headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Early Lineage Priming by Trisomy of Erg Leads to Myeloproliferation in a Down Syndrome Model | journal.pgen.1005211 | null | [
[
"Down syndrome ( DS ) is the commonest human aneuploidy [1] .",
"DS infants with trisomy of human chromosome 21 ( HSA21 ) are uniquely predisposed to a transient myeloproliferative disorder ( DS-TMD ) and acute megakaryocytic leukemia ( DS-AMKL ) [2] .",
"DS-TMD , usually characterised by the presence... | [
"Down syndrome ( DS ) , with trisomy of chromosome 21 ( HSA21 ) , is the commonest human aneuploidy .",
"Pre-leukemic myeloproliferative changes in DS foetal livers precede the acquisition of GATA1 mutations , transient myeloproliferative disorder ( DS-TMD ) and acute megakaryocytic leukemia ( DS-AMKL ) .",
"Tr... | [
"An excess number of genes in trisomy on human chromosome 21 leads to the development of specific diseases in human Down syndrome .",
"An excess copy of the gene , ERG , an ETS family transcription factor , has been implicated in abnormal blood system development in Down syndrome .",
"In this study we show how ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"urology",
"medicine and health sciences",
"pathology and laboratory medicine",
"immunology",
"microbiology",
"immunodeficiency viruses",
"urologic infections",
"infectious diseases",
"medical microbiology",
"hiv",
"microbial pathogens",
"pathogenesis",
"microbial ecology",
"immunopatholog... | The Semen Microbiome and Its Relationship with Local Immunology and Viral Load in HIV Infection | journal.ppat.1004262 | null | [
[
"Semen is an important vector in the sexual transmission of HIV [1] , and the risk of transmission increases with the semen HIV RNA viral load ( VL ) [2] , [3] .",
"The semen VL is more variable over time than that of blood , and the two are only moderately correlated [4]–[8] .",
"Therefore , since th... | [
"Semen is a major vector for HIV transmission , but the semen HIV RNA viral load ( VL ) only correlates moderately with the blood VL .",
"Viral shedding can be enhanced by genital infections and associated inflammation , but it can also occur in the absence of classical pathogens .",
"Thus , we hypothesized tha... | [
"The classical paradigm of HIV infectivity centers on the blood HIV RNA viral load .",
"However , while other fluid compartments such as semen and cerebrospinal fluid can have distinct viral loads from blood , the causes of localized HIV shedding are not fully understood .",
"Since the semen viral load is an in... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"legs",
"tropical diseases",
"geographical locations",
"limbs (anatomy)",
"parasitic diseases",
"health care",
"ethnicities",
"age groups",
"neglected tropical diseases",
"ethiopia",
"supervisors",
"africa",
"morbidity",
"musculoskeletal system",
"elepha... | Integrated morbidity mapping of lymphatic filariasis and podoconiosis cases in 20 co-endemic districts of Ethiopia | journal.pntd.0006491 | null | [
[
"Lymphatic filariasis ( LF ) and podoconiosis are neglected tropical diseases ( NTDs ) that affect the world’s poorest people and pose a significant economic burden to developing countries [1] .",
"Responsible for 90% of cases worldwide , Wuchereria bancrofti is the causative agent of LF in Africa , and i... | [
"Lymphatic filariasis ( LF ) and podoconiosis are neglected tropical diseases ( NTDs ) that pose a significant physical , social and economic burden to endemic communities .",
"Patients affected by the clinical conditions of LF ( lymphoedema and hydrocoele ) and podoconiosis ( lymphoedema ) need access to morbidi... | [
"Patients affected by the clinical conditions of lymphatic filariasis ( lymphoedema and hydrocoele ) and podoconiosis ( lymphoedema ) require access to a minimum package of care to prevent progression of the disease , and to improve their quality of life .",
"Clear estimates of the number and location of these pa... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biophysics/biomacromolecule-ligand interactions",
"computational biology/sequence motif analysis",
"computational biology/transcriptional regulation"
] | Inferring Binding Energies from Selected Binding Sites | journal.pcbi.1000590 | null | [
[
"The bimolecular interaction between a DNA binding protein , TF , and a particular DNA binding sequence , Si , is governed by two rate constants , kon for the formation of the complex , and koff for the dissociation rate: The equilibrium binding constant of the TF to the site Si is:where concentrations are in... | [
"We employ a biophysical model that accounts for the non-linear relationship between binding energy and the statistics of selected binding sites .",
"The model includes the chemical potential of the transcription factor , non-specific binding affinity of the protein for DNA , as well as sequence-specific paramete... | [
"The DNA binding sites of transcription factors that control gene expression are often predicted based on a collection of known or selected binding sites .",
"The most commonly used methods for inferring the binding site pattern , or sequence motif , assume that the sites are selected in proportion to their affin... | 2009 |
[
"Introduction",
"Results",
"Examples from the paper [",
"Discussion",
"Methods"
] | [
"control theory",
"chemical compounds",
"engineering and technology",
"integrative physiology",
"carbohydrates",
"organic compounds",
"glucose",
"control engineering",
"systems science",
"mathematics",
"algebra",
"polynomials",
"computer and information sciences",
"vector spaces",
"chemi... | Dynamic compensation, parameter identifiability, and equivariances | journal.pcbi.1005447 | null | [
[
"We formally state definitions in the language of dynamical systems with inputs and outputs , the standard paradigm in control systems theory [17]:",
"x ˙ = f ( x , u , p ) , y = h ( x , u , p ) , x ( 0 ) = ξ p , ( 1 )",
"or , more explicitly ,",
"d x d t ( t ) = f ( x ( t ) , u ( t ) , p ) , y ( ... | [
"A recent paper by Karin et al . introduced a mathematical notion called dynamical compensation ( DC ) of biological circuits .",
"DC was shown to play an important role in glucose homeostasis as well as other key physiological regulatory mechanisms .",
"Karin et al . went on to provide a sufficient condition t... | [
"A recently introduced mathematical notion called dynamical compensation of biological circuits was shown to play an important role in glucose homeostasis and other key physiological regulatory mechanisms .",
"This paper explains how dynamical compensation can be formulated in terms of a well-known concept in sys... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"clinical research design",
"genetics",
"molecular genetics",
"biology",
"human genetics",
"genetics and genomics"
] | Novel Loci for Adiponectin Levels and Their Influence on Type 2 Diabetes and Metabolic Traits: A Multi-Ethnic Meta-Analysis of 45,891 Individuals | journal.pgen.1002607 | null | [
[
"Adiponectin is a highly abundant adipocyte-derived plasma protein whose levels correlate inversely with a range of important clinical parameters including blood glucose , indices of insulin resistance , proatherogenic dyslipidemia , and risk of type 2 diabetes ( T2D ) , stroke and coronary artery disease [1]... | [
"Circulating levels of adiponectin , a hormone produced predominantly by adipocytes , are highly heritable and are inversely associated with type 2 diabetes mellitus ( T2D ) and other metabolic traits .",
"We conducted a meta-analysis of genome-wide association studies in 39 , 883 individuals of European ancestry... | [
"Serum adiponectin levels are highly heritable and are inversely correlated with the risk of type 2 diabetes ( T2D ) , coronary artery disease , stroke , and several metabolic traits .",
"To identify common genetic variants associated with adiponectin levels and risk of T2D and metabolic traits , we conducted a m... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"vero cells",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"biological cultures",
"dna-binding proteins",
"microbiology",
"viruses",
"dna viruses",
"epigenetics",
"herpesviruses",
"chromatin",
"research and analysis methods",
"chromosome biology",
"pr... | Chromatin remodeling controls Kaposi's sarcoma-associated herpesvirus reactivation from latency | journal.ppat.1007267 | null | [
[
"Kaposi’s sarcoma-associated herpesvirus ( KSHV ) , also known as human herpesvirus 8 , is the causative agent of three human malignancies , the endothelial cell cancer Kaposi’s sarcoma ( KS ) , as well as two B cell cancers , primary effusion lymphoma ( PEL ) and multicentric Castleman’s disease ( reviewed i... | [
"Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the etiologic agent of three human malignancies , the endothelial cell cancer Kaposi’s sarcoma , and two B cell cancers , Primary Effusion Lymphoma and multicentric Castleman’s disease .",
"KSHV has latent and lytic phases of the viral life cycle , and while bo... | [
"Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the causative agent of three human malignancies .",
"KSHV establishes latent infection but can be reactivated from latency to the lytic phase of the viral life cycle to propagate .",
"KSHV reactivation from latency is controlled by epigenetic changes at the p... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"sequencing techniques",
"infographics",
"split-decomposition method",
"population genetics",
"computational biology",
"alleles",
"multiple alignment calculation",
"platinum",
"genome analysis",
"molecular biology techniques",
"population biology",
"research and analysis methods",
"sequence ... | High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs | journal.pcbi.1005151 | null | [
[
"Genetic variation at HLA loci , both classical and non-classical , is associated with many medical phenotypes including risk of autoimmune [1–3] and infectious [4] disease , adverse drug reactions [5 , 6] , success of tissue and organ transplants [7] , and , via epitope presentation preferences , the success... | [
"Genetic variation at the Human Leucocyte Antigen ( HLA ) genes is associated with many autoimmune and infectious disease phenotypes , is an important element of the immunological distinction between self and non-self , and shapes immune epitope repertoires .",
"Determining the allelic state of the HLA genes ( HL... | [
"Determining an individual’s HLA type ( the sequence of the exons of the HLA genes ) is important in many areas of biomedical research .",
"For example , HLA types shape immune epitope repertoires , which are relevant in cancer immunotherapy , and influence autoimmune and infectious disease risk .",
"Whole-geno... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"biological cultures",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"rna viruses",
"dna replication",
"molecular biology techniques",
"... | Integrated and Total HIV-1 DNA Predict Ex Vivo Viral Outgrowth | journal.ppat.1005472 | null | [
[
"Current antiretroviral therapy ( ART ) successfully suppresses viral replication and reduces HIV-1 transmission , but fails to completely eliminate HIV-1 [1] .",
"Even after long-term ART , a latent reservoir of HIV-1 DNA persists and remains fully competent to refuel viral rebound when ART is stopped [2... | [
"The persistence of a reservoir of latently infected CD4 T cells remains one of the major obstacles to cure HIV .",
"Numerous strategies are being explored to eliminate this reservoir .",
"To translate these efforts into clinical trials , there is a strong need for validated biomarkers that can monitor the rese... | [
"Current HIV-1 research aims to find a cure for HIV-1 , either by pursuing viral eradication or by attempting to attain an immune-mediated functional cure .",
"For the purpose of interpreting the findings of these eradication strategies , a validated representative biomarker of the replication-competent latent HI... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine and health sciences",
"pathology and laboratory medicine",
"infectious disease epidemiology",
"pathogens",
"sociology",
"signaling networks",
"social sciences",
"animals",
"circadian oscillators",
"simulation and modeling",
"network analysis",
"social networks",
... | Short-term activity cycles impede information transmission in ant colonies | journal.pcbi.1005527 | null | [
[
"Cyclical activity patterns are found at every level of biological organization , from genes to cells , organs , and societies , and span many orders of magnitude in space and time .",
"For instance , cyclical activity is found at the smallest spatial scale in the regulation of circadian Clock genes [1] ,... | [
"Rhythmical activity patterns are ubiquitous in nature .",
"We study an oscillatory biological system: collective activity cycles in ant colonies .",
"Ant colonies have become model systems for research on biological networks because the interactions between the component parts are visible to the naked eye , an... | [
"Many complex biological systems , from cardiac tissues to entire animal populations , exhibit rhythmical oscillations .",
"Here we studied a textbook example of a complex living system–colonies of Leptothorax ants , which exhibit short ( 15 minute ) collective activity cycles .",
"In ant colonies , information... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/animal genetics",
"genetics and genomics/disease models",
"genetics and genomics/genetics of disease",
"genetics and genomics",
"genetics and genomics/medical genetics"
] | A Missense Mutation in the SERPINH1 Gene in Dachshunds with Osteogenesis Imperfecta | journal.pgen.1000579 | null | [
[
"Collagen I is the most abundant protein in the human body and its highly ordered fibril structure is responsible for its special mechanical properties .",
"Together with inorganic hydroxylapatite it is the main component of bones and gives them elasticity while the hydroxylapatite alone would be very bri... | [
"Osteogenesis imperfecta ( OI ) is a hereditary disease occurring in humans and dogs .",
"It is characterized by extremely fragile bones and teeth .",
"Most human and some canine OI cases are caused by mutations in the COL1A1 and COL1A2 genes encoding the subunits of collagen I . Recently , mutations in the CRT... | [
"Osteogenesis imperfecta ( OI ) is a genetic condition of humans and dogs characterized by extremely fragile bones and teeth .",
"Most human OI cases are caused by defects in one of two collagen genes .",
"Mutations in two other genes related to collagen maturation can also lead to OI in some patients .",
"We... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A KSHV microRNA Directly Targets G Protein-Coupled Receptor Kinase 2 to Promote the Migration and Invasion of Endothelial Cells by Inducing CXCR2 and Activating AKT Signaling | journal.ppat.1005171 | null | [
[
"Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is a gammaherpesvirus associated with Kaposi’s sarcoma ( KS ) commonly seen in AIDS patients [1] .",
"KSHV is also linked to other lymphoproliferative diseases including primary effusion lymphoma ( PEL ) and multicentric Castleman’s disease ( MCD ) [1–3] .... | [
"Kaposi's sarcoma ( KS ) is a highly disseminated angiogenic tumor of endothelial cells linked to infection by Kaposi's sarcoma-associated herpesvirus ( KSHV ) .",
"KSHV encodes more than two dozens of miRNAs but their roles in KSHV-induced tumor dissemination and metastasis remain unknown .",
"Here , we found ... | [
"Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma ( KS ) .",
"KS is a highly disseminated tumor often involved with visceral organs .",
"Experimentally , KSHV infection induces the invasiveness of endothelial cells .",
"KSHV encodes twelve precursor miRNAs ( pre-mi... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/cellular microbiology and pathogenesis",
"immunology/antigen processing and recognition",
"immunology/leukocyte development",
"cell biology/cell signaling",
"immunology/immunomodulation",
"immunology/immune response",
"immunology/innate immunity",
"immunology/leukocyte signaling and gene e... | Immune Evasion by Yersinia enterocolitica: Differential Targeting of Dendritic Cell Subpopulations In Vivo | journal.ppat.1001212 | null | [
[
