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",
"Methods"
] | [
"neuroscience/behavioral neuroscience",
"neuroscience/motor systems",
"neuroscience/neurodevelopment",
"neuroscience/neuronal signaling mechanisms",
"neuroscience"
] | Mitochondrial Morphogenesis, Dendrite Development, and Synapse Formation in Cerebellum Require both Bcl-w and the Glutamate Receptor δ2 | journal.pgen.1000097 | null | [
[
"Mitochondria have been shown to undergo morphological changes in many neurodegenerative and psychiatric diseases , suggesting their vital role in maintaining the normal function of neuron cells .",
"One of the morphological changes in mitochondria is the length or size , which can be controlled by mitoch... | [
"Bcl-w belongs to the prosurvival group of the Bcl-2 family , while the glutamate receptor δ2 ( Grid2 ) is an excitatory receptor that is specifically expressed in Purkinje cells , and required for Purkinje cell synapse formation .",
"A recently published result as well as our own findings have shown that Bcl-w c... | [
"A neuron cell is composed of cell body , axons , and dendrites .",
"Dendritic spines on dendrites form synapses with axons of other neurons , establishing communication between neuron cells .",
"Dendrite development and synapse formation are therefore important for neuronal function .",
"Although many genes ... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/embryology",
"developmental biology",
"molecular biology/transcription initiation and activation",
"developmental biology/cell differentiation",
"developmental biology/organogenesis"
] | Dynamic Chromatin Organization during Foregut Development Mediated by the Organ Selector Gene PHA-4/FoxA | journal.pgen.1001060 | null | [
[
"Selector genes govern the fates of groups of cells related to each other by virtue of their cell type , position or affiliation to an organ [1] .",
"Genomic methods have revealed that selector genes directly control hundreds , even thousands , of target genes , which define the characteristics of a parti... | [
"Central regulators of cell fate , or selector genes , establish the identity of cells by direct regulation of large cohorts of genes .",
"In Caenorhabditis elegans , foregut ( or pharynx ) identity relies on the FoxA transcription factor PHA-4 , which activates different sets of target genes at various times and... | [
"Central regulators of cell fate establish the identity of cells by direct regulation of large cohorts of genes .",
"In Caenorhabditis elegans , foregut ( or pharynx ) identity relies on the FoxA transcription factor PHA-4 , which activates different target genes in different cellular environments .",
"An outst... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"humoral immunity",
"animal models of infection",
"viral vaccines",
"mechanisms of resistance and susceptibility",
"immunity",
"virology",
"innate immunity",
"immune defense",
"biology",
"microbiology",
"viral evolution",
"pathogenesis"
] | Noninfectious Retrovirus Particles Drive the Apobec3/Rfv3 Dependent Neutralizing Antibody Response | journal.ppat.1002284 | null | [
[
"Millions of years of co-evolution of retroviruses and mammalian hosts has led to the emergence of retroviral host restriction factors , some of which were discovered following major efforts to understand key steps in the HIV life cycle .",
"Most of these genes , such as TRIM5α [1] , Tetherin/Bst2 [2] and... | [
"Members of the APOBEC3 family of deoxycytidine deaminases counteract a broad range of retroviruses in vitro through an indirect mechanism that requires virion incorporation and inhibition of reverse transcription and/or hypermutation of minus strand transcripts in the next target cell .",
"The selective advantag... | [
"Members of the APOBEC3 gene family can potently inhibit a broad range of retroviruses , including HIV-1 .",
"In cell culture , APOBEC3 counteracts retroviruses by: ( 1 ) reducing the infectivity of virions; and ( 2 ) inducing lethal G-to-A hypermutation in the next target cell .",
"The selective advantage to t... | 2011 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"biotechnology",
"medicine",
"biochemistry",
"infectious diseases",
"public health and epidemiology",
"ecology",
"global health",
"genetics",
"immunology",
"biology",
"microbiology",
"molecular cell biology",
"public health",
"genetics and genomics"
] | Wolbachia Infections Are Virulent and Inhibit the Human Malaria Parasite Plasmodium Falciparum in Anopheles Gambiae | journal.ppat.1002043 | null | [
[
"Bacterial associates are ubiquitous among insects , including mosquitoes [1] .",
"Wolbachia are obligate endosymbiotic bacteria that infect numerous insects , many of which are vectors of pathogenic microorganisms .",
"Much interest has centered around Wolbachia as a means of reducing arthropod-borne... | [
"Endosymbiotic Wolbachia bacteria are potent modulators of pathogen infection and transmission in multiple naturally and artificially infected insect species , including important vectors of human pathogens .",
"Anopheles mosquitoes are naturally uninfected with Wolbachia , and stable artificial infections have n... | [
"Infection with Wolbachia bacteria has been shown to reduce pathogen levels in multiple mosquito species .",
"Anopheles mosquitoes ( the obligate vectors of human malaria ) are naturally uninfected with Wolbachia , and stable artificial infections have not yet succeeded in this genus; however somatic infections c... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"plant science",
