pgen.1000863	null	[ [ "Cdks associate with cyclins to form heterodimers that are sequentially activated during the cell cycle .", "Metazoan cells have multiple Cdks and cyclins that are temporally regulated [1] , [2] .", "In normal cell cycles , Cdk4 and Cdk6 pair with D-type cyclins during G1 , Cdk2 pairs with E- and A-ty...	[ "The activation of phase-specific cyclin-dependent kinases ( Cdks ) is associated with ordered cell cycle transitions .", "Among the mammalian Cdks , only Cdk1 is essential for somatic cell proliferation .", "Cdk1 can apparently substitute for Cdk2 , Cdk4 , and Cdk6 , which are individually dispensable in mice ...	[ "Metazoan cells contain multiple Cdks that regulate cell cycle progression .", "Recent studies have shown that mouse cells can grow normally with just Cdk1 .", "The roles of the non-essential Cdks remain a fundamental question .", "In this study , we describe the generation and detailed characterization of CD...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "systems biology", "biology" ]	Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model	journal.pcbi.1003451	null	[ [ "Cancer is one of the most important diseases affecting human health today [1] .", "Although cancer is considered a genetic disease [2] , with a variety of oncogenes and tumour suppressor genes identified , the specific genomic alterations vary wildly between and within cancer types .", "In 2008 , thr...	[ "One of the major breakthroughs in oncogenesis research in recent years is the discovery that , in most patients , oncogenic mutations are concentrated in a few core biological functional pathways .", "This discovery indicates that oncogenic mechanisms are highly related to the dynamics of biologic regulatory net...	[ "Among complex genetic diseases affecting humans , cancer is a major cause of death .", "In 2008 , a genome-wide analysis of hundreds of tumour samples showed that oncogenic mutations are concentrated in a few core functional pathways , revealing a new conceptual framework for cancer biology research , where the ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Functional Analysis of the Unique Cytochrome P450 of the Liver Fluke Opisthorchis felineus	journal.pntd.0004258	null	[ [ "The heme-containing enzymes cytochromes P450 ( CYPs ) are widely distributed in living organisms from bacteria to mammals [reviewed in Refs . 1 , 2–3] .", "CYP enzymes act as components of a monooxygenase system; they display biological functions ranging from detoxification of environmental pollutants to...	[ "The basic metabolic cytochrome P450 ( CYP ) system is essential for biotransformation of sterols and xenobiotics including drugs , for synthesis and degradation of signaling molecules in all living organisms .", "Most eukaryotes including free-living flatworms have numerous paralogues of the CYP gene encoding he...	[ "The basic metabolic system CYP ( cytochrome P450 ) is essential for biotransformation of sterols and xenobiotics , for synthesis and degradation of signaling molecules in all living organisms .", "Most eukaryotes including free-living flatworms evolved numerous paralogues of the CYP gene .", "Notably , by cont...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "motor systems", "computational neuroscience", "biology", "neuroscience", "neurophysiology" ]	Priors Engaged in Long-Latency Responses to Mechanical Perturbations Suggest a Rapid Update in State Estimation	journal.pcbi.1003177	null	[ [ "Neural transmission delays present a major challenge because the brain cannot directly use sensory feedback to guide motor actions .", "In order to compensate for feedback delays , the brain must build internal models of the dynamical interaction between the body and the environment , including sensory a...	[ "In every motor task , our brain must handle external forces acting on the body .", "For example , riding a bike on cobblestones or skating on irregular surface requires us to appropriately respond to external perturbations .", "In these situations , motor predictions cannot help anticipate the motion of the bo...	[ "It is commonly assumed that the brain uses internal estimates of the state of the body to adjust motor commands and perform successful movements .", "A problem arises when external disturbances deviate the limb from the ongoing task .", "In such cases , the estimated state of the body must be corrected based o...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "hela cells", "gene regulation", "cell cycle and cell division", "biological cultures", "immunology", "cell processes", "dna damage", "mitosis", "dna replication", "cell cultures", "dna", "molecular biology techniques", "re...	Rescue of collapsed replication forks is dependent on NSMCE2 to prevent mitotic DNA damage	journal.pgen.1007942	null	[ [ "Replication-associated DNA damage is common in human cells and can lead to the development of somatic mutations .", "DNA damage during replication can be induced by DNA lesion-producing chemicals , proteins bound to the DNA , DNA polymerase inhibitors , or nucleotide limitation [1] .", "Hydroxyurea (...	[ "NSMCE2 is an E3 SUMO ligase and a subunit of the SMC5/6 complex that associates with the replication fork and protects against genomic instability .", "Here , we study the fate of collapsed replication forks generated by prolonged hydroxyurea treatment in human NSMCE2-deficient cells .", "Double strand breaks ...	[ "DNA damage encountered by the replication fork causes fork stalling and is a major source of mutations when not adequately repaired .", "Fork stalling can lead to fork collapse , that is , a state of the fork in which normal DNA synthesis cannot be resumed at the site of stalling .", "Collapsed forks must be r...	2019