"Host defense against microbial pathogens relies on the concerted action of both antigen-independent innate immunity and antigen-specific adaptive immunity [1]–[3] .",
"Key features of the innate immune system include the ability to rapidly recognize pathogens and/or tissue injury and to signal the presen... | [
"CD4+ T cells are essential for the control of Yersinia enterocolitica ( Ye ) infection in mice .",
"Ye can inhibit dendritic cell ( DC ) antigen uptake and degradation , maturation and subsequently T-cell activation in vitro .",
"Here we investigated the effects of Ye infection on splenic DCs and T-cell prolif... | [
"Dendritic cells ( DCs ) are crucial in promoting immune responses against pathogens .",
"Mouse DCs consist of different subpopulations but their role in immunity to pathogens and immune evasion is largely unclear .",
"The enteric pathogen Yersinia enterocolitica ( Ye ) was shown to evade DC functions in bone m... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"cell motility",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"gene regulation",
"regulatory proteins",
"immunology",
"dna-binding proteins",
"microbiology",
"signs and symptoms",
"transcription factors",
"cytotoxic t cells",
"white bl... | Equine arteritis virus long-term persistence is orchestrated by CD8+ T lymphocyte transcription factors, inhibitory receptors, and the CXCL16/CXCR6 axis | journal.ppat.1007950 | null | [
[
"Equine arteritis virus ( EAV ) is a positive-sense , single-stranded RNA virus that belongs to the family Arteriviridae , order Nidovirales [1] .",
"EAV is the causative agent of equine viral arteritis ( EVA ) , an economically important systemic , reproductive and respiratory disease of equids [2–8] .",... | [
"Equine arteritis virus ( EAV ) has the unique ability to establish long-term persistent infection in the reproductive tract of stallions and be sexually transmitted .",
"Previous studies showed that long-term persistent infection is associated with a specific allele of the CXCL16 gene ( CXCL16S ) and that persis... | [
"A distinctive feature of equine arteritis virus ( EAV ) is its ability to establish long-term persistent infection in the stallion reproductive tract in the presence of strong immune and inflammatory responses .",
"The data presented herein provides insight into the molecular signature of the inflammatory respon... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"tropical diseases",
"diet",
"anemia",
"health care",
"bacterial diseases",
"physiological processes",
"nutrition",
"neglected tropical diseases",
"public and occupational health",
"infectious diseases",
"food",
"hematology",
"food consumption",
"socioecon... | Dietary diversity and poverty as risk factors for leprosy in Indonesia: A case-control study | journal.pntd.0006317 | null | [
[
"Leprosy has long been known as a disease of poverty , yet the mechanism underlying this interaction remains unclear .",
"Most of the affected countries are underdeveloped , in which people affected by leprosy are born and raised in poor environments and continue being pushed into poverty due to the stigm... | [
"Poverty has long been considered a risk factor for leprosy and is related to nutritional deficiencies .",
"In this study , we aim to investigate the association between poverty-related diet and nutrition with leprosy .",
"In rural leprosy-endemic areas in Indonesia , we conducted a household-based case-control... | [
"Despite the suggestion that nutritional deficiencies may impair host immune responses against Mycobacterium leprae , there has not been any systematic study on how various aspects of poverty interact and associate with nutrition and leprosy .",
"In poor rural areas in Indonesia that have the highest proportion o... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"learning",
"medicine and health sciences",
"neural networks",
"brain",
"social sciences",
"neuroscience",
"learning and memory",
"cognitive psychology",
"network analysis",
"hallucinations",
"vision",
"neuronal tuning",
"computer and information sciences",
"animal cells",
"visual cortex... | Optimal Information Representation and Criticality in an Adaptive Sensory Recurrent Neuronal Network | journal.pcbi.1004698 | null | [
[
"The anatomical abundance of lateral interactions [1 , 2] between neurons of the local cerebral circuit ( referred in this text as recurrent connections ) suggest they play a fundamental role in cortical function .",
"Indirect physiological evidence of their involvement in memory [3 , 4] , sensory process... | [
"Recurrent connections play an important role in cortical function , yet their exact contribution to the network computation remains unknown .",
"The principles guiding the long-term evolution of these connections are poorly understood as well .",
"Therefore , gaining insight into their computational role and i... | [
"The recurrent interactions among cortical neurons shape the representation of incoming information but the principles governing their evolution are yet unclear .",
"We investigate the computational role of recurrent connections in the context of sensory processing .",
"Specifically , we study a neuronal networ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"developmental biology",
"model organisms",
"genetics",
"biology",
"genetics and genomics",
"cardiovascular"
] | Bmp and Nodal Independently Regulate lefty1 Expression to Maintain Unilateral Nodal Activity during Left-Right Axis Specification in Zebrafish | journal.pgen.1002289 | null | [
[
"In vertebrates the internal organs are positioned asymmetrically along the left-right ( LR ) axis .",
"For example , in humans , the heart is positioned on the left side , as is the stomach whilst the liver is positioned on the right side .",
"Within organs LR asymmetry also exists .",
"For examp... | [
"In vertebrates , left-right ( LR ) axis specification is determined by a ciliated structure in the posterior region of the embryo .",
"Fluid flow in this ciliated structure is responsible for the induction of unilateral left-sided Nodal activity in the lateral plate mesoderm , which in turn regulates organ later... | [
"Although vertebrates are bilaterally symmetric when observed from the outside , inside the body cavity the organs are positioned asymmetrically with respect to the left and right sides .",
"Cases where all the organs are mirror imaged , known as situs inversus , are not associated with any medical defects .",
... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immunology/immunity to infections",
"neurological disorders"
] | Predicting Neuropathy and Reactions in Leprosy at Diagnosis and Before Incident Events—Results from the INFIR Cohort Study | journal.pntd.0000500 | null | [
[
"Leprosy is a disease of skin and peripheral nerves , as well as other organs , resulting from the interaction between Mycobacterium leprae and the host response .",
"The involvement of the skin aids early detection and diagnosis while the injury to the motor , sensory and autonomic function of peripheral... | [
"Leprosy is a disease of skin and peripheral nerves .",
"The process of nerve injury occurs gradually through the course of the disease as well as acutely in association with reactions .",
"The INFIR ( ILEP Nerve Function Impairment and Reactions ) Cohort was established to identify clinically relevant neurolog... | [
"Leprosy is a disease of skin and peripheral nerves .",
"The skin changes aid early detection and diagnosis , while the nerve damage leads to progressive impairment and disability .",
"The aim of this study was to identify new risk factors at diagnosis and during follow-up that would predict which patients woul... | 2009 |
[
"Introduction",
"Methods and materials",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"legs",
"feet",
"pathology and laboratory medicine",
"tropical diseases",
"geographical locations",
"parasitic diseases",
"filariasis",
"signs and symptoms",
"neglected tropical diseases",
"ethiopia",
"body limbs",
"edema",
"lymphatic filariasis",
"africa"... | Community based cross sectional study of podoconiosis and associated factors in Dano district, Central Ethiopia | journal.pntd.0007050 | null | [
[
"Neglected tropical diseases ( NTDs ) are prevalent in many tropical and sub-tropical developing countries where poverty is rampant .",
"Evidence showed that one–sixth of the world’s population , mostly in developing countries , are infected with one or more of the NTDs .",
"The World Health Organizat... | [
"Podoconiosis , affects lower limb , is an entirely preventable non-communicable tropical disease common in low income countries .",
"Globally it is estimated that there are 4 million peoples with podoconiosis and nationally it is estimated that there are 1 . 56 million cases of podoconiosis .",
"Even though na... | [
"Podoconiosis ( endemic non-filarial elephantiasis ) is one of a disabling and stigmatizing neglected tropical disease ( NTD ) which affects the lower limb found mostly in low income countries .",
"Even though there were mostly prevalence studies and disease mapping , there was no report , especially on factors a... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"body fluids",
"cancer treatment",
"immunology",
"cancers and neoplasms",
"oncology",
"hematologic cancers and related disorders",
"animal models",
"model organisms",
"lymphomas",
"immunologic techniques",
"research and analysi... | PD-1/CTLA-4 Blockade Inhibits Epstein-Barr Virus-Induced Lymphoma Growth in a Cord Blood Humanized-Mouse Model | journal.ppat.1005642 | null | [
[
"The human herpesvirus , Epstein-Barr virus ( EBV ) , causes the clinical syndrome , infectious mononucleosis , but is usually well controlled by the host after recovery from the initial infection .",
"However , in a small number of infected patients , EBV contributes to the development of a variety of di... | [
"Epstein-Barr virus ( EBV ) infection causes B cell lymphomas in humanized mouse models and contributes to a variety of different types of human lymphomas .",
"T cells directed against viral antigens play a critical role in controlling EBV infection , and EBV-positive lymphomas are particularly common in immunoco... | [
"EBV is a human herpesvirus that remains in the host for life , but is normally well controlled by the host immune response .",
"Nevertheless , EBV causes lymphomas in certain individuals , particularly when T cell function is impaired .",
"Antibodies against two different inhibitory receptors on T cells , PD-1... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Regulation of Oncogene Expression in T-DNA-Transformed Host Plant Cells | journal.ppat.1004620 | null | [
[
"Agrobacterium tumefaciens is a pathogenic bacterium that infects several plant species .",
"A region in the tumor inducing ( Ti ) plasmid , the transfer DNA ( T-DNA ) , is integrated into the plant genome causing crown gall disease [1] .",
"There are essentially two groups of genes encoded on the T-D... | [
"Virulent Agrobacterium tumefaciens strains integrate their T-DNA into the plant genome where the encoded agrobacterial oncogenes are expressed and cause crown gall disease .",
"Essential for crown gall development are IaaH ( indole-3-acetamide hydrolase ) , IaaM ( tryptophan monooxygenase ) and Ipt ( isopentenyl... | [
"Crown gall development requires the expression of agrobacterial genes in the plant host .",
"These genes are transferred by the T-DNA of the plant pathogen Agrobacterium tumefaciens and include the oncogenes IaaH , IaaM and Ipt , which , according to the tumor-inducing principle , are essential for crown gall de... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"trophozoites",
"parasite groups",
"medicine and health sciences",
"innate immune system",
"immune physiology",
"cytokines",
"enzyme-linked immunoassays",
"complement system",
"spleen",
"immunology",
"vertebrates",
"animals",
"mammals",
"parasitology",
"parasitic protozoans",
"developm... | Evaluation of the C-Terminal Fragment of Entamoeba histolytica Gal/GalNAc Lectin Intermediate Subunit as a Vaccine Candidate against Amebic Liver Abscess | journal.pntd.0004419 | null | [
[
"Amebiasis caused by infection with Entamoeba histolytica is one of the most problematic parasitic diseases affecting people in both developing and developed countries .",
"E . histolytica causes an estimated 50 million collective cases of dysentery , colitis , and extraintestinal abscesses resulting in 4... | [
"Entamoeba histolytica is an intestinal protozoan parasite that causes amoebiasis , including amebic dysentery and liver abscesses .",
"E . histolytica invades host tissues by adhering onto cells and phagocytosing them depending on the adaptation and expression of pathogenic factors , including Gal/GalNAc lectin ... | [
"Amebiasis , a neglected tropical disease caused by the protozoan parasite Entamoeba histolytica , is the second leading cause of death from protozoan diseases .",
"Vaccination is considered as an effective strategy against amebiasis; however , clinical vaccines have yet to be developed .",
"We previously repor... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell death",
"invertebrates",
"medicine and health sciences",
"reproductive system",
"gonads",
"caenorhabditis",
"cell processes",
"animals",
"germ cells",
"animal models",
"caenorhabditis elegans",
"oocytes",
"model organisms",
"experimental organism systems",
"mitochondria",
"bioene... | Binucleate germ cells in Caenorhabditis elegans are removed by physiological apoptosis | journal.pgen.1007417 | null | [
[
"Apoptosis is a universal feature of animal development , and allows the controlled demolition of damaged or unnecessary cells and the subsequent removal of those cells by phagocytes [1] .",
"The major molecular components of the apoptosis and corpse-removal pathways are conserved evolutionarily , and man... | [
"Cell death plays a major role during C . elegans oogenesis , where over half of the oogenic germ cells die in a process termed physiological apoptosis .",
"How germ cells are selected for physiological apoptosis , or instead become oocytes , is not understood .",
"Most oocytes produce viable embryos when apopt... | [
"Many germ cells die by apoptosis during the development of animal oocytes , including more than half of all germ cells in the model system C . elegans .",
"How individual germ cells are selected for apoptosis , or survival , is not known .",
"Here we study the cell biology of apoptosis .",
"The C . elegans g... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"meiosis",
"molecular cell biology",
"cell biology",
"chromosome biology",
"genetics",
"plant genetics",
"biology",
"genetics and genomics",
"gene function"
] | The Arabidopsis HEI10 Is a New ZMM Protein Related to Zip3 | journal.pgen.1002799 | null | [
[
"From a diploid mother cell , meiosis generates four haploid products from which gametes differentiate .",
"This ploidy reduction is a direct consequence of two rounds of chromosomal segregation ( meiosis I and meiosis II ) following a single S phase .",
"The first meiotic division separates homologou... | [
"In numerous species , the formation of meiotic crossovers is largely under the control of a group of proteins known as ZMM .",
"Here , we identified a new ZMM protein , HEI10 , a RING finger-containing protein that is well conserved among species .",
"We show that HEI10 is structurally and functionally related... | [
"During meiosis two successive chromosomal divisions follow a single S phase , resulting in the formation of four haploid cells , each with half of the parental genetic material .",
"This ploidy reduction occurs during the first meiotic division , when homologous chromosomes ( paternal and maternal ) are separate... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"deletion mutation",
"enzymes",
"enzymology",
"epistasis",
"mutation",
"substitution mutation",
"proteins",
"molecular evolution",
"chemistry",
"evolutionary genetics",
"biochemistry",
"point mutation",
"hydrolysis",
"heredity",
"genetics",
"biology and life sciences",
"chemical reac... | Functional Trade-Offs in Promiscuous Enzymes Cannot Be Explained by Intrinsic Mutational Robustness of the Native Activity | journal.pgen.1006305 | null | [
[
"The evolution of new enzymatic functions commonly occurs via the modification of existing enzymes that exhibit a promiscuous activity , increasing this activity through adaptive mutations , and eventually duplicating the encoding gene to generate a new enzyme [1–6] .",