"cell biology",
"plant development",
"plant growth and development",
"plant cell biology",
"biology and life sciences",
"molecular cell biology",
"molecular biology"
] | SEEDSTICK is a Master Regulator of Development and Metabolism in the Arabidopsis Seed Coat | journal.pgen.1004856 | null | [
[
"Seeds are essential units for plant propagation .",
"Their development is an intricate process that requires the coordinated development of the embryo , the endosperm and the seed coat .",
"The seed coat is derived from the maternal integuments and surrounds the embryo providing the latter protection... | [
"The role of secondary metabolites in the determination of cell identity has been an area of particular interest over recent years , and studies strongly indicate a connection between cell fate and the regulation of enzymes involved in secondary metabolism .",
"In Arabidopsis thaliana , the maternally derived see... | [
"Plant secondary metabolites accumulate in seeds to protect the developing embryo .",
"Using an RNA sequencing approach in conjunction with enrichment analyses we identified the homeotic MADS-domain gene SEEDSTICK ( STK ) as a regulator of metabolic processes during seed development .",
"We analyzed the role of... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"evolutionary biology",
"molecular biology",
"genetics and genomics"
] | Strong Purifying Selection in Transmission of Mammalian Mitochondrial DNA | journal.pbio.0060010 | We have used a genetic mouse model with a proofreading-deficient mitochondrial polymerase to mutagenize the mouse mitochondrial genome. The inherited mutations are subject to rapid purifying selection against amino acid substitutions. | [
[
"Mammalian mitochondrial DNA ( mtDNA ) has a high mutation rate and is inherited in a non-Mendelian manner only from the mother [1 , 2] .",
"Though there are reports of mitochondrial recombination in mammals , it is thought to be quite rare , and it is currently not known whether this phenomenon would be ... | [
"There is an intense debate concerning whether selection or demographics has been most important in shaping the sequence variation observed in modern human mitochondrial DNA ( mtDNA ) .",
"Purifying selection is thought to be important in shaping mtDNA sequence evolution , but the strength of this selection has b... | [
"Mammalian mitochondrial DNA ( mtDNA ) is maternally transmitted and does not undergo bi-parental recombination in the germ line .",
"This asexual mode of transmission , together with a high rate of mutation , should eventually lead to the accumulation of numerous deleterious mtDNA mutations and a “mutational mel... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"children",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"geographical locations",
"microbiology",
"mathematical models",
"viruses",
"preventive medicine",
"vaccines",
"age groups",
"rna viruses",
"vaccination and immunization",
"africa"... | Preventing Vaccine-Derived Poliovirus Emergence during the Polio Endgame | journal.ppat.1005728 | null | [
[
"Global and synchronous withdrawal of all live-attenuated oral poliovirus vaccines ( OPV ) is one of the major objectives of the global Polio Eradication & Endgame Strategic Plan 2013–2018 [1] and part of the global transition from OPV to inactivated poliovirus vaccine ( IPV ) .",
"Serotype 2 will be the ... | [
"Reversion and spread of vaccine-derived poliovirus ( VDPV ) to cause outbreaks of poliomyelitis is a rare outcome resulting from immunisation with the live-attenuated oral poliovirus vaccines ( OPVs ) .",
"Global withdrawal of all three OPV serotypes is therefore a key objective of the polio endgame strategic pl... | [
"Global , coordinated withdrawal of serotype-2 OPV ( OPV2 ) is planned for April 2016 and will mark a major milestone for the Global Polio Eradication Initiative ( GPEI ) .",
"Because OPV2 withdrawal will leave cohorts of young children susceptible to serotype-2 poliovirus , minimising the risk of new serotype-2 ... | 2016 |
[
"Introduction",
"Model",
"Results",
"Discussion",
"Materials and Methods"
] | [
"phosphorylation",
"egfr signaling",
"mathematical models",
"simulation and modeling",
"cellular structures and organelles",
"research and analysis methods",
"erk signaling cascade",
"proteins",
"mathematical and statistical techniques",
"ras signaling",
"cytoplasm",
"biochemistry",
"biochem... | Modeling Cellular Noise Underlying Heterogeneous Cell Responses in the Epidermal Growth Factor Signaling Pathway | journal.pcbi.1005222 | null | [
[
"Intracellular signaling pathways must respond appropriately to various signals from the external environment .",
"However , a variety of noise inside and outside of the cells can evoke heterogeneous responses in individual cells even when exposed to the same stimuli [1 , 2] .",
"Although such heterog... | [
"Cellular heterogeneity , which plays an essential role in biological phenomena , such as drug resistance and migration , is considered to arise from intrinsic ( i . e . , reaction kinetics ) and extrinsic ( i . e . , protein variability ) noise in the cell .",
"However , the mechanistic effects of these types of... | [
"Individual cell behaviors are controlled by a variety of noise , such as fluctuations in biochemical reactions , protein variability , molecular diffusion , transcriptional noise , cell-to-cell contact , temperature , and pH . Such cellular noise often interferes with signal responses from external stimuli , and s... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"systems biology",