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "morphogenic segmentation", "gene regulation", "animals", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "insect vectors", "morphogenesis", "drosophila", "research and analysis methods", "epidemiology...	Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution	journal.pgen.1006052	null	[ [ "Molecular phylogenies based on protein coding genes have greatly enhanced evolutionary theory , and in favorable cases even allow a reconstruction of the last common ancestral gene or even full evolutionary pathways [1] .", "However regulatory sequence evolves more rapidly than coding sequence and the fu...	[ "Molecular evolution is an established technique for inferring gene homology but regulatory DNA turns over so rapidly that inference of ancestral networks is often impossible .", "In silico evolution is used to compute the most parsimonious path in regulatory space for anterior-posterior patterning linking two Di...	[ "The last common ancestor of the fruit fly ( Drosophila ) and mosquito ( Anopheles ) lived more than 200 Million years ago .", "Can we use available data on insects alive today to infer what their ancestor looked like ?", "In this manuscript , we focus on early embryonic development , when stripes of genetic ex...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chromosome structure and function", "dna damage", "telomeres", "mutation", "sumoylation", "dna replication", "dna", "research and analysis methods", "sequence analysis", "sequence alignment", "bioinformatics", "proteins", "chromosome biology", "chromosomal aberrations", "biochemistry", ...	SUMO E3 ligase Mms21 prevents spontaneous DNA damage induced genome rearrangements	journal.pgen.1007250	null	[ [ "The Small Ubiquitin-like MOdifier ( SUMO ) regulates many biological processes through its covalent attachment to lysine residues on target proteins via a cascade of an E1-activating enzyme ( Aos1-Uba2 in Saccharomyces cerevisiae ) , an E2-conjugating enzyme Ubc9 , and one of several SUMO E3 ligases [1] .", ...	[ "Mms21 , a subunit of the Smc5/6 complex , possesses an E3 ligase activity for the Small Ubiquitin-like MOdifier ( SUMO ) .", "Here we show that the mms21-CH mutation , which inactivates Mms21 ligase activity , causes increased accumulation of gross chromosomal rearrangements ( GCRs ) selected in the dGCR assay ....	[ "Chromosomal rearrangement is a hallmark of cancer .", "Saccharomyces cerevisiae Mms21 is an E3 ligase for Small Ubiquitin like MOdifer ( SUMO ) , which has been shown to have a major role in preventing chromosomal rearrangement .", "Despite extensive studies about the function of Mms21 in regulating the repair...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "flow cytometry", "chemical compounds", "phosphates", "cell processes", "mutation", "fungi", "substitution mutation", "model organisms", "cell growth", "experimental organism systems", "molecular biology techniques", "research and analysis methods", "saccharomyces", "spectrum analysis tech...	Dual role of starvation signaling in promoting growth and recovery	journal.pbio.2002039	null	[ [ "Growing cells require an influx of nutrients from their environment to sustain metabolic activity .", "Depletion of essential nutrients arrests cell growth until the nutrients are replenished [1] .", "Prior to this arrest , a starvation program that regulates the expression and activity of multiple g...	[ "Growing cells are subject to cycles of nutrient depletion and repletion .", "A shortage of nutrients activates a starvation program that promotes growth in limiting conditions .", "To examine whether nutrient-deprived cells prepare also for their subsequent recovery , we followed the transcription program acti...	[ "Cells must have sufficient nutrients in order to perform their different functions .", "This becomes particularly critical when the nutrient composition in their environment changes .", "To accommodate such changes , cells have evolved specialized adaptation pathways that sense the nutrients available in their...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine and health sciences", "enzyme-linked immunoassays", "pathology and laboratory medicine", "tropical diseases", "database searching", "research design", "age groups", "mathematics", "signs and symptoms", "statistics (mathematics)", "cohort studies", "neglected tropical di...	Tourniquet Test for Dengue Diagnosis: Systematic Review and Meta-analysis of Diagnostic Test Accuracy	journal.pntd.0004888	null	[ [ "Dengue is an arboviral infection ubiquitous to tropical and sub-tropical regions , [1–3] where it is transmitted by domesticated day-biting mosquitoes including Aedes aegypti .", "After an incubation period of 4–10 days ( mean , 7 days ) , illness onset is abrupt ( with headache , fever , myalgia/arthral...	[ "Dengue fever is a ubiquitous arboviral infection in tropical and sub-tropical regions , whose incidence has increased over recent decades .", "In the absence of a rapid point of care test , the clinical diagnosis of dengue is complex .", "The World Health Organisation has outlined diagnostic criteria for makin...	[ "Dengue is an infectious disease transmitted by mosquitoes in the Tropics .", "There are 2 . 5 billion people around the world at risk .", "Dengue presents as an acute febrile illness with symptoms including headache , bone or joint and muscular pains and rash .", "The objective of this study is to perform a ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology", "mitosis", "model organisms", "cell division", "chromosome biology", "biology", "molecular biology", "signal transduction", "pka signaling cascade", "cell biology", "yeast and fungal models", "molecular cell biology", "signaling cascades" ]	Proteins in the Nutrient-Sensing and DNA Damage Checkpoint Pathways Cooperate to Restrain Mitotic Progression following DNA Damage	journal.pgen.1002176	null	[ [ "Progression through mitosis in yeast requires the ordered destruction of two inhibitors: securin or Pds1 and the mitotic or B type cyclin , Clb2 .", "The inhibitors are ubiquitinated and targeted for destruction by the anaphase promoting complex or cyclosome ( APC/C ) in conjunction with the specificity ...	[ "Checkpoint pathways regulate genomic integrity in part by blocking anaphase until all chromosomes have been completely replicated , repaired , and correctly aligned on the spindle .", "In Saccharomyces cerevisiae , DNA damage and mono-oriented or unattached kinetochores trigger checkpoint pathways that bifurcate...	[ "Previous studies showed that phosphorylation of a subset of regulatory ( R ) subunits of the cAMP-dependent protein kinase ( PKA ) occurred under conditions that down-regulate global PKA activity , including growth on non-fermentable carbon sources .", "However , the role of the phosphorylation sites has not bee...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "methods and resources", "sleep", "anesthesiology", "brain electrophysiology", "brain", "electrophysiology", "neuroscience", "physiological processes", "clinical medicine", "pharmaceutics", "anesthesia", "gamma spectrometry", "brain mapping", "bioassays an...	