"This process has driven the emerge... | [
"The extent to which an emerging new function trades off with the original function is a key characteristic of the dynamics of enzyme evolution .",
"Various cases of laboratory evolution have unveiled a characteristic trend; a large increase in a new , promiscuous activity is often accompanied by only a mild redu... | [
"Understanding how enzymes evolve is a fundamental question that can help us decipher not only the mechanisms of evolution on a higher level , i . e . , whole organisms , but also advances our knowledge of sequence-structure-function relationships as a guide to artificial evolution in the test tube .",
"An import... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | K-homology Nuclear Ribonucleoproteins Regulate Floral Organ Identity and Determinacy in Arabidopsis | journal.pgen.1004983 | null | [
[
"Development of multicellular organisms relies on exquisitely controlled transcriptional and post-transcriptional regulatory actions to govern gene expression and accurately respond to endogenous and environmental fluctuations .",
"As exemplified in the reference plant Arabidopsis thaliana ( Arabidopsis h... | [
"Post-transcriptional control is nowadays considered a main checking point for correct gene regulation during development , and RNA binding proteins actively participate in this process .",
"Arabidopsis thaliana FLOWERING LOCUS WITH KH DOMAINS ( FLK ) and PEPPER ( PEP ) genes encode RNA-binding proteins that cont... | [
"Unlike animals , angiosperms ( flowering plants ) lack a germline that is set-aside early in embryo development .",
"Contrariwise , reproductive success relies on the formation of flowers during adult life , which provide the germ cells and the means for fertilization .",
"Therefore , timing of flowering and f... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Material and Methods"
] | [
"cell death",
"rna interference",
"viruses and cancer",
"microbiology",
"host-pathogen interaction",
"gene expression",
"biology",
"molecular biology",
"rna",
"cell biology",
"nucleic acids",
"virology",
"molecular cell biology"
] | Kaposi's Sarcoma Herpesvirus microRNAs Target Caspase 3 and Regulate Apoptosis | journal.ppat.1002405 | null | [
[
"The development of cancer is linked to six major hallmarks that explain how cells transgress from a normal to a neoplastic state , including",
"( i ) sustained proliferative signaling ,",
"( ii ) evasion of growth suppression ,",
"( iii ) activated invasion and metastasis ,",
"( iv ) enabled ... | [
"Kaposi's sarcoma herpesvirus ( KSHV ) encodes a cluster of twelve micro ( mi ) RNAs , which are abundantly expressed during both latent and lytic infection .",
"Previous studies reported that KSHV is able to inhibit apoptosis during latent infection; we thus tested the involvement of viral miRNAs in this process... | [
"MiRNAs are small , non-coding RNAs that regulate gene expression post-transcriptionally via binding to complementary sites in target mRNAs .",
"This evolutionary conserved regulatory system is present in most eukaryotes , and it has recently been shown that certain viruses have evolved to express their own miRNA... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Fungal Exopolysaccharide Galactosaminogalactan Mediates Virulence by Enhancing Resistance to Neutrophil Extracellular Traps | journal.ppat.1005187 | null | [
[
"Invasive aspergillosis ( IA ) is the most common invasive mold infection in humans .",
"In immunocompromised patients , the inhalation of airborne spores of Aspergillus species leads to a necrotizing fungal pneumonia that can disseminate hematogenously to the brain and other organs [1] .",
"Although ... | [
"Of the over 250 Aspergillus species , Aspergillus fumigatus accounts for up to 80% of invasive human infections .",
"A . fumigatus produces galactosaminogalactan ( GAG ) , an exopolysaccharide composed of galactose and N-acetyl-galactosamine ( GalNAc ) that mediates adherence and is required for full virulence .... | [
"The ubiquitous mold A . fumigatus is isolated in over 80% of all patients with invasive aspergillosis ( IA ) .",
"A . nidulans is a relatively non-pathogenic species that rarely causes IA except in patients with chronic granulomatous disease ( CGD ) , a hereditary disease characterized by impaired neutrophil fun... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"viruses",
"infectious diseases",
"public health and epidemiology",
"virology",
"mus (mouse)",
"insects"
] | Mosquitoes Inoculate High Doses of West Nile Virus as They Probe and Feed on Live Hosts | journal.ppat.0030132 | null | [
[
"West Nile virus ( WNV ) has become the most prevalent arbovirus in the United States , causing more than 24 , 000 reported human cases and 960 deaths since it was first detected in New York in 1999 [1] .",
"The virus is maintained in an enzootic cycle involving birds and mosquitoes ( primarily Culex spec... | [
"West Nile virus ( WNV ) is transmitted to vertebrate hosts by mosquitoes as they take a blood meal .",
"The amount of WNV inoculated by mosquitoes as they feed on a live host is not known .",
"Previous estimates of the amount of WNV inoculated by mosquitoes ( 101 . 2–104 . 3 PFU ) were based on in vitro assays... | [
"Since it was first introduced into the United States in 1999 , West Nile virus ( WNV ) has caused significant disease in humans , horses , and other animals .",
"WNV is transmitted to humans and other vertebrate hosts by female mosquitoes as they take a blood meal .",
"Currently , the amount of virus inoculate... | 2007 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"engineering and technology",
"immunology",
"tropical diseases",
"geographical locations",
"vertebrates",
"social sciences",
"malawi",
"dogs",
"animals",
"mammals",
"cell phones",
"vaccines",
"preventive medicine",
"rabies",
"neglected tropical diseases"... | The Vaccination of 35,000 Dogs in 20 Working Days Using Combined Static Point and Door-to-Door Methods in Blantyre, Malawi | journal.pntd.0004824 | null | [
[
"Rabies is a devastating disease which is estimated to kill approximately 60 , 000 people a year [1] .",
"Globally , rabies is estimated to cause 3 . 7 million disability-adjusted life years and results in 8 . 6 billion US dollars of economic losses annually [1] .",
"Successful treatment of patients w... | [
"An estimated 60 , 000 people die of rabies annually .",
"The vast majority of cases of human rabies develop following a bite from an infected dog .",
"Rabies can be controlled in both human and canine populations through widespread vaccination of dogs .",
"Rabies is particularly problematic in Malawi , costi... | [
"Rabies is a devastating disease that is estimated to result in the death of approximately 60 , 000 people every year .",
"Most humans contract rabies following a bite from an infected dog and it has been demonstrated that provided a large enough proportion of the dog population is vaccinated; rabies incidence ca... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics",
"biology and life sciences",
"comparative genomics",
"genomics",
"computational biology"
] | The Population Structure of Vibrio cholerae from the Chandigarh Region of Northern India | journal.pntd.0002981 | null | [
[
"Cholera , caused by the Gram-negative bacterium Vibrio cholerae , is classically associated with rapidly dehydrating watery diarrhoea .",
"Although more than 200 serogroups of V . cholerae have been identified; only the O1 and O139 serogroups are associated with epidemic and pandemic outbreaks .",
"H... | [
"Cholera infection continues to be a threat to global public health .",
"The current cholera pandemic associated with Vibrio cholerae El Tor has now been ongoing for over half a century .",
"Thirty-eight V . cholerae El Tor isolates associated with a cholera outbreak in 2009 from the Chandigarh region of India ... | [
"Vibrio cholerae is a diarrheal pathogen that is responsible for substantial morbidity and mortality worldwide .",
"Historically , seven pandemics of cholera have been recognized , with classical biotype strains associated with the sixth and the El Tor biotype with the seventh ( current ) pandemic .",
"Recently... | 2014 |
[
"Introduction",
"Results and Discussion",
"Methods"
] | [] | Combining Regulatory T Cell Depletion and Inhibitory Receptor Blockade Improves Reactivation of Exhausted Virus-Specific CD8+ T Cells and Efficiently Reduces Chronic Retroviral Loads | journal.ppat.1003798 | null | [
[
"Cytotoxic CD8+ T cells are crucial for the control of most virus infections .",
"However , in several chronic virus infections , like HIV or hepatitis C virus ( HCV ) in humans , the virus evades destruction by CD8+ T cells .",
"Mostly these infections are associated with an appearance of functionall... | [
"Chronic infections with human viruses , such as HIV and HCV , or mouse viruses , such as LCMV or Friend Virus ( FV ) , result in functional exhaustion of CD8+ T cells .",
"Two main mechanisms have been described that mediate this exhaustion: expression of inhibitory receptors on CD8+ T cells and expansion of reg... | [
"A loss of function , the so-called ‘exhaustion’ of CD8+ T cells , is a hallmark of many chronic infections .",
"The T cell exhaustion is mediated by two main mechanisms , the expression of inhibitory receptors on CD8+ T cells and virus-induced expansion of regulatory T cells ( Tregs ) , which suppress CD8+ T cel... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/disease models",
"genetics and genomics/epigenetics",
"neurological disorders/neurogenetics",
"genetics and genomics/medical genetics"
] | CTCF cis-Regulates Trinucleotide Repeat Instability in an Epigenetic Manner: A Novel Basis for Mutational Hot Spot Determination | journal.pgen.1000257 | null | [
[
"Trinucleotide repeat expansion is the cause of at least 25 inherited neurological disorders , including Huntington's disease ( HD ) , fragile X mental retardation , and myotonic dystrophy ( DM1 ) [1] .",
"One intriguing aspect of trinucleotide repeat disorders is ‘anticipation’ – a phenomenon whereby inc... | [
"At least 25 inherited disorders in humans result from microsatellite repeat expansion .",
"Dramatic variation in repeat instability occurs at different disease loci and between different tissues; however , cis-elements and trans-factors regulating the instability process remain undefined .",
"Genomic fragments... | [
"The human genome contains many repetitive sequences .",
"In 1991 , we discovered that excessive lengthening of a three-nucleotide ( trinucleotide ) repeat sequence could cause a human genetic disease .",
"We now know that this unique type of genetic mutation , known as a “repeat expansion , ” occurs in at leas... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Randomized Single-Blinded Non-inferiority Trial Of 7 mg/kg Pentamidine Isethionate Versus 4 mg/kg Pentamidine Isethionate for Cutaneous Leishmaniaisis in Suriname | journal.pntd.0003592 | null | [
[
"With a global yearly incidence around 1 . 5 million cases , Cutaneous leishmaniasis ( CL ) is the most common clinical presentation of Leishmania infection . [1]",
"The bite of an infected female sandfly of the genus Phlebotomus and Lutzomyia transmit the protozoan Leishmania parasites . [2]",
"In Su... | [
"Standard treatment of cutaneous leishmaniasis ( CL ) in Suriname entails three injections of pentamidine isethionate ( PI ) 4 mg/kg per injection in 7 days ( 7 day regimen ) .",
"Compliance to treatment is low and may contribute to increasing therapy failure .",
"A 3 day regimen , including 2 injections of 7 m... | [
"Cutaneous Leishmaniasis ( CL ) , caused by the single cellular protozoan parasite of the genus Leishmania , is treated in Suriname with pentamidine isethionate ( PI ) .",
"Standard treatment consists of 3 intramuscular injections of 4 mg per kg bodyweight given in 7 days .",
"Compliance to treatment is low whi... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular complexes",
"cell cycle and cell division",
"cell processes",
"microbiology",
"escherichia coli",
"prokaryotic models",
"model organisms",
"cytokinesis",
"bacterial pathogens",
"research and analysis methods",
"medical microbiology",
"microbial pathogens",
"biophysics",
"molecul... | Evidence for Divisome Localization Mechanisms Independent of the Min System and SlmA in Escherichia coli | journal.pgen.1004504 | null | [
[
"Cell division is an essential cellular process that requires accurate spatial and temporal positioning of cytokinetic proteins .",
"Assembly of the cell division apparatus , the divisome , must be coordinated closely with replication and segregation of chromosomes to ensure that each daughter cell receiv... | [
"Cell division in Escherichia coli starts with assembly of FtsZ protofilaments into a ring-like structure , the Z-ring .",
"Positioning of the Z-ring at midcell is thought to be coordinated by two regulatory systems , nucleoid occlusion and the Min system .",
"In E . coli , nucleoid occlusion is mediated by the... | [
"Cell division in Escherichia coli begins with the assembly of FtsZ proteins into a ring-like structure , the Z-ring .",
"Remarkably , the Z-ring localizes with very high precision at midcell .",
"Currently , two molecular systems , nucleoid occlusion and the Min system , are known to localize the Z-ring .",
... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"molecular biology",
"infectious diseases/epidemiology and control of infectious diseases",
"genetics and genomics/population genetics"
] | Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin | journal.ppat.1001343 | null | [
[
"Cryptococcus neoformans ( Cn ) is an encapsulated basidiomycetous yeast , and the etiological agent of the invasive fungal infection cryptococcosis .",
"The first clinical discovery of Cn was in 1894 , and this pathogen has since become one of the leading causes of mycotic morbidity and mortality worldwi... | [
"The global burden of HIV-associated cryptococcal meningitis is estimated at nearly one million cases per year , causing up to a third of all AIDS-related deaths .",
"Molecular epidemiology constitutes the main methodology for understanding the factors underpinning the emergence of this understudied , yet increas... | [
"Cryptococcus neoformans is a species complex of often highly pathogenic fungi that cause significant disease in humans .",
"Cryptococcus is notable in the degree that virulence differs amongst genotypes , and highly-virulent emerging lineages are changing patterns of disease in time and space .",
"Cryptococcus... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"prion diseases"
] | Highly Efficient Prion Transmission by Blood Transfusion | journal.ppat.1002782 | null | [
[
"In 1996 , a new form of CJD , named variant CJD ( v-CJD ) was identified in humans [1] , [2] .",
"The presence of the v-CJD agent in lymphoid tissues of patients incubating the disease raised the possibility of blood borne v-CJD transmission .",
"Since then , four v-CJD cases were reported in patient... | [
"It is now clearly established that the transfusion of blood from variant CJD ( v-CJD ) infected individuals can transmit the disease .",
"Since the number of asymptomatic infected donors remains unresolved , inter-individual v-CJD transmission through blood and blood derived products is a major public health con... | [
"In the UK , several v-CJD cases have been identified in patients that received blood or blood-derived products prepared from incubating asymptomatic donors .",
"Since there is no screening test to identify infected donors , procedural risk reduction measures remain the only protection against v-CJD transfusion r... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"public health and epidemiology/epidemiology",
"infectious diseases/viral infections",
"public health and epidemiology/infectious diseases",
"public health and epidemiology/social and behavioral determinants of health",
"ecology/population ecology",
"in... | Water Use Practices Limit the Effectiveness of a Temephos-Based Aedes aegypti Larval Control Program in Northern Argentina | journal.pntd.0000991 | null | [
[
"Dengue is currently the most important arboviral disease in the world; it affects an estimated 50 million people and causes 30 , 000 deaths per year [1] , [2] .",