"medicine",
"gene expression",
"genetics",
"atherosclerosis",
"biology",
"genetics and genomics",
"cardiovascular"
] | Novel Loci for Metabolic Networks and Multi-Tissue Expression Studies Reveal Genes for Atherosclerosis | journal.pgen.1002907 | null | [
[
"Five years of genome-wide association studies ( GWAS ) have successfully identified common variants at >1 , 000 genomic loci robustly associated with a wide range of human conditions and quantitative traits [1] .",
"Despite this progress , one limitation is that almost all GWAS performed to date have foc... | [
"Association testing of multiple correlated phenotypes offers better power than univariate analysis of single traits .",
"We analyzed 6 , 600 individuals from two population-based cohorts with both genome-wide SNP data and serum metabolomic profiles .",
"From the observed correlation structure of 130 metabolite... | [
"In this study , we aim to identify novel genetic variants for metabolism , characterize their effects on nearby genes , and show that the nearby genes are associated with metabolism and atherosclerosis .",
"To discover new genetic variants , we use an alternative approach to traditional genome-wide association s... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"functional genomics",
"rna interference",
"protein interactions",
"dna-binding proteins",
"dna transcription",
"gene function",
"animal models",
"mitosis",
"model organisms",
"cell division",
"proteins",
"gene expression",
"biology",
"mouse",
"molecular biology",
"biochemistry",
"ce... | A Synthetic Interaction Screen Identifies Factors Selectively Required for Proliferation and TERT Transcription in p53-Deficient Human Cancer Cells | journal.pgen.1003151 | null | [
[
"The p53 tumor suppressor ( also called TP53; NP_000537 . 3 ) plays a pivotal role in regulating multiple cellular processes including cell cycle arrest , apoptosis , cell metabolism and senescence ( reviewed in [1] ) .",
"Activated p53 can either induce cell cycle arrest and inhibit cell growth or promot... | [
"Numerous genetic and epigenetic alterations render cancer cells selectively dependent on specific genes and regulatory pathways , and represent potential vulnerabilities that can be therapeutically exploited .",
"Here we describe an RNA interference ( RNAi ) –based synthetic interaction screen to identify genes ... | [
"The conversion of a normal cell into a cancer cell involves activating genes that promote cancer growth ( oncogenes ) and/or inactivating genes that normally act to inhibit cancer growth ( tumor suppressor genes ) .",
"The tumor suppressor gene p53 is the most frequently mutated gene in human cancers , being ina... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"flow cytometry",
"medicine and health sciences",
"immune cells",
"immune physiology",
"pathology and laboratory medicine",
"cd coreceptors",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"rna viruses",
"immunoprecipitation",
"tcr signaling cascade"... | HTLV-1 bZIP Factor Enhances T-Cell Proliferation by Impeding the Suppressive Signaling of Co-inhibitory Receptors | journal.ppat.1006120 | null | [
[
"Human T-cell leukemia virus type 1 ( HTLV-1 ) belongs to the delta type retrovirus group , which also includes bovine leukemia virus and HTLV-2 .",
"HTLV-1 causes adult T-cell leukemia-lymphoma ( ATL ) and inflammatory diseases [1–4] .",
"This virus induces clonal proliferation of infected cells to e... | [
"Human T-cell leukemia virus type 1 ( HTLV-1 ) causes adult T-cell leukemia-lymphoma ( ATL ) and inflammatory diseases .",
"To enhance cell-to-cell transmission of HTLV-1 , the virus increases the number of infected cells in vivo .",
"HTLV-1 bZIP factor ( HBZ ) is constitutively expressed in HTLV-1 infected cel... | [
"Since HTLV-1 infects only through cell-to-cell transmission , increasing the number of infected cells is critical for transmission of HTLV-1 .",
"Proliferation of HTLV-1 infected cells is critical for development of leukemia and inflammatory diseases .",
"In this study , we showed that HBZ promotes the prolife... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell physiology",
"medicine and health sciences",
"myofibrils",
"muscle tissue",
"cardiovascular anatomy",
"nervous system",
"molecular probe techniques",
"junctional complexes",
"electrophysiology",
"cloning",
"neuroscience",
"animal models",
"gap junctions",
"electrocardiography",
"mo... | HSPB7 prevents cardiac conduction system defect through maintaining intercalated disc integrity | journal.pgen.1006984 | null | [
[
"HSPB7 , also known as cardiovascular heat-shock protein ( cvHsp ) , is a member of the small heat-shock protein ( sHSP or HSPB in mammals ) family that shares a conserved α-crystallin domain in the C-terminal region [1 , 2] .",
"The sHSPs characteristically function as ATP-independent molecular chaperone... | [
"HSPB7 is a member of the small heat-shock protein ( HSPB ) family and is expressed in the cardiomyocytes from cardiogenesis onwards .",
"A dramatic increase in HSPB7 is detected in the heart and blood plasma immediately after myocardial infarction .",
"Additionally , several single-nucleotide polymorphisms of ... | [
"The intercalated disc is an indispensable structure that connects neighboring cardiomyocytes .",
"It is also considered to be a single functional unit for cellular electric , mechanical , and signaling communication to maintain cardiomyocyte rigidity and synchrony .",