Harnessing olfactory bulb oscillations to perform fully brain-based sleep-scoring and real-time monitoring of anaesthesia depth	journal.pbio.2005458	null	[ [ "Defining the different states of brain activity and describing how they impact the computations performed by neural networks is an ongoing challenge in neuroscience .", "In our day-to-day lives , the most dramatic change of state is found at the frontier between sleep and wakefulness , which involves sub...	[ "Real-time tracking of vigilance states related to both sleep or anaesthesia has been a goal for over a century .", "However , sleep scoring cannot currently be performed with brain signals alone , despite the deep neuromodulatory transformations that accompany sleep state changes .", "Therefore , at heart , th...	[ "Real-time tracking of vigilance states related to wake , sleep , and anaesthesia has been a goal for over a century .", "However identification of wakefulness and different sleep states cannot currently be performed routinely with brain signals and instead relies on motor activity .", "Here we demonstrate that...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "fungal genetics", "symbiosis", "trees", "fungi", "plant science", "genome analysis", "plant pathology", "plants", "mycology", "genomics", "pines", "gene expression", "pathogenesis", "plant fungal pathogens", "host-...	Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus	journal.pgen.1006348	null	[ [ "Growing evidence has shown that many symbiotic plant-microbial associations including pathogenic as well as mutualistic symbioses are governed by similar genetic interaction mechanisms [1 , 2] .", "For example , in many groups of pathogenic fungi and oomycetes , coevolution with their plant hosts has res...	[ "Ectomycorrhizal fungi ( EMF ) represent one of the major guilds of symbiotic fungi associated with roots of forest trees , where they function to improve plant nutrition and fitness in exchange for plant carbon .", "Many groups of EMF exhibit preference or specificity for different plant host genera; a good exam...	[ "Ectomycorrhizal fungi ( EMF ) comprise the dominant group of symbiotic fungi associated with plant roots in temperate and boreal forests .", "We examined host-specificity and gene-expression of five EMF Suillus species that exhibited strong patterns of mycorrhizal compatibility/incompatibility with either white ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/animal genetics", "biochemistry", "genetics and genomics/animal genetics", "physiology/renal, fluid, and electrolyte physiology", "physiology/gastroenterology and hepatology" ]	Mutations in the SLC2A9 Gene Cause Hyperuricosuria and Hyperuricemia in the Dog	journal.pgen.1000246	null	[ [ "Uric acid is the predominant product of purine metabolism in humans , great apes and one breed of dog , the Dalmatian; all other mammals excrete allantoin .", "During primate evolution , urate oxidase ( UOX ) , which catalyzes the oxidation of uric acid into allantoin , accumulated several independent no...	[ "Allantoin is the end product of purine catabolism in all mammals except humans , great apes , and one breed of dog , the Dalmatian .", "Humans and Dalmatian dogs produce uric acid during purine degradation , which leads to elevated levels of uric acid in blood and urine and can result in significant diseases in ...	[ "Animals excrete waste products in their urine .", "When most mammals metabolize compounds , called purines , they produce allantoin as one waste product in their urine .", "Humans , great apes , and Dalmatian dogs produce a different breakdown product , uric acid .", "This leads to high levels of uric acid i...	2008
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "humoral immunity", "sequencing", "medicine", "clinical laboratory sciences", "protein interactions", "immunology", "microbiology", "parastic protozoans", "glycoproteins", "sequence analysis", "synthetic peptide", "biology", "proteomics", "biochemistry", "trypanosoma", "diagnostic medi...	Identification of Peptide Mimotopes of Trypanosoma brucei gambiense Variant Surface Glycoproteins	journal.pntd.0001189	null	[ [ "Human African trypanosomiasis ( HAT ) , or sleeping sickness , is caused by the protozoan flagellar parasites Trypanosoma brucei ( T . b . ) gambiense and T . b . rhodesiense .", "The disease is transmitted by tsetse flies ( Glossina spp . ) and therefore only occurs in sub-Saharan Africa .", "The nu...	[ "The current antibody detection tests for the diagnosis of gambiense human African trypanosomiasis ( HAT ) are based on native variant surface glycoproteins ( VSGs ) of Trypanosoma brucei ( T . b . ) gambiense .", "These native VSGs are difficult to produce , and contain non-specific epitopes that may cause cross...	[ "The control of human African trypanosomiasis or sleeping sickness , a deadly disease in sub-Saharan Africa , mainly depends on a correct diagnosis and treatment .", "The aim of our study was to identify mimotopic peptides ( mimotopes ) that may replace the native proteins in antibody detection tests for sleeping...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models of infection", "antiviral therapeutics", "viral persistence and latency", "virology", "biology and life sciences", "microbiology" ]	Persistence of Virus Reservoirs in ART-Treated SHIV-Infected Rhesus Macaques after Autologous Hematopoietic Stem Cell Transplant	journal.ppat.1004406	null	[ [ "The introduction of antiretroviral therapy ( ART ) has dramatically reduced the morbidity and mortality associated with HIV infection and AIDS .", "However , currently available ART requires life long treatment with significant potential side effects and a cost that places an inordinate burden on public ...	[ "Despite many advances in AIDS research , a cure for HIV infection remains elusive .", "Here , we performed autologous hematopoietic stem cell transplantation ( HSCT ) in three Simian/Human Immunodeficiency Virus ( SHIV ) -infected , antiretroviral therapy ( ART ) -treated rhesus macaques ( RMs ) using HSCs colle...	[ "While antiretroviral therapy ( ART ) can reduce HIV replication , it does not eradicate the virus from an infected individual .", "Replication-competent viruses persist on ART and our incomplete understanding of these viral reservoirs greatly complicates the generation of a cure for HIV .", "In this study we p...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse transcriptase-polymerase chain reaction", "medicine and health sciences", "leptospira", "body fluids", "pathology and laboratory medicine", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "dogs", "urine", "molecular biology techniques", "kidneys", "bacteria", ...	