"In Argentina , the regional context of increasing dengue incidence led in 2009 to the most severe and extended DF epidemic ever recorded [3] ... | [
"A five-year citywide control program based on regular application of temephos significantly reduced Aedes aegypti larval indices but failed to maintain them below target levels in Clorinda , northern Argentina .",
"Incomplete surveillance coverage and reduced residuality of temephos were held as the main putativ... | [
"Dengue is currently the most important viral disease of humans transmitted by arthropods worldwide .",
"Aedes aegypti , a human-biting mosquito dwelling in artificial domestic containers , is the main vector of dengue .",
"Ae .",
"aegypti larval control programs are frequently based on the application of the... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"decision making",
"tropical diseases",
"social sciences",
"parasitic diseases",
"neuroscience",
"cognitive psychology",
"cognition",
"neglected tropical diseases",
"infectious disease control",
"information technology",
"infectious diseases",
"computer and in... | Integrating evidence, models and maps to enhance Chagas disease vector surveillance | journal.pntd.0006883 | null | [
[
"Chagas disease is a neglected tropical disease ( NTD ) endemic to the Americas with a current estimated prevalence of six to nine million people worldwide [1 , 2] and 70 million more at risk [3] .",
"An estimated 30% of those with Chagas disease will develop serious cardiac and/or gastrointestinal proble... | [
"Until recently , the Chagas disease vector , Triatoma infestans , was widespread in Arequipa , Perú , but as a result of a decades-long campaign in which over 70 , 000 houses were treated with insecticides , infestation prevalence is now greatly reduced .",
"To monitor for T . infestans resurgence , the city is ... | [
"Chagas disease is a serious infection that is spread by blood-sucking insects called ‘kissing bugs . ’ These bugs live in and around human homes , and until recently , they infested thousands of human homes throughout Arequipa , the second largest city in Perú .",
"However , a decades-long control campaign drast... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"medicine and health sciences",
"reproductive system",
"rna interference",
"neuroscience",
"animals",
"animal models",
"drosophila melanogaster",
"model organisms",
"stem cells",
"membrane receptor signaling",
"hormone receptor signaling",
"epigenetics",
"drosophila",
"r... | Mating-Induced Increase in Germline Stem Cells via the Neuroendocrine System in Female Drosophila | journal.pgen.1006123 | null | [
[
"Gametogenesis is modulated by stimuli from environments surrounding individual organisms .",
"One such example is mating stimulus , which accelerates egg production [1] .",
"Because mating is a process that utilizes many eggs , it is plausible that mating may modulate the process of gametogenesis .",... | [
"Mating and gametogenesis are two essential components of animal reproduction .",
"Gametogenesis must be modulated by the need for gametes , yet little is known of how mating , a process that utilizes gametes , may modulate the process of gametogenesis .",
"Here , we report that mating stimulates female germlin... | [
"In many animals , gametogenesis is supported by germline stem cells ( GSCs ) .",
"Since GSCs are the fundamental cell population for successful reproduction , how such special GSCs are precisely proliferated is a long-standing question in biology .",
"In the fruit fly Drosophila melanogaster , it is known that... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Reprogramming of Yersinia from Virulent to Persistent Mode Revealed by Complex In Vivo RNA-seq Analysis | journal.ppat.1004600 | null | [
[
"Yersinia pseudotuberculosis is a food borne pathogen that can penetrate the intestinal epithelium and cause gastroenteritis .",
"This enteropathogen invades lymphoid follicles of Peyer’s patches and cecum , where it survives extracellularly before breaking the barrier and becoming systemic [1 , 2] .",
... | [
"We recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections .",
"We performed in vivo RNA-seq of bacteria in small cecal tissue biopsies at early and persistent stages of infection to determine strategies associated with persistence .",
"Comprehensive analysis o... | [
"To establish infection and colonize within a host , infecting pathogens have to cope with a variety of destructive surroundings .",
"The food-borne pathogen Y . pseudotuberculosis can cause persistent infection in mice .",
"Upon infection , Y . pseudotuberculosis passes the anti-microbial gastrointestinal mili... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"salmonella typhi",
"health care",
"organisms",
"bacterial diseases",
"signs and symptoms",
"enterobacteriaceae",
"convalescence",
"molecular biology techniques",
"bacteria",
... | Ascertaining the burden of invasive Salmonella disease in hospitalised febrile children aged under four years in Blantyre, Malawi | journal.pntd.0007539 | null | [
[
"Both Salmonella Typhi and nontyphoidal Salmonellae remain prominent contributors to the large burden of bloodstream infection ( BSI ) in sub-Saharan Africa ( sSA ) [1–4] .",
"Until recently nontyphoidal serovars Salmonella Typhimurium and Salmonella Enteritidis were the most prevalent in sSA , mainly aff... | [
"Typhoid fever is endemic across sub-Saharan Africa .",
"However , estimates of the burden of typhoid are undermined by insufficient blood volumes and lack of sensitivity of blood culture .",
"Here , we aimed to address this limitation by exploiting pre-enrichment culture followed by PCR , alongside routine blo... | [
"There are increasing reports of typhoid fever epidemics in sub-Saharan Africa frequently affecting young adults and children aged between 5 and 16 years .",
"In Asia where typhoid is hyperendemic , children aged 0 to 4 years also have a high burden of typhoid fever .",
"Diagnosis of typhoid in young children i... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics and genomics/genomics",
"genetics and genomics/comparative genomics",
"evolutionary biology/evolutionary and comparative genetics",
"computational biology/comparative sequence analysis",
"evolutionary biology/genomics",
"genetics and genomics/bioinformatics"
] | Mutations of Different Molecular Origins Exhibit Contrasting Patterns of Regional Substitution Rate Variation | journal.pcbi.1000015 | null | [
[
"Elucidating causes of regional variation of substitution rates is a prominent topic in molecular evolutionary studies [1]–[6] .",
"While most studies consider all types of point mutations together , different types of mutations arise from distinctive molecular processes .",
"In this paper , we contra... | [
"Transitions at CpG dinucleotides , referred to as “CpG substitutions” , are a major mutational input into vertebrate genomes and a leading cause of human genetic disease .",
"The prevalence of CpG substitutions is due to their mutational origin , which is dependent on DNA methylation .",
"In comparison , other... | [
"Mutations are raw materials of evolution .",
"Earlier studies have shown that mutations occur at different frequencies in different genomic regions .",
"By investigating the patterns and causes of such “regional” variation of mutations , we can better understand the mechanisms of underlying mutagenesis .",
"... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"test evaluation",
"veterinary diseases",
"diagnostic medicine",
"veterinary parasitology",
"veterinary diagnostics",
"leishmaniasis",
"neglected tropical diseases",
"quantitative parasitology",
"veterinary science",
"veterinary medicine"
] | Evaluation of rK39 Rapid Diagnostic Tests for Canine Visceral Leishmaniasis: Longitudinal Study and Meta-Analysis | journal.pntd.0001992 | null | [
[
"Zoonotic visceral leishmaniasis ( ZVL ) is a potentially fatal disease caused by the intracellular protozoan parasite Leishmania infantum , which is endemic in South and Central America , the Mediterranean basin and parts of Asia .",
"The domestic dog is the most important reservoir host , and infection ... | [
"There is a need for sensitive and specific rapid diagnostic tests ( RDT ) for canine visceral leishmaniasis .",
"The aims of this study were to evaluate the diagnostic performance of immunochromatographic dipstick RDTs using rK39 antigen for canine visceral leishmaniasis by",
"( i ) investigating the sensitivi... | [
"Canine visceral leishmaniasis is a vector-borne disease caused by the intracellular parasite Leishmania infantum .",
"It is an important veterinary disease , and dogs are also the main animal reservoir for human infection .",
"The disease is widespread in the Mediterranean area , and parts of Asia and South an... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"molecular neuroscience",
"neuroscience",
"animals",
"dna transcription",
"animal models",
"drosophila melanogaster",
"model organisms",
"drosophila",
"research and analysis methods",
"gene expression",
"insects",
"arthropoda",
"cell biology",
"gene regulatory networks",... | Synergistic Interactions between the Molecular and Neuronal Circadian Networks Drive Robust Behavioral Circadian Rhythms in Drosophila melanogaster | journal.pgen.1004252 | null | [
[
"Most organisms use 24-hr circadian clocks to keep temporal order and anticipate daily environmental changes .",
"These clocks are based on self-sustained biochemical oscillators that manifest at the molecular , physiological and behavioral levels [for review see [1] , [2]] .",
"Circadian clocks have ... | [
"Most organisms use 24-hr circadian clocks to keep temporal order and anticipate daily environmental changes .",
"In Drosophila melanogaster CLOCK ( CLK ) and CYCLE ( CYC ) initiates the circadian system by promoting rhythmic transcription of hundreds of genes .",
"However , it is still not clear whether high a... | [
"Circadian clocks allow organisms to predict daily environmental changes .",
"These clocks time the sleep/wake cycles and many other physiological and cellular pathways to 24hs rhythms .",
"The current model states that circadian clocks keep time by the use of biochemical feedback loops .",
"These feedback lo... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases/bacterial infections",
"genetics and genomics/microbial evolution and genomics",
"evolutionary biology/microbial evolution and genomics",
"microbiology/microbial evolution and genomics"
] | Within-Host Evolution of Burkholderia pseudomallei in Four Cases of Acute Melioidosis | journal.ppat.1000725 | null | [
[
"In vivo studies of pathogen evolution have provided important insights into the dynamic adaptability of infectious agents during the course of an infection .",
"To date , the overwhelming majority of within-host evolution work has focused upon monitoring pathogen adaptations concomitant with chronic infe... | [
"Little is currently known about bacterial pathogen evolution and adaptation within the host during acute infection .",
"Previous studies of Burkholderia pseudomallei , the etiologic agent of melioidosis , have shown that this opportunistic pathogen mutates rapidly both in vitro and in vivo at tandemly repeated l... | [
"While both viral and bacterial pathogens have been shown to undergo genetic changes over the course of a chronic infection , this phenomenon has not been studied during an acute infection and as such is not well understood .",
"Here , we examined within-host evolution of the pathogen Burkholderia pseudomallei du... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"bacterial biofilms",
"microbial pathogens",
"biology",
"microbiology",
"host-pathogen interaction"
] | Bap, a Biofilm Matrix Protein of Staphylococcus aureus Prevents Cellular Internalization through Binding to GP96 Host Receptor | journal.ppat.1002843 | null | [
[
"Staphylococcus aureus is a regular commensal of the skin of animals and human population and it persistently colonizes the anterior nares of around 25% of human adults [1] .",
"S . aureus is harmless in these locations , but it turns into an extremely threatening pathogen when it traverses the epithelial... | [
"The biofilm matrix , composed of exopolysaccharides , proteins , nucleic acids and lipids , plays a well-known role as a defence structure , protecting bacteria from the host immune system and antimicrobial therapy .",
"However , little is known about its responsibility in the interaction of biofilm cells with h... | [
"Staphylococcus aureus is a pathogen responsible for a wide variety of infections , some of which become chronic due to the capacity of this bacteria to form multicellular communities that grow embedded in a self-produced extracellular matrix , referred to as biofilms .",
"Numerous evidences have demonstrated tha... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"cell biology/cell growth and division",
"computational biology/genomics",
"mathematics/statistics",
"cell biology/gene expression"
] | Predicting Cellular Growth from Gene Expression Signatures | journal.pcbi.1000257 | null | [
[
"Cellular growth is typically quantified in one of two experimental environments:",
"batch culture or the chemostat .",
"In a batch culture , cells are provided with a",
"saturating amount of nutrient [1] .",
"Growth is quantified by measuring the optical",
"density ( OD ) of the culture o... | [
"Maintaining balanced growth in a changing environment is a fundamental",
"systems-level challenge for cellular physiology , particularly in microorganisms .",
"While the complete set of regulatory and functional pathways supporting growth",
"and cellular proliferation are not yet known , portions of them are... | [
"A major challenge for living organisms is the regulation of cellular growth in a",
"fluctuating environment .",
"Sudden changes in nutrient availability or the presence",
"of stress factors typically require rapid adjustments of cellular growth .",
"The",
"misregulation of growth control in higher organi... | 2009 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"physics",
"protein folding",
"biophysics theory",
"biophysics"
] | Folding Pathways of a Knotted Protein with a Realistic Atomistic Force Field | journal.pcbi.1003002 | null | [
[
"Natively-knotted proteins are increasingly studied as a new paradigm of “multiscale” folding coordination , which leads to establishing the native knot in the native position starting from the unknotted newly-translated state [1]–[4] .",
"Intuitively , the pathways associated to this process appear so im... | [
"We report on atomistic simulation of the folding of a natively-knotted protein , MJ0366 , based on a realistic force field .",
"To the best of our knowledge this is the first reported effort where a realistic force field is used to investigate the folding pathways of a protein with complex native topology .",
... | [
"It has been recently observed that the native structure of proteins can contain knots .",
"These are formed during the folding process and are tightened in a specific ( i . e . native ) location , along the poly-peptide chain .",
"The existence of knots hence implies a high degree coordination of local and glo... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Arabidopsis DNA Polymerase δ Has a Role in the Deposition of Transcriptionally Active Epigenetic Marks, Development and Flowering | journal.pgen.1004975 | null | [
[
"Arabidopsis is a facultative long-day ( LD ) plant , meaning that LDs accelerate flowering whereas in short days ( SD ) flowering is delayed .",
"Flowering in spring ( LDs ) is therefore promoted by GIGANTEA ( GI ) , CONSTANS ( CO ) and FLOWERING LOCUS T ( FT ) which constitute the so called “photoperiod... | [
"DNA replication is a key process in living organisms .",
"DNA polymerase α ( Polα ) initiates strand synthesis , which is performed by Polε and Polδ in leading and lagging strands , respectively .",
"Whereas loss of DNA polymerase activity is incompatible with life , viable mutants of Polα and Polε were isolat... | [
"Three DNA polymerases replicate DNA in Eukaryotes .",
"DNA polymerase α ( Polα ) initiates strand synthesis , which is performed by Polε and Polδ in leading and lagging strands , respectively .",