"Mutation or defect in intercalated disc c... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology",
"medicine",
"immune evasion",
"basic cancer research",
"virology",
"biology",
"microbiology"
] | The EBV Immunoevasins vIL-10 and BNLF2a Protect Newly Infected B Cells from Immune Recognition and Elimination | journal.ppat.1002704 | null | [
[
"Epstein-Barr virus ( EBV ) is a ubiquitous human herpes virus with strong tropism for human B cells .",
"EBV persists in an infected host for life by establishing a latent infection in B cells that represent an immunologically silent reservoir .",
"Eventual reactivation of these cells into the lytic ... | [
"Lifelong persistence of Epstein-Barr virus ( EBV ) in infected hosts is mainly owed to the virus' pronounced abilities to evade immune responses of its human host .",
"Active immune evasion mechanisms reduce the immunogenicity of infected cells and are known to be of major importance during lytic infection .",
... | [
"Despite strong cellular and humoral immune responses , herpesviruses persist in their hosts for a lifetime .",
"Epstein-Barr virus ( EBV ) is a herpesvirus that infects human B cells .",
"This results in a latent infection where only a minimal set of viral proteins is expressed and infected cells cannot be era... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"microbial mutation",
"enzyme-linked immunoassays",
"immune physiology",
"pathology and laboratory medicine",
"nervous system",
"pathogens",
"immunology",
"microbiology",
"viruses",
"mutation",
"substitution mutation",
"rna viruses",
"antibodies",
"immunol... | Shortening of Zika virus CD-loop reduces neurovirulence while preserving antigenicity | journal.pntd.0007212 | null | [
[
"Zika virus ( ZIKV ) is a positive-sense single-stranded RNA flavivirus .",
"Though first isolated in 1947 and after years of relatively benign infections throughout Southeast Asia , ZIKV was identified in large human disease outbreaks in Yap Island , French Polynesia , and then the Americas [1–5] .",
... | [
"Zika virus ( ZIKV ) is a mosquito-borne positive sense RNA virus .",
"Recently , ZIKV emerged into the Western hemisphere as a human health threat , with severe disease associated with developmental and neurological complications .",
"The structural envelope protein of ZIKV and other neurotropic flaviviruses c... | [
"Zika virus ( ZIKV ) is a mosquito-transmitted virus that was recently introduced in Brazil and subsequently spread throughout the Americas .",
"ZIKV is highly similar to the related dengue virus but causes unique disease outcomes including neurological disease in adults and fetal developmental complications .",
... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immune response",
"biology and life sciences",
"immunology"
] | The CD14+CD16+ Inflammatory Monocyte Subset Displays Increased Mitochondrial Activity and Effector Function During Acute Plasmodium vivax Malaria | journal.ppat.1004393 | null | [
[
"Plasmodium vivax is the most widely distributed malaria parasite and responsible for approximately 70–80 million cases , annually .",
"In addition , P . vivax is responsible for the majority of malaria cases and represents a significant impediment to social and economic development in Latin America and A... | [
"Infection with Plasmodium vivax results in strong activation of monocytes , which are important components of both the systemic inflammatory response and parasite control .",
"The overall goal of this study was to define the role of monocytes during P . vivax malaria .",
"Here , we demonstrate that P . vivax–i... | [
"Malaria , caused by a protozoa parasite , Plasmodium , affects more than 200 million people per year .",
"The infection triggers an acute febrile illness , the paroxysms , occurring every 48 or 72 hours depending on the species .",
"Plasmodium vivax , in most cases , does not cause severe malaria , but it is t... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"medicine and health sciences",
"ecuador",
"tropical diseases",
"geographical locations",
"sand flies",
"parasitic diseases",
"parasitic protozoans",
"protozoans",
"leishmania",
"phylogenetic analysis",
"neglected tropical diseases",
"molecular biology techniques",
... | First Human Cases of Leishmania (Viannia) lainsoni Infection and a Search for the Vector Sand Flies in Ecuador | journal.pntd.0004728 | null | [
[
"Leishmaniases are caused by infection with protozoan parasites of the genus Leishmania transmitted by bites of female sand flies [1 , 2] .",
"The genus Leishmania is further divided into two subgenera , Leishmania ( Leishmania ) and Leishmania ( Viannia ) , originally distinguished by their development i... | [
"An epidemiological study of leishmaniasis was performed in Amazonian areas of Ecuador since little information on the prevalent Leishmania and sand fly species responsible for the transmission is available .",
"Of 33 clinical specimens from patients with cutaneous leishmaniasis ( CL ) , causative parasites were ... | [
"In Ecuador , leishmaniasis is endemic in Pacific coast subtropical , Amazonian , and Andean highland areas .",
"Seven Leishmania species , Leishmania ( Leishmania ) mexicana , L . ( L . ) amazonensis , L . ( L . ) major-like , Leishmania ( Viannia ) guyanensis , L . ( V . ) panamensis , L . ( V . ) braziliensis ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"microbiology",
"homo (human)",
"eubacteria"
] | Yersinia Controls Type III Effector Delivery into Host Cells by Modulating Rho Activity | journal.ppat.0040003 | null | [
[