Identification of Tenrec ecaudatus, a Wild Mammal Introduced to Mayotte Island, as a Reservoir of the Newly Identified Human Pathogenic Leptospira mayottensis	journal.pntd.0004933	null	[ [ "Leptospirosis is a bacterial zoonosis caused by pathogenic spirochetes of the genus Leptospira .", "Human infection is common in tropical countries where warm and humid conditions favour the survival of Leptospira spp .", "in water and soil .", "Furthermore , human populations in these countries ...	[ "Leptospirosis is a bacterial zoonosis of major concern on tropical islands .", "Human populations on western Indian Ocean islands are strongly affected by the disease although each archipelago shows contrasting epidemiology .", "For instance , Mayotte , part of the Comoros Archipelago , differs from the other ...	[ "Islands are exceptionally prone to species introduction , including pathogens with detrimental public health consequences for which the invasive alien species could act as reservoirs .", "Our study shows how the local non-native mammal fauna of Mayotte Island is associated with the introduction and epidemiology ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "biochemistry", "immune system proteins", "veterinary diseases", "zoonoses", "medicine and health sciences", "antibody isotypes", "proteins", "leishmaniasis", "protozoan infections", "biology and life sciences", "immunology", "antibodies", "parasitic diseases", "veterinary s...	IgG1 as a Potential Biomarker of Post-chemotherapeutic Relapse in Visceral Leishmaniasis, and Adaptation to a Rapid Diagnostic Test	journal.pntd.0003273	null	[ [ "The leishmaniases are widespread neglected infectious diseases of major public health importance , caused by protozoan parasites of the Leishmania ( Leishmania ) and Leishmania ( Viannia ) subgenera .", "There are two principal symptomatic clinical presentations of leishmaniasis:", "a ) visceral ( ka...	[ "Visceral leishmaniasis ( VL ) , caused by protozoa of the Leishmania donovani complex , is a widespread parasitic disease of great public health importance; without effective chemotherapy symptomatic VL is usually fatal .", "Distinction of asymptomatic carriage from progressive disease and the prediction of rela...	[ "Visceral leishmaniasis ( VL ) is a systemic disease with highest prevalence in South Asia , East Africa , and Brazil .", "VL is caused by protozoan ( unicellular ) parasites of the Leishmania donovani complex , transmitted to humans when an infected sandfly takes a bloodmeal .", "Within the human host , the pa...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "neuroscience", "homo (human)" ]	Mental Training Affects Distribution of Limited Brain Resources	journal.pbio.0050138	Intensive training in Vipassana meditation enhances one's ability to allocate attention efficiently in order to detect visual targets accurately. Behavioral and event-related potential evidence for a causal link between behavioral training and brain plasticity in adults is shown.	[ [ "A major limitation in human information processing arises from the time required to consciously identify and consolidate a visual stimulus in short-term memory [1] .", "This process can take more than a half-second before it is free for a second stimulus , as is revealed by the attentional-blink paradigm...	[ "The information processing capacity of the human mind is limited , as is evidenced by the so-called “attentional-blink” deficit: When two targets ( T1 and T2 ) embedded in a rapid stream of events are presented in close temporal proximity , the second target is often not seen .", "This deficit is believed to res...	[ "Meditation includes the mental training of attention , which involves the selection of goal-relevant information from the array of inputs that bombard our sensory systems .", "One of the major limitations of the attentional system concerns the ability to process two temporally close , task-relevant stimuli .", ...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/bacterial infections", "immunology/immunity to infections" ]	CD8+ T Cells Restrict Yersinia pseudotuberculosis Infection: Bypass of Anti-Phagocytosis by Targeting Antigen-Presenting Cells	journal.ppat.1000573	null	[ [ "Three Yersinia species cause disease in humans: Y . pestis , Y . pseudotuberculosis , and Y . enterocolitica [1] .", "Plague results from Y . pestis , introduced via fleabite or contaminated aerosols , and manifests in bubonic , septicemia , and pneumonic forms [2] .", "Oral ingestion of Y . pseudotu...	[ "All Yersinia species target and bind to phagocytic cells , but uptake and destruction of bacteria are prevented by injection of anti-phagocytic Yop proteins into the host cell .", "Here we provide evidence that CD8+ T cells , which canonically eliminate intracellular pathogens , are important for restricting Yer...	[ "Pathogenic Yersinia are bacteria that cause diverse diseases such as gastroenteritis and plague .", "Yersinia binds to specialized immune cells called macrophages , which attempt to engulf and destroy the bacteria .", "The bacteria resist destruction by injecting proteins called Yops into macrophages , which s...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "centrosomes", "vesicles", "caenorhabditis", "animals", "animal models", "developmental biology", "caenorhabditis elegans", "dyneins", "molecular motors", "model organisms", "mathematics", "statistics (mathematics)", "experimental organism systems", "embryos", "tubulin...	Dynactin binding to tyrosinated microtubules promotes centrosome centration in C. elegans by enhancing dynein-mediated organelle transport	journal.pgen.1006941	null	[ [ "Cytoplasmic dynein 1 ( dynein ) is the major microtubule ( MT ) minus-end directed motor in animals and transports various cargo from the cell periphery to the cell interior .", "The motor also moves and positions intracellular structures such as nuclei and centrosomes by pulling on the MTs to which they...	[ "The microtubule-based motor dynein generates pulling forces for centrosome centration and mitotic spindle positioning in animal cells .", "How the essential dynein activator dynactin regulates these functions of the motor is incompletely understood .", "Here , we dissect the role of dynactin's microtubule bind...	[ "Animal cells rely on molecular motor proteins to distribute intracellular components and organize their cytoplasmic content .", "The motor cytoplasmic dynein 1 ( dynein ) uses microtubule filaments as tracks to transport cargo from the cell periphery to the cell center , where the microtubule minus ends are embe...