"Not only the information encoded in the DNA , but also the inheritance of chromatin states is essential during dev... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"visual system",
"computational neuroscience",
"biology and life sciences",
"sensory systems",
"computational biology",
"neuroscience",
"neuronal tuning",
"coding mechanisms"
] | Orientation Selectivity in Inhibition-Dominated Networks of Spiking Neurons: Effect of Single Neuron Properties and Network Dynamics | journal.pcbi.1004045 | null | [
[
"Orientation selectivity ( OS ) , namely the selectivity of neurons in primary visual cortex ( V1 ) of mammals to oriented stimuli [1]–[5] , is the result of a simple computation in an early sensory cortex .",
"However , thanks to its experimental and theoretical tractability , it provides a unique window... | [
"The neuronal mechanisms underlying the emergence of orientation selectivity in the primary visual cortex of mammals are still elusive .",
"In rodents , visual neurons show highly selective responses to oriented stimuli , but neighboring neurons do not necessarily have similar preferences .",
"Instead of a smoo... | [
"It is not yet fully clear how sensory information is being processed when it arrives in primary cortical areas .",
"We studied this general question in the context of rodent vision .",
"We focused on the example of orientation selectivity , namely the selectivity of cortical neurons for specific orientations o... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology/plant genetics and gene expression",
"molecular biology/dna repair",
"cell biology/cell signaling"
] | Regulation and Role of Arabidopsis CUL4-DDB1A-DDB2 in Maintaining Genome Integrity upon UV Stress | journal.pgen.1000093 | null | [
[
"Plants are subjected to many different environmental stresses due to their sessile life styles .",
"As obligate prototroph they need to take benefit of the sunlight containing ultra-violets ( UV ) for photosynthesis but concomitantly , have to prevent UV irradiation from inducing irreversible damage espe... | [
"Plants use the energy in sunlight for photosynthesis , but as a consequence are exposed to the toxic effect of UV radiation especially on DNA .",
"The UV-induced lesions on DNA affect both transcription and replication and can also have mutagenic consequences .",
"Here we investigated the regulation and the fu... | [
"Recent research revealed strong links between Cullin4 ( CUL4 ) –based cullin-RING ubiquitin ligases ( CRLs ) and chromatin biology , including DNA replication and DNA repair .",
"During Nucleotide Excision Repair ( NER ) , CUL4 together with DDB1 ( DNA Damage Binding protein 1 ) ubiquitylate an increasingly larg... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"action potentials",
"medicine and health sciences",
"membrane potential",
"brain",
"electrophysiology",
"mathematical models",
"neuroscience",
"optimization",
"mathematics",
"computational neuroscience",
"neuronal tuning",
"coding mechanisms",
"research and analysis methods",
"random walk... | An efficient coding theory for a dynamic trajectory predicts non-uniform allocation of entorhinal grid cells to modules | journal.pcbi.1005597 | null | [
[
"A central goal of systems neuroscience is to unravel the principles of encoding in the brain .",
"It has been conjectured that the neural circuitry in primary sensory areas implements coding schemes that maximize information about sensory inputs , while constraining neural resources such as the number of... | [
"Grid cells in the entorhinal cortex encode the position of an animal in its environment with spatially periodic tuning curves with different periodicities .",
"Recent experiments established that these cells are functionally organized in discrete modules with uniform grid spacing .",
"Here we develop a theory ... | [
"Grid cells encode a mammal’s estimate of position by firing in multiple locations .",
"These locations are arranged on the vertices of a triangular lattice .",
"Lattices vary in spacing and therefore represent position over different spatial scales .",
"We suggest that grid cells encode position while taking... | 2017 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"model organisms",
"chromosome biology",
"gene expression",
"genetics",
"epigenetics",
"biology",
"genomics",
"yeast and fungal models",
"saccharomyces cerevisiae",
"chromatin",
"genetics and genomics",
"microbiology",
"dna transcription"
] | ISWI and CHD Chromatin Remodelers Bind Promoters but Act in Gene Bodies | journal.pgen.1003317 | null | [
[
"Nucleosome remodelers use the energy of ATP hydrolysis to alter histone-DNA contacts , slide nucleosomes , and exchange or remove histones and entire nucleosomes .",
"They are ubiquitous throughout eukaryotic evolution [1] , and alterations in their expression are found in human congenital anomaly syndro... | [
"ATP-dependent nucleosome remodelers influence genetic processes by altering nucleosome occupancy , positioning , and composition .",
"In vitro , Saccharomyces cerevisiae ISWI and CHD remodelers require ∼30–85 bp of extranucleosomal DNA to reposition nucleosomes , but linker DNA in S . cerevisiae averages <20 bp ... | [
"Eukaryotic genomes are compacted into chromatin , which restricts access to DNA .",
"In order for cells to transcribe , replicate , and repair DNA , chromatin structure must be altered .",
"Eukaryotes have evolved chromatin remodeling enzymes that use energy derived from ATP hydrolysis to modulate chromatin st... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Yersinia pestis Activates Both IL-1β and IL-1 Receptor Antagonist to Modulate Lung Inflammation during Pneumonic Plague | journal.ppat.1004688 | null | [
[
"The innate immune system plays an integral role in controlling microbial infection , providing the first layer of defense against invading pathogens and incorporating multiple levels of threat detection .",
"Sentinel cells such as macrophages and neutrophils use pattern recognition receptors ( PRRs ) tha... | [
"Pneumonic plague is the most rapid and lethal form of Yersinia pestis infection .",
"Increasing evidence suggests that Y . pestis employs multiple levels of innate immune evasion and/or suppression to produce an early “pre-inflammatory” phase of pulmonary infection , after which the disease is highly inflammator... | [
"Inhalation of respiratory droplets containing Yersinia pestis results in a rapidly developing and lethal pneumonia .",
"Interestingly , early interactions between Y . pestis and host cells in the lung contribute to significant immune evasion , but also ultimately result in severe innate immune activation .",
"... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology/gastrointestinal cancers",
"genetics and genomics/cancer genetics",
"genetics and genomics/comparative genomics",
"molecular biology/dna repair"
] | Ultradeep Sequencing of a Human Ultraconserved Region Reveals Somatic and Constitutional Genomic Instability | journal.pbio.1000275 | Ultradeep sequencing of genomes permits the detection of very low-level genomic instability in non-neoplastic tissues of patients with the most common form of inherited colorectal cancer. | [
[
"Genomic instability is a common trait of cancer cells and plays a pivotal role in promoting carcinogenesis in several hereditary tumours .",
"One of the best-known examples is the Lynch syndrome , an autosomal dominant condition associated with heterozygous mutations in mismatch repair ( MMR ) genes [1] ... | [
"Early detection of cancer-associated genomic instability is crucial , particularly in tumour types in which this instability represents the essential underlying mechanism of tumourigenesis .",
"Currently used methods require the presence of already established neoplastic cells because they only detect clonal mut... | [
"In hereditary non-polyposis colorectal cancer ( HNPCC ) , a germline mutation in one allele of a gene responsible for repairing DNA damage predisposes the host to cancer , because subsequent somatic inactivation of the one wild-type allele leads to genomic instability that favours tumourigenesis .",
"Nonneoplast... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | New Insights into the Molecular Epidemiology and Population Genetics of Schistosoma mansoni in Ugandan Pre-school Children and Mothers | journal.pntd.0002561 | null | [
[
"The neglected tropical disease schistosomiasis , remains a significant public health problem , particularly in sub-Saharan Africa ( SSA ) , and is caused by infection with parasites of the genus Schistosoma [1] .",
"In SSA Schistosoma mansoni is responsible for intestinal schistosomiasis and is associate... | [
"Significant numbers of pre-school children are infected with Schistosoma mansoni in sub-Saharan Africa and are likely to play a role in parasite transmission .",
"However , they are currently excluded from control programmes .",
"Molecular phylogenetic studies have provided insights into the evolutionary origi... | [
"Many pre-school children in sub-Saharan Africa are infected with the parasite Schistosoma mansoni , which causes intestinal schistosomiasis .",
"However , there has been no work published on the molecular epidemiology of Schistosoma in children under six or the role that these children play in parasite transmiss... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology",
"medicine",
"functional genomics",
"molecular cell biology",
"metastasis",
"dna modification",
"basic cancer research",
"gene expression",
"biology",
"genomics",
"molecular biology",
"genetics and genomics"
] | Integrative Genomics in Combination with RNA Interference Identifies Prognostic and Functionally Relevant Gene Targets for Oral Squamous Cell Carcinoma | journal.pgen.1003169 | null | [
[
"Metastatic spread to the cervical lymph nodes is a major feature associated with tumor aggressiveness in oral squamous cell carcinoma ( OSCC ) , reducing 5-year survival by about 50% [1]–[3] .",
"For these patients , treatment intensification with radiation and chemotherapy results in improved survival o... | [
"In oral squamous cell carcinoma ( OSCC ) , metastasis to lymph nodes is associated with a 50% reduction in 5-year survival .",
"To identify a metastatic gene set based on DNA copy number abnormalities ( CNAs ) of differentially expressed genes , we compared DNA and RNA of OSCC cells laser-microdissected from non... | [
"Neck lymph node metastasis is the most important prognostic factor in oral squamous cell carcinoma ( OSCC ) .",
"To identify genes associated with this critical step of OSCC progression , we compared DNA copy number aberrations and gene expression differences between tumor cells found in metastatic lymph nodes v... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"yeast two-hybrid assays",
"protein interactions",
"social sciences",
"neuroscience",
"fungi",
"protein interaction assays",
"immunoprecipitation",
"seedlings",
"co-immunoprecipitation",
"molecular biology techniques",
"plants",
"research and analysis methods",
"animal c... | The blue light-induced interaction of cryptochrome 1 with COP1 requires SPA proteins during Arabidopsis light signaling | journal.pgen.1007044 | null | [
[
"Plants constantly adjust their growth and development to the ambient light environment .",
"To sense light , plants have evolved several sets of photoreceptors which include the blue light-absorbing cryptochromes , phototropins and the ZEITLUPE family , the red/far-red responsive phytochromes and the UV-... | [
"Plants constantly adjust their growth , development and metabolism to the ambient light environment .",
"Blue light is sensed by the Arabidopsis photoreceptors CRY1 and CRY2 which subsequently initiate light signal transduction by repressing the COP1/SPA E3 ubiquitin ligase .",
"While the interaction between c... | [
"Plants sense ambient light conditions through several photoreceptors that induce a complex signaling cascade to vastly alter gene expression , growth and development .",
"Blue light activates two cryptochrome photoreceptors which subsequently inactivate an E3 ubiquitin ligase consisting of COP1 and SPA proteins ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neurological disorders/prion diseases"
] | Protease-Sensitive Synthetic Prions | journal.ppat.1000736 | null | [
[
"Prions are infectious proteins that cause heritable , sporadic , and transmissible disease in humans and other mammals [1] .",
"The molecular basis of prion disease is a conformational change in the normal , cellular prion protein , denoted PrPC , to a disease-causing form , denoted PrPSc [2] , [3] .",
... | [
"Prions arise when the cellular prion protein ( PrPC ) undergoes a self-propagating conformational change; the resulting infectious conformer is designated PrPSc .",
"Frequently , PrPSc is protease-resistant but protease-sensitive ( s ) prions have been isolated in humans and other animals .",
"We report here t... | [
"Prions are infectious proteins that cause heritable , sporadic , and transmissible diseases in humans and other mammals .",
"These infectious proteins arise when the normal form of the prion protein ( PrP ) adopts a self-perpetuating conformation .",
"This disease-causing PrP form is frequently distinguished f... | 2010 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"reverse transcriptase-polymerase chain reaction",
"invertebrates",
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"togaviruses",
"laboratory equipment",
"engineering and technology",
"pathogens",
"microbiology",
"saliva",
"animals",
"alphaviruses",
"vi... | Mosquito excreta: A sample type with many potential applications for the investigation of Ross River virus and West Nile virus ecology | journal.pntd.0006771 | null | [
[
"It has been estimated that vector-borne diseases account for almost 20% of the global burden of infectious diseases , with more than 80% of the world’s population living in areas at risk [1] .",
"Mosquitoes are the most important vectors of arthropod-borne viruses ( arboviruses ) globally .",
"In rec... | [
"Emerging and re-emerging arthropod-borne viruses ( arboviruses ) cause human and animal disease globally .",
"Field and laboratory investigation of mosquito-borne arboviruses requires analysis of mosquito samples , either individually , in pools , or a body component , or secretion such as saliva .",
"We asses... | [
"Testing for the presence of arboviruses in mosquitoes used in laboratory experiments or surveillance usually involves collecting samples , from pools of hundreds of mosquitoes to the legs and wings of an individual mosquito and testing them by different methods .",
"These methods can be labour intensive and cost... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"humoral immunity",
"medicine",
"public health and epidemiology",
"infectious disease epidemiology",
"immunity to infections",
"immunology",
"parasitic diseases",
"mathematics",
"infectious diseases",
"epidemiology",
"biology",
"infectious disease modeling",
"differential equations",
"schi... | Explaining Observed Infection and Antibody Age-Profiles in Populations with Urogenital Schistosomiasis | journal.pcbi.1002237 | null | [
[
"Urogenital schistosomiasis , which is caused by the blood fluke Schistosoma haematobium , is a tropical disease of great public health importance , infecting more than 100 million people in sub-Saharan Africa [1] , [2] .",
"S . haematobium has a complex lifecycle , which includes free-living stages in th... | [
"Urogenital schistosomiasis is a tropical disease infecting more than 100 million people in sub-Saharan Africa .",
"Individuals in endemic areas endure repeated infections with long-lived schistosome worms , and also encounter larval and egg stages of the life cycle .",
"Protective immunity against infection de... | [
"Urogenital schistosomiasis is a tropical infectious disease caused by schistosome blood flukes , infecting more than 100 million people in sub-Saharan Africa .",
"Protective immunity develops against schistosomes , but takes many years to do so , with children acquiring multiple infections with long-lived parasi... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"vertebrates",
"neuroscience",
"animals"
] | Retinal Ganglion Cells Can Rapidly Change Polarity from Off to On | journal.pbio.0050065 | A peripheral image shift produces a transient switch in retinal ganglion cell responses from Off-dominated to On-dominated. This modulation is exerted at least in part presynaptically, presumably at the bipolar cell synaptic terminal. | [