"A great spectrum of Gram-negative bacteria depends on a specialized secretion mechanism to establish a successful infection in the host .",
"This machinery is known as the type III secretion system ( TTSS ) , and is present in organisms that are pathogenic for animals or plants , as well as in symbiotic ... | [
"Yersinia pseudotuberculosis binds to β1 integrin receptors , and uses the type III secretion proteins YopB and YopD to introduce pores and to translocate Yop effectors directly into host cells .",
"Y . pseudotuberculosis lacking effectors that inhibit Rho GTPases , YopE and YopT , have high pore forming activity... | [
"The type III secretion system ( TTSS ) is essential for the virulence of a number of Gram-negative human pathogens of enormous clinical significance .",
"The molecular mechanisms by which TTSS effector proteins are translocated into the host cell are not well understood .",
"The work presented here proposes a ... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"dimers (chemical physics)",
"chemical bonding",
"crystal structure",
"electricity",
"condensed matter physics",
"fungal structure",
"electrostatics",
"crystallography",
"thermodynamics",
"hydrogen bonding",
"physical chemistry",
"mycology",
"solid state physics",
"chemistry",
"biophysic... | Induced Fit in Protein Multimerization: The HFBI Case | journal.pcbi.1005202 | null | [
[
"Hydrophobins are small ( 7–15 kDa ) proteins produced by filamentous fungi .",
"They are globular and rigid proteins containing four disulfide bridges which stabilize the structure .",
"Hydrophobins perform a variety of biological roles at interfaces that help fungi to adapt to their environment incl... | [
"Hydrophobins , produced by filamentous fungi , are small amphipathic proteins whose biological functions rely on their unique surface-activity properties .",
"Understanding the mechanistic details of the multimerization process is of primary importance to clarify the interfacial activity of hydrophobins .",
"W... | [
"Fungi proliferate by creating a complex hyphal network growing within a wet environment .",
"However , for most fungi to colonize new territories , they must produce spores carried by aerial hyphae and spread them into the air .",
"Aerial structures need to overcome the surface tension of the surrounding water... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry/cell signaling and trafficking structures",
"cell biology/cell signaling"
] | Using Structural Information to Change the Phosphotransfer Specificity of a Two-Component Chemotaxis Signalling Complex | journal.pbio.1000306 | Analysis of the crystal structure of a phosphotransfer complex from the Rhodobacter sphaeroides chemotaxis pathway allowed reengineering of molecular recognition in a two-component signalling system. | [
[
"Bacteria , Archaea , and some eukaryotes use two-component signalling pathways to detect environmental conditions and bring about appropriate changes in cellular behaviour [1] , [2] .",
"Two-component pathways comprise sensor histidine kinases ( HPK ) and response regulators ( RRs ) .",
"Environmenta... | [
"Two-component signal transduction pathways comprising histidine protein kinases ( HPKs ) and their response regulators ( RRs ) are widely used to control bacterial responses to environmental challenges .",
"Some bacteria have over 150 different two-component pathways , and the specificity of the phosphotransfer ... | [
"The ability to respond to environmental stimuli is a universal feature of living cells .",
"Evolution has created a vast array of signalling mechanisms that enable cells to react in many ways to extracellular changes .",
"In bacteria , two-component signalling mechanisms , comprising a sensor protein kinase pa... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"innate immune system",
"medicine and health sciences",
"immune physiology",
"cytokines",
"pathology and laboratory medicine",
"hela cells",
"gene regulation",
"pathogens",
"biological cultures",
"immunology",
"microbiology",
"shigella",
"bacterial diseases",
"developmental biology",
"si... | ALPK1 controls TIFA/TRAF6-dependent innate immunity against heptose-1,7-bisphosphate of gram-negative bacteria | journal.ppat.1006224 | null | [
[
"Intestinal epithelial cells ( IECs ) are not considered to be professional immune cells .",
"However , they play an important role in immuno-surveillance and contribute to the initial phase of inflammation after infection by invasive bacteria or viruses .",
"They can sense the presence of pathogens a... | [
"During infection by invasive bacteria , epithelial cells contribute to innate immunity via the local secretion of inflammatory cytokines .",
"These are directly produced by infected cells or by uninfected bystanders via connexin-dependent cell-cell communication .",
"However , the cellular pathways underlying ... | [
"Epithelial cells line internal body cavities of multicellular organisms .",
"They represent the first line of defense against various pathogens including bacteria and viruses .",
"They can sense the presence of invasive pathogens and initiate the recruitment of immune cells to infected tissues via the local se... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"medicine",
"epidemiology",
"genetics",
"biology",
"human genetics",
"genetics of disease",
"pulmonology",
"genetic epidemiology"
] | Causal and Synthetic Associations of Variants in the SERPINA Gene Cluster with Alpha1-antitrypsin Serum Levels | journal.pgen.1003585 | null | [
[