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "machine learning algorithms", "action potentials", "medicine and health sciences", "neural networks", "applied mathematics", "membrane potential", "electrophysiology", "neuroscience", "simulation and modeling", "algorithms", "mathematics", "artificial intelligence", "ranking algorithms", ...	Community-based benchmarking improves spike rate inference from two-photon calcium imaging data	journal.pcbi.1006157	null	[ [ "Two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations [1 , 2] .", "Indeed , the latest advances in scanning technologies make it now possible to record neural activity from hundreds or even thousands of cells simul...	[ "In recent years , two-photon calcium imaging has become a standard tool to probe the function of neural circuits and to study computations in neuronal populations .", "However , the acquired signal is only an indirect measurement of neural activity due to the comparatively slow dynamics of fluorescent calcium in...	[ "Two-photon calcium imaging is one of the major tools to study the activity of large populations of neurons in the brain .", "In this technique , a fluorescent calcium indicator changes its brightness when a neuron fires an action potential due to an associated increase in intracellular calcium .", "However , w...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "b vitamins", "chemical compounds", "enzymes", "enzymology", "organic compounds", "phosphatases", "serine", "genetic elements", "basic amino acids", "amino acids", "cobalamins", "genomics", "proteins", "chemistry", "vitamins", "methionine", "sulfur containing amino acids", "biochem...	Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics	journal.pgen.1007147	null	[ [ "Although it has been known for decades how the model bacterium Escherichia coli synthesizes all 20 of the standard amino acids , novel pathways for amino acid biosynthesis continue to be discovered in other bacteria and in archaea .", "For example , unlike E . coli , most bacteria use tRNA-dependent path...	[ "For many bacteria with sequenced genomes , we do not understand how they synthesize some amino acids .", "This makes it challenging to reconstruct their metabolism , and has led to speculation that bacteria might be cross-feeding amino acids .", "We studied heterotrophic bacteria from 10 different genera that ...	[ "For a few bacteria , it is well known how they can make all 20 of the standard amino acids ( the building blocks of proteins ) .", "For many other bacteria , their genome sequence implies that there are gaps in these biosynthetic pathways , so that the bacteria cannot make all of the amino acids and would need t...	2018
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[]	PKCη/Rdx-driven Phosphorylation of PDK1: A Novel Mechanism Promoting Cancer Cell Survival and Permissiveness for Parvovirus-induced Lysis	journal.ppat.1004703	null	[ [ "Protoparvoviruses ( PVs ) are non-enveloped icosahedral particles 24 nm in diameter , with a 5 . 1 kb linear single-stranded DNA genome encoding two capsid ( VP ) and several nonstructural ( NS ) proteins .", "Many rodent PVs , including H-1PV , were initially discovered as opportunistic infectants of hu...	[ "The intrinsic oncotropism and oncosuppressive activities of rodent protoparvoviruses ( PVs ) are opening new prospects for cancer virotherapy .", "Virus propagation , cytolytic activity , and spread are tightly connected to activation of the PDK1 signaling cascade , which delays stress-induced cell death and sus...	[ "The H-1 protoparvovirus ( H-1PV ) is the first replication-competent member of the Parvoviridae family to undergo a phase I/IIa clinical trial in patients suffering from glioblastoma multiforme .", "Although the intrinsic oncotropism and oncolytic activity of protoparvoviruses are well known , the underlying mol...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "phosphorylation", "medicine and health sciences", "vesicular stomatitis virus", "pathology and laboratory medicine", "molecular probe techniques", "gene regulation", "pathogens", "immunology", "immunoblotting", "microbiology", "immune receptor signaling", "viruses", "rna viruses", "membra...	Pivotal role for the ESCRT-II complex subunit EAP30/SNF8 in IRF3-dependent innate antiviral defense	journal.ppat.1006713	null	[ [ "The early induction of interferons ( IFNs ) and proinflammatory cytokines and chemokines is a hallmark of host innate immune responses to viral infections [1] .", "This process starts with the detection of viral components , most notably nucleic acids , by immune sentinel molecules termed pattern recogni...	[ "The activation of interferon ( IFN ) -regulatory factor-3 ( IRF3 ) , characterized by phosphorylation and nuclear translocation of the latent transcription factor , is central to initiating innate antiviral responses .", "Whereas much has been learned about the upstream pathways and signaling mechanisms leading ...	[ "The induction of IFN antiviral response is a hallmark of immediate host immune responses to viral infections .", "In a majority of cell types , eliciting this intrinsic defense mechanism depends on activation of IRF3 , characterized by C-terminal phosphorylation , dimerization and subsequent nuclear translocatio...	2017
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "neglected tropical diseases", "leprosy" ]	PARK2 Mediates Interleukin 6 and Monocyte Chemoattractant Protein 1 Production by Human Macrophages	journal.pntd.0002015	null	[ [ "Leprosy , also called Hansen's disease , is a persistent infectious disease caused by Mycobacterium leprae .", "While leprosy can be transmitted by armadillos in the Southern United States [1] humans are the most important reservoir for M . leprae and the more common route is human-human transmission .",...	[ "Leprosy is a persistent infectious disease caused by Mycobacterium leprae that still affects over 200 , 000 new patients annually .", "The host genetic background is an important risk factor for leprosy susceptibility and the PARK2 gene is a replicated leprosy susceptibility candidate gene .", "The protein pro...	[ "Leprosy is an infectious disease with a strong host genetic component .", "The identification of host genetic lesions predisposing to disease is a powerful approach for mapping key junctions in the host pathogen interplay .", "Genetic variants located in the promoter region of the PARK2 gene are replicated lep...