[
"In the retina , signals flow along parallel , spatially distributed pathways [1] .",
"A major split occurs at the very first synapse: On bipolar cells and Off bipolar cells respond to light with the opposite sign .",
"Retinal ganglion cells receive excitatory input from On or Off bipolars within thei... | [
"Retinal ganglion cells are commonly classified as On-center or Off-center depending on whether they are excited predominantly by brightening or dimming within the receptive field .",
"Here we report that many ganglion cells in the salamander retina can switch from one response type to the other , depending on st... | [
"The eye communicates to the brain all the information needed for vision in the form of electrical pulses , or spikes , on optic nerve fibers .",
"These spikes are produced by retinal ganglion cells , the output neurons of the retina .",
"In a popular view of retinal function , each ganglion cell responds to a ... | 2007 |
[
"Introduction",
"Models",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell binding",
"cell physiology",
"chemical characterization",
"neural networks",
"nucleases",
"engineering and technology",
"deoxyribonucleases",
"enzymes",
"signal processing",
"gene regulation",
"regulatory proteins",
"dna-binding proteins",
"enzymology",
"neuroscience",
"signal filt... | Imputation for transcription factor binding predictions based on deep learning | journal.pcbi.1005403 | null | [
[
"Transcription factors ( TFs ) play a central role in regulating gene expression .",
"Although TF binding to chromatin is primarily dictated by the DNA sequence , the binding patterns can be cell-specific through cooperative interactions between many different TFs .",
"Mutations in cis-regulatory elem... | [
"Understanding the cell-specific binding patterns of transcription factors ( TFs ) is fundamental to studying gene regulatory networks in biological systems , for which ChIP-seq not only provides valuable data but is also considered as the gold standard .",
"Despite tremendous efforts from the scientific communit... | [
"Transcription factors play a central role in regulating various cellular processes .",
"They bind to DNA in a cell-specific way .",
"To study where a TF would bind to DNA , ChIP-seq experiment has been developed and widely adopted by the science community to study genome-wide in vivo protein-DNA interactions .... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"systems biology",
"genome expression analysis",
"genomics",
"protein interactions",
"proteins",
"biology",
"computational biology",
"structural genomics"
] | Distinct Types of Disorder in the Human Proteome: Functional Implications for Alternative Splicing | journal.pcbi.1003030 | null | [
[
"While it is well established that a protein's three-dimensional structure determines its function , a large fraction of proteins and protein regions lack stable structure .",
"Such intrinsically disordered proteins contain extended regions that do not fold into a native fixed conformation [1] .",
"Th... | [
"Intrinsically disordered regions have been associated with various cellular processes and are implicated in several human diseases , but their exact roles remain unclear .",
"We previously defined two classes of conserved disordered regions in budding yeast , referred to as “flexible” and “constrained” conserved... | [
"A protein's cellular and molecular function is typically determined by its folded structure .",
"However , a large fraction of proteomes lack stably folded structure .",
"These regions are referred to as intrinsically disordered .",
"Protein disorder has largely been understudied , although it is emerging to... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"invertebrates",
"medicine and health sciences",
"ecology and environmental sciences",
"immune cells",
"parasite evolution",
"immunology",
"parasitic diseases",
"animals",
"parasitology",
"animal models",
"developmental biology",
"drosophila melanogaster",
"model organisms",... | Parallel and costly changes to cellular immunity underlie the evolution of parasitoid resistance in three Drosophila species | journal.ppat.1006683 | null | [
[
"Considerable genetic variation in susceptibility to infection exists both within and between populations [1] .",
"This variation determines the burden of disease within populations , and represents the raw material from which populations can evolve resistance in nature and during the selective breeding o... | [
"A priority for biomedical research is to understand the causes of variation in susceptibility to infection .",
"To investigate genetic variation in a model system , we used flies collected from single populations of three different species of Drosophila and artificially selected them for resistance to the parasi... | [
"We have found that three species of fruit fly evolve resistance to parasitic wasps ( parasitoids ) by increasing investment in their immune defences but they achieve this in different ways .",
"Resistance always involved increases in the number of the circulating hemocytes , which are the blood cells that kill p... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Material and Methods"
] | [
"molecular biology/histone modification",
"biochemistry",
"molecular biology/chromatin structure"
] | Histone H2A C-Terminus Regulates Chromatin Dynamics, Remodeling, and Histone H1 Binding | journal.pgen.1001234 | null | [
[
"In the eukaryotic nucleus , DNA is stored in a nucleoprotein complex referred to as chromatin .",
"This packaging of DNA does not only serve to condense DNA into a highly compacted form , it is also fundamental for the regulation of all DNA-dependent processes such as transcription , replication and DNA ... | [
"The tails of histone proteins are central players for all chromatin-mediated processes .",
"Whereas the N-terminal histone tails have been studied extensively , little is known about the function of the H2A C-terminus .",
"Here , we show that the H2A C-terminal tail plays a pivotal role in regulating chromatin... | [
"Histones are the main protein components of chromatin .",
"The N-terminal tails of histones stick out from the nucleosomes , the building blocks of chromatin , and are involved in the regulation of all DNA–dependent processes .",
"Only Histone H2A has an additional C-terminal tail and currently very little is ... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Evidence for Finely-Regulated Asynchronous Growth of Toxoplasma gondii Cysts Based on Data-Driven Model Selection | journal.pcbi.1003283 | null | [
[
"Toxoplasma gondii , an obligate intracellular protozoan parasite , is an important foodborne pathogen that can cause various diseases including lymphadenitis and congenital infection of the fetuses in humans .",
"Infection occurs through ingestion of food or water contaminated with cysts or oocysts .",
... | [
"Toxoplasma gondii establishes a chronic infection by forming cysts preferentially in the brain .",
"This chronic infection is one of the most common parasitic infections in humans and can be reactivated to develop life-threatening toxoplasmic encephalitis in immunocompromised patients .",
"Host-pathogen intera... | [
"A large portion of people worldwide are chronically infected with T . gondii .",
"Chronic infection with this parasite is characterized by formation of tissue cysts .",
"Bradyzoites slowly replicate within cysts during the chronic stage of infection leading to a corresponding increase in cyst size .",
"Cysts... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/plant genetics and gene expression",
"developmental biology/plant growth and development",
"developmental biology/stem cells"
] | ARGONAUTE10 and ARGONAUTE1 Regulate the Termination of Floral Stem Cells through Two MicroRNAs in Arabidopsis | journal.pgen.1001358 | null | [
[
"Stem cells are key to morphogenesis in multicellular organisms and understanding the mechanisms governing their maintenance or termination is a major goal in developmental biology .",
"In plants , small populations of pluripotent stem cells are found in meristems located at the tips of roots , shoots , o... | [
"Stem cells are crucial in morphogenesis in plants and animals .",
"Much is known about the mechanisms that maintain stem cell fates or trigger their terminal differentiation .",
"However , little is known about how developmental time impacts stem cell fates .",
"Using Arabidopsis floral stem cells as a model... | [
"Stem cells have the capacity to self renew while producing daughter cells that undergo differentiation .",
"While some stem cells remain as stem cells throughout the life of an organism , others are programmed to terminate within developmental contexts .",
"It is presumed that stem cell termination is simply t... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"solomon islands",
"ecology and environmental sciences",
"water resources",
"pathology and laboratory medicine",
"immunology",
"tropical diseases",
"geographical locations",
"health care",
"vaccines",
"preventive medicine",
"bacterial diseases",
"diarrhea",
... | Knowledge, Attitudes, and Practices regarding Diarrhea and Cholera following an Oral Cholera Vaccination Campaign in the Solomon Islands | journal.pntd.0004937 | null | [
[
"From July 2009 until late 2011 , an outbreak of cholera in Papua New Guinea ( PNG ) resulted in >15 , 500 cases and >500 deaths in 8 of 20 province-level divisions and the Autonomous Region of Bougainville , situated in the western archipelago of the Solomon Islands in the South Pacific ( Fig 1 ) [1] .",
... | [
"In response to a 2011 cholera outbreak in Papua New Guinea , the Government of the Solomon Islands initiated a cholera prevention program which included cholera disease prevention and treatment messaging , community meetings , and a pre-emptive cholera vaccination campaign targeting 11 , 000 children aged 1–15 yea... | [
"We assessed knowledge , attitudes and practices of diarrhea and cholera disease and prevention in two areas of the Solomon Islands near Papua New Guinea .",
"Both areas were ‘at risk’ for cholera disease and received messages about cholera prevention .",
"Later , one of the areas also received vaccination agai... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Preferential Allele Expression Analysis Identifies Shared Germline and Somatic Driver Genes in Advanced Ovarian Cancer | journal.pgen.1005755 | null | [
[
"Identifying genes contributing to tumor biology ( driver genes ) underlies the design of targeted therapies .",
"The advent of large-scale tumor sequencing in 2006 [1] followed by integrated multi-dimensional TCGA studies [2] brought a wealth of molecular data in different cancers at the somatic mutation... | [
"Identifying genes where a variant allele is preferentially expressed in tumors could lead to a better understanding of cancer biology and optimization of targeted therapy .",
"However , tumor sample heterogeneity complicates standard approaches for detecting preferential allele expression .",
"We therefore dev... | [
"Identifying genes that contribute to cancer biology is complicated partly because cancers can have dozens of somatic mutations and thousands of germline variants .",
"Somatic mutations are gene variants that arise after conception in an organism while germline variants are gene variants present at conception in ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biomacromolecule-ligand interactions",
"humoral immunity",
"immunity to infections",
"immunology",
"microbiology",
"viral structure",
"immunodeficiency viruses",
"mechanisms of resistance and susceptibility",
"viral immune evasion",
"biology",
"biophysics",
"immune response",
"viral envelop... | Contribution of Intrinsic Reactivity of the HIV-1 Envelope Glycoproteins to CD4-Independent Infection and Global Inhibitor Sensitivity | journal.ppat.1002101 | null | [
[
"The entry of human immunodeficiency virus type 1 ( HIV-1 ) into cells is mediated by the envelope glycoprotein complex on the viral membrane [1] .",
"This complex is a trimer of heterodimeric subunits , each composed of a gp120 surface glycoprotein and a gp41 transmembrane glycoprotein [2] .",
"In th... | [
"Human immunodeficiency virus ( HIV-1 ) enters cells following sequential activation of the high-potential-energy viral envelope glycoprotein trimer by target cell CD4 and coreceptor .",
"HIV-1 variants differ in their requirements for CD4; viruses that can infect coreceptor-expressing cells that lack CD4 have be... | [
"Human immunodeficiency virus ( HIV-1 ) , the cause of acquired immunodeficiency syndrome ( AIDS ) , enters cells by attaching its major surface component , the envelope glycoprotein spike , to a receptor protein on the target cell called CD4 .",
"This attachment promotes cell entry by allowing the envelope prote... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"rna interference",
"chromosome structure and function",
"gene regulation",
"cell differentiation",
"developmental biology",
"epigenetics",
"sex chromosomes",
"chromosome biology",
"genetic interference",
"gene expression",
"x chromosomes",
"autosomes",
"biochemistry",
"rna",
"cell biolo... | Anchoring of Heterochromatin to the Nuclear Lamina Reinforces Dosage Compensation-Mediated Gene Repression | journal.pgen.1006341 | null | [
[
"Expression of genes must be tightly regulated both spatially and temporarily to ensure normal development .",
"While our understanding of gene regulation at the level of transcription factor binding and modulation of chromatin structure is supported by an abundance of data , the contribution of the spati... | [
"Higher order chromosome structure and nuclear architecture can have profound effects on gene regulation .",
"We analyzed how compartmentalizing the genome by tethering heterochromatic regions to the nuclear lamina affects dosage compensation in the nematode C . elegans .",
"In this organism , the dosage compen... | [
"DNA isolated from the nucleus of a single human cell , if stretched out , would be 3 meters long .",
"This amount of DNA must be packaged into a nucleus , which is orders of magnitude smaller .",
"DNA of active genes tends to be loosely packed and localized internally within the nucleus , while DNA of inactive... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/cellular death and stress responses",
"computational biology",
"computational biology/systems biology",
"cell biology/cell signaling"
] | Rule-Based Cell Systems Model of Aging using Feedback Loop Motifs Mediated by Stress Responses | journal.pcbi.1000820 | null | [
[
"Approaches to model aging computationally are challenged by an inherent complexity through involvement of a wide range of molecular processes , pathways , oxidative damage , dysfunction of organelles and dysregulation .",
"Therefore , systems level representations combining experimental observations , co... | [
"Investigating the complex systems dynamics of the aging process requires integration of a broad range of cellular processes describing damage and functional decline co-existing with adaptive and protective regulatory mechanisms .",
"We evolve an integrated generic cell network to represent the connectivity of ke... | [
"The global process of aging disturbs a broad range of cellular mechanisms in a complex fashion and is not well understood .",
"One important goal of computational approaches in aging is to develop integrated models in terms of a unifying aging theory , predicting progression of aging phenotypes grounded on molec... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public and occupational health",
"medicine and health sciences",
"simulation and modeling",
"biology and life sciences",
"parasitology",
"research and analysis methods"
] | Bayesian Risk Mapping and Model-Based Estimation of Schistosoma haematobium–Schistosoma mansoni Co-distribution in Côte d′Ivoire | journal.pntd.0003407 | null | [
[
"The fight against schistosomiasis has been stepped up with global awareness of the burden inflicted upon people who mainly live in rural settings of tropical and sub-tropical countries .",
"Control measures aim to prevent and reduce morbidity due to chronic infection .",
"Whenever resources allow , i... | [