"Alpha1-antitrypsin ( AAT ) is a serum marker for inflammation produced in the liver .",
"Its main function is to inhibit neutrophil elastase and consequently protect pulmonary tissue .",
"The SERPINA1 gene encoding the AAT protein is known to be polymorphic in the general population .",
"The best... | [
"Several infrequent genetic polymorphisms in the SERPINA1 gene are known to substantially reduce concentration of alpha1-antitrypsin ( AAT ) in the blood .",
"Since low AAT serum levels fail to protect pulmonary tissue from enzymatic degradation , these polymorphisms also increase the risk for early onset chronic... | [
"Low levels of alpha1-antitrypsin ( AAT ) in the blood are a well-established risk factor for accelerated loss in lung function and chronic obstructive pulmonary disease .",
"While a few infrequent genetic polymorphisms are known to influence the serum levels of this enzyme , the role of common genetic variants h... | 2013 |
[
"Introduction",
"Methods",
"Results and Discussion"
] | [
"parastic protozoans",
"leishmania",
"parasitology",
"protozoology",
"biology",
"microbiology",
"host-pathogen interaction",
"microbial growth and development"
] | Leishmania Metacyclogenesis Is Promoted in the Absence of Purines | journal.pntd.0001833 | null | [
[
"Protozoan parasites from Leishmania genus are the causative agents of leishmaniasis , a broad spectrum disease that range from asymptomatic infections to disfiguring forms such as diffuse or mucosal leishmaniasis as well as visceral leishmaniasis , which can be fatal if not adequately treated .",
"The ou... | [
"Leishmania parasites , the causative agent of leishmaniasis , are transmitted through the bite of an infected sand fly .",
"Leishmania parasites present two basic forms known as promastigote and amastigote which , respectively , parasitizes the vector and the mammalian hosts .",
"Infection of the vertebrate ho... | [
"Leishmania parasites are the causative agent of a spectrum of diseases characterized by severe lesions in skin or life threatening visceral infections .",
"In the parasite life cycle , a range of morphological transitions can be found such as amastigotes ( hosted in humans and others mammals ) and promastigotes ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"cell biology",
"molecular biology",
"hematology"
] | Coordinate Gene Regulation during Hematopoiesis Is Related to Genomic Organization | journal.pbio.0050309 | Coordinate gene regulation is required for cellular differentiation. Is the genome nonrandomly organized to accomplish this? | [
[
"The nucleus appears to be organized according to the many functions it performs [1 , 2] .",
"The nucleolus , for example , is a subcompartment that exists as a result of its activities: rDNA transcription and ribosomal biogenesis [1] .",
"Gene loci reflect this functional organization in that their s... | [
"Gene loci are found in nuclear subcompartments that are related to their expression status .",
"For instance , silent genes are often localized to heterochromatin and the nuclear periphery , whereas active genes tend to be found in the nuclear center .",
"Evidence also suggests that chromosomes may be specific... | [
"How are genomes—and the chromosomes that comprise them—organized in the eukaryotic nucleus ?",
"This long-standing question in cell biology has gained renewed interest due to observations that gene regulation is correlated with the nonrandom distribution of gene loci linearly along chromosomes and spatially with... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"gram negative",
"immune cells",
"nk cells",
"immunity",
"immune activation",
"innate immunity",
"immunology",
"biology",
"microbiology",
"host-pathogen interaction",
"bacterial pathogens",
"gram positive"
] | A LysM and SH3-Domain Containing Region of the Listeria monocytogenes p60 Protein Stimulates Accessory Cells to Promote Activation of Host NK Cells | journal.ppat.1002368 | null | [
[
"NK cells are lymphocytes that help control infections and tumors and regulate autoimmune responses through both cytotoxic and cytokine-secreting effector functions .",
"Through the use of Fas , TRAIL , and secretion of perforin and granzyme B , NK cells induce apoptosis or lysis of distressed somatic cel... | [
"Listeria monocytogenes ( Lm ) infection induces rapid and robust activation of host natural killer ( NK ) cells .",
"Here we define a region of the abundantly secreted Lm endopeptidase , p60 , that potently but indirectly stimulates NK cell activation in vitro and in vivo .",
"Lm expression of p60 resulted in ... | [
"Pathogens have evolved diverse strategies to influence host immune responses .",
"By studying these strategies , we may learn how to therapeutically intervene to manipulate immune responses during infectious and other diseases .",
"In this study , we investigated how the bacterial pathogen Listeria monocytogen... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Sigma Factor SigB Is Crucial to Mediate Staphylococcus aureus Adaptation during Chronic Infections | journal.ppat.1004870 | null | [
[
"S . aureus is a major human pathogen that can infect almost every organ in the body and cause destructive infections [1] .",
"Besides tissue damage the ability to develop persisting and therapy-refractory infections poses a major problem in clinical practice , such as endovascular and bone infections [2 ... | [
"Staphylococcus aureus is a major human pathogen that causes a range of infections from acute invasive to chronic and difficult-to-treat .",