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "histology", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	Role of the Gut Endoderm in Relaying Left-Right Patterning in Mice	journal.pbio.1001276	Analysis of Sox17 mutant mice reveals that gap junction coupling across the gut endoderm of the embryo transmits the left-right asymmetric signal from the node to the site of asymmetric organogenesis in mice.	[ [ "The elaboration of the major axes of the embryo ( anterior-posterior , dorsal-ventral , and left-right ) occurs at the time of gastrulation , the morphogenetic process that forms the primary germ layers ( ectoderm , mesoderm , and definitive endoderm ) .", "The molecular definition of a left-right ( LR )...	[ "Establishment of left-right ( LR ) asymmetry occurs after gastrulation commences and utilizes a conserved cascade of events .", "In the mouse , LR symmetry is broken at a midline structure , the node , and involves signal relay to the lateral plate , where it results in asymmetric organ morphogenesis .", "How ...	[ "Superficially , humans , like other vertebrates , are bilaterally symmetrical .", "Nonetheless , the internal configuration of visceral organs reveals a stereotypical asymmetry .", "For example , human hearts are generally located on the left and the liver on the right side within the body cavity .", "How th...	2012
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "biofilms", "bacteriology", "medicine and health sciences", "toxins", "crystal structure", "pathology and laboratory medicine", "chemical compounds", "pathogens", "vibrio", "condensed matter physics", "microbiology", "carbohydrates", "organic compounds", "toxicology", "toxic agents", "...	Structural basis of mammalian glycan targeting by Vibrio cholerae cytolysin and biofilm proteins	journal.ppat.1006841	null	[ [ "The recognition of carbohydrate receptors on host cell-surfaces is an important strategy for achieving the selectivity and potency of virulence factors including adhesion molecules , toxins , and biofilm proteins [1–3] .", "Often mediated by a canonical set of lectin domains with conserved folds , these ...	[ "Vibrio cholerae is an aquatic gram-negative microbe responsible for cholera , a pandemic disease causing life-threatening diarrheal outbreaks in populations with limited access to health care .", "Like most pathogenic bacteria , V . cholerae secretes virulence factors to assist colonization of human hosts , seve...	[ "Bacterial pathogens secrete multiple virulence factors to aid in infection including adhesion molecules , effector proteins , enzymes , toxins and biofilm proteins .", "To increase the potency and specificity of these molecules , many factors contain binding sites for host cell-surface receptors .", "This stud...	2018
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "meiosis", "yeast two-hybrid assays", "rna interference", "cell cycle and cell division", "cell processes", "animals", "animal models", "germ cells", "oocytes", "drosophila melanogaster", "model organisms", "protein interaction assays", "experimental organism systems", "...	Narya, a RING finger domain-containing protein, is required for meiotic DNA double-strand break formation and crossover maturation in Drosophila melanogaster	journal.pgen.1007886	null	[ [ "Homologous recombination is an essential feature of meiosis and is required to ensure proper chromosome segregation .", "Although several core aspects of meiosis are highly conserved , many of the proteins and structures that mediate meiosis have features that are unique to each model organism .", "T...	[ "Meiotic recombination , which is necessary to ensure that homologous chromosomes segregate properly , begins with the induction of meiotic DNA double-strand breaks ( DSBs ) and ends with the repair of a subset of those breaks into crossovers .", "Here we investigate the roles of two paralogous genes , CG12200 an...	[ "Errors in chromosome segregation during meiosis are the leading cause of miscarriages and can result in genetic abnormalities like Down syndrome or Turner syndrome .", "For chromosomes to segregate faithfully , they must recombine with their homolog during the early steps of meiosis .", "An essential component...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "cancer genetics", "genetics", "biology", "basic cancer research", "genetics and genomics" ]	Estrogen Mediated-Activation of miR-191/425 Cluster Modulates Tumorigenicity of Breast Cancer Cells Depending on Estrogen Receptor Status	journal.pgen.1003311	null	[ [ "MicroRNAs ( miRNAs ) are a class of evolutionarily conserved regulatory RNAs that pleiotropically suppress gene expression at post-transcriptional level [1] .", "MiRNAs control the expression of 10–30% of the human transcriptome and are crucial regulators of both physiologic and pathologic processes [2]–...	[ "MicroRNAs ( miRNAs ) , single-stranded non-coding RNAs , influence myriad biological processes that can contribute to cancer .", "Although tumor-suppressive and oncogenic functions have been characterized for some miRNAs , the majority of microRNAs have not been investigated for their ability to promote and modu...	[ "MicroRNAs are small noncoding RNAs that act as posttranscriptional repressors of gene expression .", "A pivotal role for miRNAs in all the molecular processes driving initiation and progression of various malignancies , including breast cancer , has been described .", "Divergent miRNA expression between normal...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Novel Mechanism of Bacterial Toxin Transfer within Host Blood Cell-Derived Microvesicles	journal.ppat.1004619	null	[ [ "Shiga toxin ( Stx ) is the major virulence factor of enterohemorrhagic Escherichia coli ( EHEC ) .", "EHEC are non-invasive bacteria [1] causing gastrointestinal infection presenting with diarrhea , hemorrhagic colitis and in severe cases leading to hemolytic uremic syndrome ( HUS ) characterized by thro...	[ "Shiga toxin ( Stx ) is the main virulence factor of enterohemorrhagic Escherichia coli , which are non-invasive strains that can lead to hemolytic uremic syndrome ( HUS ) , associated with renal failure and death .", "Although bacteremia does not occur , bacterial virulence factors gain access to the circulation...	[ "Shiga toxin-producing enterohemorrhagic Escherichia coli are non-invasive bacteria that , after ingestion , cause disease by systemic release of toxins and other virulence factors .", "These infections cause high morbidity , including hemolytic uremic syndrome with severe anemia , low platelet counts , renal fai...