"Schistosoma haematobium and Schistosoma mansoni are blood flukes that cause urogenital and intestinal schistosomiasis , respectively .",
"In Côte d′Ivoire , both species are endemic and control efforts are being scaled up .",
"Accurate knowledge of the geographical distribution , including delineation of high-... | [
"Two types of blood-dwelling parasitic worms that cause schistosomiasis ( i . e . , Schistosoma haematobium and Schistosoma mansoni ) are endemic in Côte d′Ivoire , West Africa .",
"Reliable information on their geographical distribution is needed to plan and guide the national control program .",
"Recently , c... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/protein folding"
] | The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau | journal.pcbi.1000155 | null | [
[
"Alzheimer's disease ( AD ) pathology is characterized by extracellular aggregates of Aβ-amyloid ( Aβ ) and intraneuronal tau aggregates , known as senile plaques and neurofibrillary tangles ( NFTs ) , respectively [1] .",
"Despite much focus on Aβ amyloid in AD research , tau seems to play an important r... | [
"Tau is a natively unfolded protein that forms intracellular aggregates in the brains of patients with Alzheimer's disease .",
"To decipher the mechanism underlying the formation of tau aggregates , we developed a novel approach for constructing models of natively unfolded proteins .",
"The method , energy-mini... | [
"Alzheimer's disease pathology is characterized by two types of protein aggregates that are found in the brain—amyloid plaques and neurofibrillary tangles .",
"Several studies suggest that these aggregates also play an active role in the disease process .",
"Thus , an understanding of disease pathogenesis may b... | 2008 |
[
"Introduction",
"Methods and Materials",
"Results",
"Discussion",
"Conclusion"
] | [
"medicine and health sciences",
"enzyme-linked immunoassays",
"body fluids",
"pathology and laboratory medicine",
"immune physiology",
"immunology",
"tropical diseases",
"geographical locations",
"uganda",
"bacterial diseases",
"eye diseases",
"neglected tropical diseases",
"antibodies",
"... | Defining Seropositivity Thresholds for Use in Trachoma Elimination Studies | journal.pntd.0005230 | null | [
[
"Trachoma is caused by ocular infection with the bacterium Chlamydia trachomatis ( Ct ) [1] .",
"It is the leading infectious cause of blindness worldwide [2] .",
"The World Health Organization ( WHO ) estimates that over 200 million people in 42 countries are at risk from trachoma blindness [3] , tha... | [
"Efforts are underway to eliminate trachoma as a public health problem by 2020 .",
"Programmatic guidelines are based on clinical signs that correlate poorly with Chlamydia trachomatis ( Ct ) infection in post-treatment and low-endemicity settings .",
"Age-specific seroprevalence of anti Ct Pgp3 antibodies has ... | [
"Trachoma is caused by the bacterium Chlamydia trachomatis ( Ct ) .",
"Individuals who have previously been infected with Ct carry specific antibodies in their blood .",
"Recent studies have suggested that these antibodies may be a good way to estimate the intensity of transmission of this bacterium in a popula... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"bacterial diseases",
"infectious diseases",
"botulism",
"microbial pathogens",
"biology",
"microbiology",
"bacterial pathogens",
"gram positive"
] | Two-Component Signal Transduction System CBO0787/CBO0786 Represses Transcription from Botulinum Neurotoxin Promoters in Clostridium botulinum ATCC 3502 | journal.ppat.1003252 | null | [
[
"Botulinum neurotoxins are the most poisonous biological substances known to mankind .",
"The neurotoxins are metalloproteases which block neurotransmission in cholinergic nerves [1] , [2] in humans and animals to cause botulism , a potentially lethal flaccid paralysis .",
"Botulinum neurotoxins are p... | [
"Blocking neurotransmission , botulinum neurotoxin is the most poisonous biological substance known to mankind .",
"Despite its infamy as the scourge of the food industry , the neurotoxin is increasingly used as a pharmaceutical to treat an expanding range of muscle disorders .",
"Whilst neurotoxin expression b... | [
"Botulinum neurotoxin produced by the spore-forming bacterium Clostridium botulinum is the most poisonous biological substance known to mankind .",
"By blocking neurotransmission , the neurotoxin causes a flaccid paralysis called botulism which may to lead to death upon respiratory muscle collapse .",
"Despite ... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"medicine and health sciences",
"leptospira",
"pathology and laboratory medicine",
"pathogens",
"tropical diseases",
"microbiology",
"bacterial diseases",
"phylogenetics",
"data management",
"phylogenetic analysis",
"genome analysis",
"neglected tropical diseases",
"bacteria",
... | Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics | journal.pntd.0007270 | null | [
[
"Leptospirosis is an emerging zoonotic disease of worldwide distribution that affects more than 1 million people with 60 , 000 deaths per year [1] .",
"In addition , numerous animal hosts ( wild and domestic ) , such as livestock , can contract leptospirosis causing economical cost to subsistence and indu... | [
"The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide .",
"One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals .",
"Soils and surface waters also host a high diversity of... | [
"Leptospirosis which is an emerging zoonotic disease worldwide , is transmitted to humans through contact with soils or surface waters contaminated with the urine of reservoir animals .",
"Species of Leptospira , which include infectious and non-infectious strains , are ubiquitous in the environment .",
"In thi... | 2019 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"genomics",
"microbial evolution",
"biology",
"evolutionary biology",
"comparative genomics",
"microbiology",
"host-pathogen interaction",
"genetics and genomics"
] | Comparative Genomics Suggests an Independent Origin of Cytoplasmic Incompatibility in Cardinium hertigii | journal.pgen.1003012 | null | [
[
"Bacterial symbionts of terrestrial arthropods are common , influential associates , known to affect fundamental aspects of the host life history , ecology , and evolution .",
"These maternally inherited bacteria may , for example , provide essential nutrients supplementing their host's diet , confer prot... | [
"Terrestrial arthropods are commonly infected with maternally inherited bacterial symbionts that cause cytoplasmic incompatibility ( CI ) .",
"In CI , the outcome of crosses between symbiont-infected males and uninfected females is reproductive failure , increasing the relative fitness of infected females and lea... | [
"Many arthropods are infected with bacterial symbionts that are maternally transmitted and have a great impact on their hosts' biology , ecology , and evolution .",
"One of the most common phenotypes of facultative symbionts appears to be cytoplasmic incompatibility ( CI ) , a type of reproductive failure in whic... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"applied mathematics",
"neurites",
"neuroscience",
"cell differentiation",
"simulation and modeling",
"algorithms",
"developmental biology",
"systems science",
"mathematics",
"signaling cascades",
"neuronal dendrites",
"research and analysis methods",
"erk signaling cascade",
"computer and... | System identification of signaling dependent gene expression with different time-scale data | journal.pcbi.1005913 | null | [
[
"In intracellular signaling systems , information of an extracellular stimulus is encoded into combinations of distinct temporal patterns of phosphorylation of intracellular signaling molecules that are selectively decoded by downstream gene expression , leading to cell fate decisions such as cell differentia... | [
"Cells decode information of signaling activation at a scale of tens of minutes by downstream gene expression with a scale of hours to days , leading to cell fate decisions such as cell differentiation .",
"However , no system identification method with such different time scales exists .",
"Here we used compre... | [
"The key points of this study are two-fold: The first point is the decoding mechanism for cell differentiation .",
"We previously demonstrated the encoding mechanism of cell fate decision information by transient and sustained ERK activation in PC12 cells , and also identified the decoding genes essential for cel... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"mathematics",
"infectious disease epidemiology",
"epidemiology",
"applied mathematics",
"biology and life sciences",
"population biology",
"physical sciences"
] | Model-Based Investigations of Different Vector-Related Intervention Strategies to Eliminate Visceral Leishmaniasis on the Indian Subcontinent | journal.pntd.0002810 | null | [
[
"Visceral leishmaniasis ( VL ) , also known as Kala-azar , is a vector-borne parasitic disease that almost always ends in death if untreated [1] .",
"Infection with the parasite , Leishmania chagasi/infantum in the New or parts of the Old World or Leishmania donovani in other regions of the Old World , oc... | [
"The elimination of infectious diseases requires reducing transmission below a certain threshold .",
"The Visceral Leishmaniasis ( VL ) Elimination Initiative in Southeast Asia aims to reduce the annual VL incidence rate below 1 case per 10 , 000 inhabitants in endemic areas by 2015 via a combination of case mana... | [
"Visceral leishmaniasis is suspected to be the second largest parasitic killer in the world after malaria .",
"On the Indian subcontinent , the vector-borne disease is caused by the protozoan flagellate Leishmania donovani and transmitted by the sand fly Phlebotomus argentipes .",
"The regional elimination prog... | 2014 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"microbiology/plant-biotic interactions",
"computational biology/sequence motif analysis",
"microbiology/microbial evolution and genomics",
"molecular biology/bioinformatics",
"public health and epidemiology/infectious diseases",
"computational biology/macromolecular sequence analysis",
"computational b... | Sequence-Based Prediction of Type III Secreted Proteins | journal.ppat.1000376 | null | [
[
"Many Gram-negative bacteria with symbiotic or parasitic lifestyles modulate their environment , the eukaryotic host cell , by the secretion of bacterial proteins into the host cell through the type III secretion system ( TTSS ) [1] .",
"The unique role of type III mediated transport for establishing as w... | [
"The type III secretion system ( TTSS ) is a key mechanism for host cell interaction used by a variety of bacterial pathogens and symbionts of plants and animals including humans .",
"The TTSS represents a molecular syringe with which the bacteria deliver effector proteins directly into the host cell cytosol .",
... | [
"Many Gram-negative bacteria live closely associated with humans , animals , or plants .",
"The pathogenic or symbiotic interactions between bacteria and host are often mediated by the secretion of bacterial proteins into the host cells .",
"The Type III secretion system ( TTSS ) is one of the best studied cell... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"bacteriology",
"medicine and health sciences",
"microbiome",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"ulcerative colitis",
"social sciences",
"colitis",
"gastroenterology and hepatology",
"bacterial genetics",
"inflammatory bowel disease",
"microbial genetics",
"... | Genetic effects on the commensal microbiota in inflammatory bowel disease patients | journal.pgen.1008018 | null | [
[
"Most genetic analyses and twin studies published to date support a genetic component of inflammatory bowel disease ( IBD ) phenotypes [1] .",
"Recent works showed an estimated heritability on the liability scale of approximately 70–80% for Crohn’s disease ( CD ) and 60–70% for ulcerative colitis ( UC ) [... | [
"Several bacteria in the gut microbiota have been shown to be associated with inflammatory bowel disease ( IBD ) , and dozens of IBD genetic variants have been identified in genome-wide association studies .",
"However , the role of the microbiota in the etiology of IBD in terms of host genetic susceptibility rem... | [
"In this study , we used observational data to explore associations between host genetics and the commensal microbiome in inflammatory bowel disease cases .",
"Our analysis identified four associations involving two genes and four bacterial taxa and replicated two of these associations in independent cohorts .",
... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer science",
"computational biology/systems biology",
"computational biology/signaling networks"
] | Organization of Physical Interactomes as Uncovered by Network Schemas | journal.pcbi.1000203 | null | [
[
"Network schemas build upon earlier pioneering work in network analysis by enabling new types of analyses that were not possible with previous methods for identifying recurrent patterns in biological networks .",
"By considering the specific roles of individual proteins , network schemas look beyond the p... | [
"Large-scale protein-protein interaction networks provide new opportunities for understanding cellular organization and functioning .",
"We introduce network schemas to elucidate shared mechanisms within interactomes .",
"Network schemas specify descriptions of proteins and the topology of interactions among th... | [
"Large-scale networks of protein-protein interactions provide a view into the workings of the cell .",
"However , these interaction maps do not come with a key for interpreting them , so it is necessary to develop methods that shed light on their functioning and organization .",
"We propose the language of netw... | 2008 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"helminths",
"gene regulation",
"dna-binding proteins",
"animals",
"parasitology",
"dna transcription",
"developmental biology",
"sporocysts",
"epigenetics",
"chromatin",
"transcriptional control",
"chromosome biology",
"proteins",... | Histone methylation changes are required for life cycle progression in the human parasite Schistosoma mansoni | journal.ppat.1007066 | null | [
[
"Parasites often display complex life cycles that involve several hosts and multiple , phenotypically distinct , developmental stages .",
"This is the case for many human endoparasites , which cause deadly diseases including malaria ( Plasmodium falciparum ) , leishmaniasis ( Leishmania spp . ) , cryptosp... | [
"Epigenetic mechanisms and chromatin structure play an important role in development .",
"Their impact is therefore expected to be strong in parasites with complex life cycles and multiple , strikingly different , developmental stages , i . e . developmental plasticity .",
"Some studies have already described h... | [
"Schistosoma mansoni is a parasitic flatworm and causative agent of intestinal schistosomiasis , a neglected tropical disease affecting 67 million people worldwide .",
"The parasite has a complex life cycle involving two consecutive obligate hosts ( a poikilotherm snail and a homeotherm mammal ) and two transitio... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | The Presence of Nuclear Cactus in the Early Drosophila Embryo May Extend the Dynamic Range of the Dorsal Gradient | journal.pcbi.1004159 | null | [
[
"Tissues in a developing animal are often patterned by long-range signaling factors called morphogens .",
"In the early ( 1–3 hr old ) Drosophila embryo , the transcription factor Dorsal ( dl; FlyBase ID: FBgn0260632 ) acts as a morphogen to pattern the embryo’s dorsal-ventral ( DV ) axis ( [1 , 2]; revie... | [
"In a developing embryo , the spatial distribution of a signaling molecule , or a morphogen gradient , has been hypothesized to carry positional information to pattern tissues .",
"Recent measurements of morphogen distribution have allowed us to subject this hypothesis to rigorous physical testing .",
"In the e... | [
"In the early stages of development , an embryo must establish the beginnings of a body plan in order to grow organs and limbs in the right places .",
"Across the fruit fly embryo , proteins known as morphogens cause chain reactions that eventually lead to the growth of many different body parts .",