"Infection strategies associated with persisting S . aureus infections are bacterial host cell invasion and the bacterial ability to dynamically change phenotypes from the a... | [
"Staphylococcus aureus is a frequent pathogen of severe invasive infections that can develop into chronicity and become extremely difficult to eradicate .",
"Chronic infections have been highly associated with altered bacterial phenotypes , i . e . , the small colony variants ( SCVs ) that dynamically appear afte... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"genetics and genomics/genomics",
"genetics and genomics/bioinformatics"
] | A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies | journal.pgen.1000529 | null | [
[
"Genome-wide association studies have identified many putative disease susceptibility loci in recent years [1]–[3] .",
"This approach to studying disease has succeeded largely because of improved catalogues of human genetic variation [4] and advances in genotyping technology , but it has also been bolster... | [
"Genotype imputation methods are now being widely used in the analysis of genome-wide association studies .",
"Most imputation analyses to date have used the HapMap as a reference dataset , but new reference panels ( such as controls genotyped on multiple SNP chips and densely typed samples from the 1 , 000 Genom... | [
"Large association studies have proven to be effective tools for identifying parts of the genome that influence disease risk and other heritable traits .",
"So-called “genotype imputation” methods form a cornerstone of modern association studies: by extrapolating genetic correlations from a densely characterized ... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/bacterial infections",
"infectious diseases/neglected tropical diseases",
"infectious diseases/tropical and travel-associated diseases",
"infectious diseases/protozoal infections"
] | The Interplay between Entamoeba and Enteropathogenic Bacteria Modulates Epithelial Cell Damage | journal.pntd.0000266 | null | [
[
"Once trophozoites of Entamoeba histolytica reach the host intestine , they can damage the mucosa epithelial layer and spread through the submucosa and the lamina propia and other tissues .",
"Neutrophils and other cells infiltrate the tissue in the vicinity of amoebic lesions increasing the inflammatory ... | [
"Mixed intestinal infections with Entamoeba histolytica , Entamoeba dispar and bacteria with exacerbated manifestations of disease are common in regions where amoebiasis is endemic .",
"However , amoeba–bacteria interactions remain largely unexamined .",
"Trophozoites of E . histolytica and E . dispar were co-c... | [
"In amoebiasis , a human disease that is a serious health problem in many developing countries , efforts have been made to identify responsible factors for the tissue damage inflicted by the parasite Entamoeba histolytica .",
"This amoeba lives in the lumen of the colon without causing damage to the intestinal mu... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Updated Global Burden of Cholera in Endemic Countries | journal.pntd.0003832 | null | [
[
"Since the early 1800s , pandemics of cholera have affected millions , with the seventh still ongoing since 1961 [1] .",
"Access to safe water and improved sanitation facilities has eliminated cholera transmission of Vibrio cholerae , the causative agent , in high-income countries .",
"However , the b... | [
"The global burden of cholera is largely unknown because the majority of cases are not reported .",
"The low reporting can be attributed to limited capacity of epidemiological surveillance and laboratories , as well as social , political , and economic disincentives for reporting .",
"We previously estimated 2 ... | [
"The global burden of cholera is largely unknown because the majority of cases are not reported .",
"The low reporting can be attributed to limited capacity of epidemiological surveillance and laboratories , as well as social , political , and economic disincentives for reporting .",
"We previously estimated 2 ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology",
"computational biology"
] | Restricted N-glycan Conformational Space in the PDB and Its Implication in Glycan Structure Modeling | journal.pcbi.1002946 | null | [
[
"Glycosylation represents one of the most important post-translational modifications [1] , [2] and is ubiquitous in all domains of life .",
"The glycosylation machinery is largely conserved in eukaryotes , and more than 50% of all eukaryotic proteins are expected to be glycosylated [3] , [4] .",
"An o... | [
"Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions .",
"Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity , computational modeling could ... | [
"An N-glycan is a carbohydrate chain covalently linked to the side chain of asparagine .",
"Due to the flexibility of carbohydrate chains , it is believed that the N-glycan chains would not have a well-defined structure .",
"However , our survey of N-glycan structures in the PDB shows that the N-glycan structur... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biochemistry",
"infectious diseases",
"bacterial diseases",
"immunity",
"enzymes",
"biology",
"microbiology",
"bacterial pathogens"
] | Group A Streptococcus Secreted Esterase Hydrolyzes Platelet-Activating Factor to Impede Neutrophil Recruitment and Facilitate Innate Immune Evasion | journal.ppat.1002624 | null | [
[
"Neutrophils are one of the first responders of innate inflammatory cells to migrate towards the site of infecting agents .",