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "luciferase", "pathology and laboratory medicine", "enzymes", "pathogens", "gene regulation", "microbiology", "enzymology", "dna transcription", "viruses", "dna replication", "dna viruses", "sequence motif analysis", "dna", "herpesviruses", "research and...	An integrative approach identifies direct targets of the late viral transcription complex and an expanded promoter recognition motif in Kaposi’s sarcoma-associated herpesvirus	journal.ppat.1007774	null	[ [ "A conserved feature of double-stranded ( ds ) DNA viruses is that they possess a set of genes that become strongly activated only following viral DNA replication [1] .", "These “late genes” generally encode factors involved in viral assembly that are essential for virion production .", "The mechanism...	[ "The structural proteins of DNA viruses are generally encoded by late genes , whose expression relies on recruitment of the host transcriptional machinery only after the onset of viral genome replication .", "β and γ-herpesviruses encode a unique six-member viral pre-initiation complex ( vPIC ) for this purpose ,...	[ "Gene expression in DNA viruses often occurs in temporal waves , with expression of essential structural proteins occurring late in infection , after viral genome replication has begun .", "Strategies underlying expression of these viral late genes are often sophisticated; for example , the β- and γ-herpesviruses...	2019
[ "Introduction", "Results", "Discussion", "Materials & methods" ]	[ "chemical bonding", "urea", "protein interactions", "chemical compounds", "enzymes", "microbiology", "enzymology", "viral structure", "organic compounds", "tartrates", "membrane proteins", "serine proteases", "cellular structures and organelles", "physical chemistry", "proteins", "stru...	The Vaccinia virion: Filling the gap between atomic and ultrastructure	journal.ppat.1007508	null	[ [ "The virion of Vaccinia , the prototypical poxvirus , is one of the largest among the animal viruses .", "While its ultrastructural characterization is the beneficiary of 60+ years of electron microscopic examination [1–3] and references therein , attempts to better understand its molecular and atomic arc...	[ "We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking , identifying 4609 unique-mass crosslink ions at an effective FDR of 0 . 33% , covering 2534 unique pairs of crosslinked protein positions , 625 of which were inter-protein .", "The data wer...	[ "Vaccinia is one of the most complex virions among the animal viruses , containing 70+ distinct gene products .", "Although virion ultrastructure has been apparent , at least in outline by electron microscopy since the year 1961 or earlier , its molecular architecture is largely unknown: Vaccinia is resistant to ...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "complex systems", "systems biology", "mathematics", "applied mathematics", "biology", "genetics and genomics" ]	The Fidelity of Dynamic Signaling by Noisy Biomolecular Networks	journal.pcbi.1002965	null	[ [ "Cells are continuously challenged by extra- and intracellular fluctuations , or ‘noise’ , [1]–[3] .", "We are only starting to unravel how fluctuating inputs and dynamic interactions with other stochastic , intracellular systems affect the behavior of biomolecular networks [4]–[9] .", "Such knowledge...	[ "Cells live in changing , dynamic environments .", "To understand cellular decision-making , we must therefore understand how fluctuating inputs are processed by noisy biomolecular networks .", "Here we present a general methodology for analyzing the fidelity with which different statistics of a fluctuating inp...	[ "Cells do not live in constant conditions , but in environments that change over time .", "To adapt to their surroundings , cells must therefore sense fluctuating concentrations and ‘interpret’ the state of their environment to see whether , for example , a change in the pattern of gene expression is needed .", ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "developmental biology", "genetics", "biology", "molecular cell biology", "genetics and genomics" ]	Histone Deacetylase 2 (HDAC2) Regulates Chromosome Segregation and Kinetochore Function via H4K16 Deacetylation during Oocyte Maturation in Mouse	journal.pgen.1003377	null	[ [ "Post-translational modifications of histones , e . g . , phosphorylation , methylation , ubiquitination , and acetylation , are critically involved in a number of cellular processes that range from regulating gene expression to repair of DNA damage [1]–[3] .", "Lysine acetylation of histones is controlle...	[ "Changes in histone acetylation occur during oocyte development and maturation , but the role of specific histone deacetylases in these processes is poorly defined .", "We report here that mice harboring Hdac1−/+/Hdac2−/− or Hdac2−/− oocytes are infertile or sub-fertile , respectively .", "Depleting maternal HD...	[ "Oocyte development is becoming of increasing interest not only in the broad research community but also within the general public due , in part , to the ever increasing demand for and use of assisted reproductive technologies ( ART ) to treat human infertility , and because the oocyte-to-embryo transition encompas...	2013
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "chemical compounds", "enzymes", "enzymology", "carbohydrates", "organic compounds", "glucose", "asparagine", "fungi", "model organisms", "materials science", "experimental organism systems", "enzyme metabolism", "acidic amino acids", "amino acids", "oligomers", "cellular structures an...	Filamentation of asparagine synthetase in Saccharomyces cerevisiae	journal.pgen.1007737	null	[ [ "Intracellular compartmentation is crucial for the function of a cell .", "In 2010 , three studies reported that the metabolic enzyme CTP synthase ( CTPS ) , forms filamentous compartments , termed cytoophidia , in fruit flies , bacteria and budding yeast cells [1–3] .", "Subsequent studies revealed t...	[ "Asparagine synthetase ( ASNS ) and CTP synthase ( CTPS ) are two metabolic enzymes crucial for glutamine homeostasis .", "A genome-wide screening in Saccharomyces cerevisiae reveal that both ASNS and CTPS form filamentous structures termed cytoophidia .", "Although CTPS cytoophidia were well documented in rece...	[ "Asparagine synthetase ( ASNS ) is an essential enzyme for biosynthesis of asparagine .", "We have recently shown that ASNS , similar to CTP synthase ( CTPS ) , can assemble into snake-shaped structures termed cytoophidia .", "In this study , we reveal that the ASNS cytoophidium stays close with the CTPS cytoop...	2018