"One specif... | 2015 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [] | How Attention Can Create Synaptic Tags for the Learning of Working Memories in Sequential Tasks | journal.pcbi.1004060 | null | [
[
"Animals like monkeys can be trained to perform complex cognitive tasks , simply by giving rewards at the right times .",
"They can learn to map sensory stimuli onto responses , to store task-relevant information and to integrate and combine unreliable sensory evidence .",
"Training induces new stimul... | [
"Intelligence is our ability to learn appropriate responses to new stimuli and situations .",
"Neurons in association cortex are thought to be essential for this ability .",
"During learning these neurons become tuned to relevant features and start to represent them with persistent activity during memory delays... | [
"Working memory is a cornerstone of intelligence .",
"Most , if not all , tasks that one can imagine require some form of working memory .",
"The optimal solution of a working memory task depends on information that was presented in the past , for example choosing the right direction at an intersection based on... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Environmental and Behavioural Determinants of Leptospirosis Transmission: A Systematic Review | journal.pntd.0003843 | null | [
[
"Leptospirosis , classified as a neglected tropical disease , is caused by a pathogenic spirochete bacterium of the genus Leptospira [1] , [2] .",
"Most mammalian species can carry leptospirosis , with no disease or only mild clinical manifestations in the maintenance hosts because they are highly adapted... | [
"Leptospirosis is one of the most widespread zoonotic diseases , which is of global medical and veterinary importance , and also a re-emerging infectious disease .",
"The main tracks of transmission are known; however , the relative importance of each of the components and the respective environmental risk factor... | [
"Leptospirosis is a bacterial disease passed from animals to people—either through direct contact with animals or indirectly via the environment .",
"The disease can be found worldwide but is more important in tropical and subtropical countries .",
"Due to their sheer genetic diversity , virtually all mammals c... | 2015 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genome projects",
"genetics and genomics/microbial evolution and genomics"
] | Genome Sequence of the Pea Aphid Acyrthosiphon pisum | journal.pbio.1000313 | The genome of the pea aphid shows remarkable levels of gene duplication and equally remarkable gene absences that shed light on aspects of aphid biology, most especially its symbiosis with Buchnera. | [
[
"Aphids are small , soft-bodied insects with elaborate life cycles that include all-female , parthenogenetic generations that alternate with sexual generations ( Figure 1 ) .",
"Aphids feed exclusively on plant phloem sap by inserting their slender mouthparts into sieve elements , the primary food conduit... | [
"Aphids are important agricultural pests and also biological models for studies of insect-plant interactions , symbiosis , virus vectoring , and the developmental causes of extreme phenotypic plasticity .",
"Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum .",
"This first pu... | [
"Aphids are common pests of crops and ornamental plants .",
"Facilitated by their ancient association with intracellular symbiotic bacteria that synthesize essential amino acids , aphids feed on phloem ( sap ) .",
"Exploitation of a diversity of long-lived woody and short-lived herbaceous hosts by many aphid sp... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"epistasis",
"genetic dominance",
"genetic polymorphism",
"quantitative trait loci",
"phenotypes",
"heredity",
"genetics",
"biology and life sciences",
"population genetics",
"population biology",
"quantitative traits",
"evolutionary biology",
"variant genotypes",
"genetic loci",
"geneti... | The Genetic Architecture of Quantitative Traits Cannot Be Inferred from Variance Component Analysis | journal.pgen.1006421 | null | [
[
"Nearly a century ago , R . A . Fisher solved the apparent discrepancy between rules of Mendelian inheritance for alleles with large effects at one or a few loci and the resemblance among relatives for quantitative traits with a continuous distribution of phenotypes in natural populations [1 , 2] .",
"He ... | [
"Classical quantitative genetic analyses estimate additive and non-additive genetic and environmental components of variance from phenotypes of related individuals without knowing the identities of quantitative trait loci ( QTLs ) .",
"Many studies have found a large proportion of quantitative trait variation can... | [
"There has been a great amount of debate over the relative importance of additivity and non-additivity in quantitative trait variation .",
"The main argument supporting the importance of additivity is the observation that the additive component of genetic variance is much greater than non-additive variance compon... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | First Evidence of a Hybrid of Leishmania (Viannia) braziliensis/L. (V.) peruviana DNA Detected from the Phlebotomine Sand Fly Lutzomyia tejadai in Peru | journal.pntd.0004336 | null | [
[
"New World Leishmanias are transmitted by phlebotomine sand flies of the genus Lutzomyia , and around 480 species have been recorded; in Peru , 149 species have been registered [1] , and some of which have been implicated as potential vectors of human Leishmanias [2–8] .",
"In Peru , cutaneous leishmanias... | [
"The natural infection of sand flies by Leishmania was examined in the Department of Huanuco of Peru , where cutaneous leishmaniasis caused by a hybrid of Leishmania ( Viannia ) braziliensis/L .",
"( V . ) peruviana is endemic .",
"A total of 2 , 997 female sand flies were captured by CDC light traps and Shanno... | [
"Leishmaniasis is a protozoan disease caused by members of the genus Leishmania , which are distributed worldwide , especially in tropical and subtropical areas .",
"More than 20 species of Leishmania are described as causative agents of human leishmaniases and clinical features are largely associated with the in... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Neural Dynamics as Sampling: A Model for Stochastic Computation in Recurrent Networks of Spiking Neurons | journal.pcbi.1002211 | null | [
[
"Attempts to understand the organization of computations in the brain from the perspective of traditional , mostly deterministic , models of computation , such as attractor neural networks or Turing machines , have run into problems: Experimental data suggests that neurons , synapses , and neural systems are ... | [
"The organization of computations in networks of spiking neurons in the brain is still largely unknown , in particular in view of the inherently stochastic features of their firing activity and the experimentally observed trial-to-trial variability of neural systems in the brain .",
"In principle there exists a p... | [
"It is well-known that neurons communicate with short electric pulses , called action potentials or spikes .",
"But how can spiking networks implement complex computations ?",
"Attempts to relate spiking network activity to results of deterministic computation steps , like the output bits of a processor in a di... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Coordinate Regulation of Lipid Metabolism by Novel Nuclear Receptor Partnerships | journal.pgen.1002645 | null | [
[
"Modern day lifestyle and diet dramatically increase the threat of chronic diseases including obesity , diabetes and atherosclerosis .",
"These metabolic disorders have been consistently linked to the imbalance between energy consumption and expenditure .",
"Growing evidence suggests that faulty regul... | [
"Mammalian nuclear receptors broadly influence metabolic fitness and serve as popular targets for developing drugs to treat cardiovascular disease , obesity , and diabetes .",
"However , the molecular mechanisms and regulatory pathways that govern lipid metabolism remain poorly understood .",
"We previously fou... | [
"Mammalian nuclear receptors are actively targeted for treatment of a range of cardiovascular diseases and obesity .",
"However , effective drug development still depends on a more exhaustive characterization of how different nuclear receptors mediate their different physiological effects in vivo .",
"Taking ad... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Role for Macro-ER-Phagy in ER Quality Control | journal.pgen.1005390 | null | [
[
"One third of all newly synthesized proteins enter the endoplasmic reticulum ( ER ) .",
"However , only a small fraction is transported to their final destination .",
"A large fraction ( 30–75% ) fails to fold and mature properly , does not pass the ER quality control ( ERQC ) and gets degraded [1] ."... | [
"The endoplasmic-reticulum quality-control ( ERQC ) system shuttles misfolded proteins for degradation by the proteasome through the well-defined ER-associated degradation ( ERAD ) pathway .",
"In contrast , very little is known about the role of autophagy in ERQC .",
"Macro-autophagy , a collection of pathways... | [
"ER-quality control ( ERQC ) ensures delivery of “native” proteins through the secretory pathway .",
"Currently , ER-associated degradation ( ERAD ) , which delivers misfolded proteins for degradation by the proteasome , is considered a major ERQC pathway , with autophagy as its backup .",
"Until now , the role... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary biology/human evolution",
"molecular biology",
"genetics and genomics/population genetics"
] | Sequences From First Settlers Reveal Rapid Evolution in Icelandic mtDNA Pool | journal.pgen.1000343 | null | [
[
"The Icelanders are one of the most studied populations in human genetics [1]–[5] .",
"According to historical and archaeological sources , Iceland was settled roughly 1100 years ago by a mixture of people that originated primarily from Scandinavia and the British Isles [6] , [7] .",
"Studies of mtDNA... | [
"A major task in human genetics is to understand the nature of the evolutionary processes that have shaped the gene pools of contemporary populations .",
"Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population ... | [
"Ancient DNA studies have great potential to shed light on the evolution of populations because they provide the opportunity to sample from the same population at different points in time .",
"However , ancient DNA studies are often based on DNA extracted from only one or a few individuals and , therefore , do no... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"parasite evolution",
"enzymes",
"immunology",
"microbiology",
"host-pathogen interaction",
"parasitology",
"animal models",
"model organisms",
"enzyme regulation",
"protozoan models",
"biology",
"mouse",
"biochemistry",
"enzyme structure",
"immunity",
"genetics",
"genetics and genom... | A Toxoplasma gondii Pseudokinase Inhibits Host IRG Resistance Proteins | journal.pbio.1001358 | A secreted kinase from the parasitic protozoan, Toxoplasma gondii, is shown to cooperate with a phylogenetically related pseudokinase to phosphorylate and inactivate a mouse resistance protein of the IRG system. | [
[
"Toxoplasma gondii ( T . gondii ) is an intracellular parasitic protozoan of the phylum Apicomplexa , a relative of the malarial Plasmodia .",
"The two groups of human parasites differ greatly in their ecology .",
"In particular , unlike Plasmodium species , which have narrow host ranges , T . gondii ... | [
"The ability of mice to resist infection with the protozoan parasite , Toxoplasma gondii , depends in large part on the function of members of a complex family of atypical large GTPases , the interferon-gamma-inducible immunity-related GTPases ( IRG proteins ) .",
"Nevertheless , some strains of T . gondii are hi... | [
"Toxoplasma gondii is an intracellular parasitic protozoan infecting about a third of humankind .",
"Humans , however , are unlikely to be important hosts in terms of the evolution of the parasite because , for completion of the parasite sexual cycle , the infected animal must be eaten by a cat .",
"Therefore ,... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/immunity to infections",
"immunology/immune response"
] | Protective Efficacy of Cross-Reactive CD8+ T Cells Recognising Mutant Viral Epitopes Depends on Peptide-MHC-I Structural Interactions and T Cell Activation Threshold | journal.ppat.1001039 | null | [
[
"Virus-specific CD8+ T cells play a critical role in host defence via the production of antiviral cytokines , the direct killing of virus-infected cells and the establishment of immunological memory [1] .",
"The selection of CD8+ T cells into an immune response requires specific interaction between the T ... | [
"Emergence of a new influenza strain leads to a rapid global spread of the virus due to minimal antibody immunity .",
"Pre-existing CD8+ T-cell immunity directed towards conserved internal viral regions can greatly ameliorate the disease .",
"However , mutational escape within the T cell epitopes is a substanti... | [
"Introduction of a new influenza strain into human circulation leads to a rapid global spread of the virus due to minimal antibody immunity .",
"Established T-cell immunity towards conserved viral regions provides some protection against influenza and promotes rapid recovery .",
"However , influenza viruses mut... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cancer detection and diagnosis",
"children",
"medicine and health sciences",
"lymphatic mapping",
"education",
"sociology",
"geographical locations",
"tropical diseases",
"social sciences",
"parasitic diseases",
"oncology",
"age groups",
"filariasis",
"pharmaceutics",
"drug administrati... | Towards elimination of lymphatic filariasis in southeastern Madagascar: Successes and challenges for interrupting transmission | journal.pntd.0006780 | null | [
[
"The world is on a path towards the elimination of lymphatic filariasis ( LF ) , a major neglected tropical disease ( NTD ) and parasitic infection transmitted by mosquitoes and caused by Wuchereria bancrofti , Brugia malayi , and B . timori .",
"LF can result in chronic disabling consequences ( e . g . h... | [
"A global strategy of mass drug administration ( MDA ) has greatly reduced the burden of lymphatic filariasis ( LF ) in endemic countries .",
"In Madagascar , the National Programme to eliminate LF has scaled-up annual MDA of albendazole and diethylcarbamazine across the country in the last decade , but its impac... | [
"Lymphatic filariasis is a neglected disease with chronic disabling consequences .",
"Endemic countries have reduced lymphatic filariasis transmission through a strategy of annual rounds of mass drug administration ( MDA ) , but the impact of such strategy has not yet been reported for Madagascar .",
"In this s... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"fish",
"molecular dynamics",
"vertebrates",
"social sciences",
"pigments",
"animals",
"neuroscience",
"animal models",
"osteichthyes",
"model organisms",
"mathematics",
"forecasting",
"statistics (mathematics)",
"materials science",
"experimental organism systems",
"vision",
"resear... | Predicting peak spectral sensitivities of vertebrate cone visual pigments using atomistic molecular simulations | journal.pcbi.1005974 | null | [
[
"Many living organisms rely upon vision as the dominant sensory modality for foraging , predator avoidance , and social behaviors including mate selection .",
"Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the neural retina of the eye .",
"Within photo... | [
"Vision is the dominant sensory modality in many organisms for foraging , predator avoidance , and social behaviors including mate selection .",
"Vertebrate visual perception is initiated when light strikes rod and cone photoreceptors within the neural retina of the eye .",
"Sensitivity to individual colors , i... | [
"Vertebrate color vision is possible when cone visual pigments with distinct peak spectral sensitivities ( λmax ) are expressed in separate cone populations and provide differential input to downstream neurons .",
"The λmax is a function of the type of chromophore ( such as 11-cis retinal ) and the amino acid seq... | 2018 |
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