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "livestock", "medicine and health sciences", "ruminants", "tropical diseases", "geographical locations", "vertebrates", "south sudan", "animals", "brucellosis", "mammals", "bacterial diseases", "neglected tropical diseases", "africa", "veterinary science", "public and occupational health...	The sero-prevalence of brucellosis in cattle and their herders in Bahr el Ghazal region, South Sudan	journal.pntd.0006456	null	[ [ "Brucellosis is described as a highly contagious zoonotic disease , and a cause of significant reproductive losses in livestock [1] .", "Brucellosis is common in Low and Middle Income Countries ( LMICs ) , characterized by poor hygiene , consumption of raw animal products ( like milk and meat ) , and lack...	[ "Brucellosis is a worldwide recognized bacterial zoonotic disease .", "There is currently no information on bovine brucellosis sero-prevalence in South Sudan regardless of the economic , social and public health impact on populations .", "Therefore , for the first time in 33 years , we report the sero-prevalenc...	[ "Enzootic brucellosis is a bacterial infectious disease , which represents millions of dollars in production losses in livestock , as well as Disability- Adjusted Life Years ( DALYS ) associated with health and treatment in the human populations for Low and Middle Income Countries ( LMICs ) .", "Despite these une...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "biophysics", "evolutionary biology/bioinformatics", "computational biology" ]	Investigating Homology between Proteins using Energetic Profiles	journal.pcbi.1000722	null	[ [ "Protein structure and function are ultimately determined by thermodynamics .", "For example , Anfinsen's seminal work [1] demonstrated that the native state of a protein exists at a minimum in Gibbs free energy of stability under physiological conditions .", "Binding and catalysis are also governed b...	[ "Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation .", "In contrast , less is known about the effects of large sequence or structure changes on the stability of a particular fold .", "Almost completely unknown is the degree to which stab...	[ "Protein structure and function are fundamentally determined by thermodynamics .", "However , for technical as well as historical reasons , current evolutionary classification schemes and bioinformatics tools do not fully utilize thermodynamic information to describe or analyze proteins .", "In this work , we a...	2010
[ "Introduction", "Methods", "Results/Discussion" ]	[ "enzymes", "condensed matter physics", "enzymology", "dismutases", "simulation and modeling", "protein structure prediction", "protein structure", "research and analysis methods", "relaxation (physics)", "proteins", "melting", "phase transitions", "molecular biology", "physics", "protein...	As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy	journal.pcbi.1005211	null	[ [ "No other scientific discipline has been so challenged to match the standard of physics-based simplicity as molecular and cell biology , perhaps in parts due to the inherent complexity of the systems under study and to our incomplete knowledge of the structure and function of the living cell .", "In narro...	[ "Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom ( AA ) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein ( HA-Gō ) , the ...	[ "Although experimentalists can now unfold single proteins in the lab by pulling them apart and measuring the force and extension , a clear idea of how the protein changes shape and loses structure during this process is currently missing .", "Molecular dynamics simulations can offer insight as to what is actually...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology/cellular microbiology and pathogenesis", "cell biology/cell signaling" ]	Chlamydial Entry Involves TARP Binding of Guanine Nucleotide Exchange Factors	journal.ppat.1000014	null	[ [ "Chlamydiae are obligate intracellular bacterial pathogens that are responsible for a number of human diseases [1] .", "Different serological variants of Chlamydia trachomatis are primarily pathogens of humans .", "Serological variants ( serovar ) A , B , Ba , and C are the etiologic agents of trachom...	[ "Chlamydia trachomatis attachment to cells induces the secretion of the elementary body–associated protein TARP ( Translocated Actin Recruiting Protein ) .", "TARP crosses the plasma membrane where it is immediately phosphorylated at tyrosine residues by unknown host kinases .", "The Rac GTPase is also activate...	[ "The human pathogen Chlamydia trachomatis is the causative agent of the most prevalent bacterial sexually transmitted disease in industrialized nations , and of the preventable blinding condition trachoma in developing countries .", "Survival and replication of chlamydial species occur exclusively inside a host c...	2008
[ "Introduction", "Results", "Discussion" ]	[ "cell physiology", "medicine and health sciences", "vesicles", "pathology and laboratory medicine", "pathogens", "microbiology", "signaling networks", "orthomyxoviruses", "viruses", "wireless sensor networks", "membrane fusion", "rna viruses", "network analysis", "molecular biology techniq...	Viral RNA Degradation and Diffusion Act as a Bottleneck for the Influenza A Virus Infection Efficiency	journal.pcbi.1005075	null	[ [ "Seasonal influenza epidemics and periodical pandemics remain a constant threat to the human population .", "Influenza A virus ( IAV ) infection is a multi-step process that critically depends on the viral spike protein hemagglutinin ( HA ) , which mediates host cell adhesion by binding to sialic acid-con...	[ "After endocytic uptake , influenza viruses transit early endosomal compartments and eventually reach late endosomes .", "There , the viral glycoprotein hemagglutinin ( HA ) triggers fusion between endosomal and viral membrane , a critical step that leads to release of the viral segmented genome destined to reach...	[ "Influenza A virus carries its segmented genome inside a lipid envelope .", "Since genome replication occurs inside the nucleus , the main goal of virus infection is to deliver all genome segments through the cytoplasm into the nucleus .", "After endocytic uptake , influenza viruses transit early endosomal comp...	2016

Subsets and Splits

No community queries yet

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