"Evasion of the neutrophil microbicidal response is critical for survival , dissemination , and infectability of bacterial pathogens .",
"Bacterial pathogens evade the neutroph... | [
"The innate immune system is the first line of host defense against invading organisms .",
"Thus , pathogens have developed virulence mechanisms to evade the innate immune system .",
"Here , we report a novel means for inhibition of neutrophil recruitment by Group A Streptococcus ( GAS ) .",
"Deletion of the ... | [
"GAS is a major human pathogen causing a variety of infections , including pharyngitis and necrotizing fasciitis .",
"GAS pathogenesis is mediated by a large array of secreted and cell-surface virulence factors .",
"However , the functions of many GAS virulence factors are poorly understood .",
"Recently , we... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results/Discussion"
] | [
"next-generation sequencing",
"genome expression analysis",
"infectious diseases",
"helminth infections",
"medicine and health sciences",
"genomics",
"foodborne trematodiases",
"diagnostic medicine",
"paragonimiasis",
"genome analysis",
"serodiagnosis",
"transcriptome analysis",
"genetics",
... | Systems Biology Studies of Adult Paragonimus Lung Flukes Facilitate the Identification of Immunodominant Parasite Antigens | journal.pntd.0003242 | null | [
[
"Paragonimiasis is an important food-borne trematode infection ( and a “neglected tropical disease” ) that is caused by lung flukes in the genus Paragonimus [1]–[3] .",
"More than 50 Paragonimus species have been described , and nine species are known to infect humans .",
"Human infections are most fr... | [
"Paragonimiasis is a food-borne trematode infection acquired by eating raw or undercooked crustaceans .",
"It is a major public health problem in the far East , but it also occurs in South Asia , Africa , and in the Americas .",
"Paragonimus worms cause chronic lung disease with cough , fever and hemoptysis tha... | [
"Paragonimiasis is a food-borne trematode infection that people acquire when they eat raw or undercooked crustaceans .",
"Disease symptoms ( including cough , fever , blood in sputum , etc . ) can be similar to those observed in patients with tuberculosis or bacterial pneumonia , frequently resulting in misdiagno... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal models",
"biochemistry",
"developmental biology",
"caenorhabditis elegans",
"model organisms",
"organism development",
"protein interactions",
"genetics",
"epigenetics",
"biology",
"proteomics",
"genetics and genomics",
"histone modification"
] | The C. elegans H3K27 Demethylase UTX-1 Is Essential for Normal Development, Independent of Its Enzymatic Activity | journal.pgen.1002647 | null | [
[
"The proper development of multicellular organisms requires strict regulation of cell-specific gene expression to ensure appropriate cell fate specification , cellular differentiation , and organogenesis .",
"In addition to transcription factors , gene expression is controlled by chromatin organization , ... | [
"Epigenetic modifications influence gene expression and provide a unique mechanism for fine-tuning cellular differentiation and development in multicellular organisms .",
"Here we report on the biological functions of UTX-1 , the Caenorhabditis elegans homologue of mammalian UTX , a histone demethylase specific f... | [
"Chromatin organization influences gene expression , and its regulation is crucial to achieve correct cellular differentiation and development in multicellular organisms .",
"Histone demethylases are among several factors responsible for regulating chromatin dynamics .",
"Here we report on the biological functi... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell division",
"gene regulation",
"genetics",
"gene expression",
"molecular genetics",
"biology",
"cyclins",
"molecular cell biology",
"chromatin",
"dna transcription",
"gene function"
] | Bck2 Acts through the MADS Box Protein Mcm1 to Activate Cell-Cycle-Regulated Genes in Budding Yeast | journal.pgen.1003507 | null | [
[
"The temporal control of transcription is likely a universal feature of cell cycles , with clear transcriptional programs in yeast , bacteria and metazoans [1]–[4] .",
"Bursts of gene expression in eukaryotes tend to be associated with major cell cycle transitions that are governed by cyclin-dependent kin... | [
"The Bck2 protein is a potent genetic regulator of cell-cycle-dependent gene expression in budding yeast .",
"To date , most experiments have focused on assessing a potential role for Bck2 in activation of the G1/S-specific transcription factors SBF ( Swi4 , Swi6 ) and MBF ( Mbp1 , Swi6 ) , yet the mechanism of g... | [
"Cell-cycle-dependent gene expression is a universal feature of cell cycles , with clear transcriptional programs in yeast , bacteria , and metazoans .",
"At the M/G1 transition , many of the up-regulated genes encode key regulators of DNA replication ( CDC6 ) and cyclins that initiate the events of cell cycle co... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Integrated Enrichment Analysis of Variants and Pathways in Genome-Wide Association Studies Indicates Central Role for IL-2 Signaling Genes in Type 1 Diabetes, and Cytokine Signaling Genes in Crohn's Disease | journal.pgen.1003770 | null | [
[
"Our approach builds on previous work that casts simultaneous analysis of genetic variants as a variable selection problem—the problem of deciding which variables ( the genetic variants ) to include in a multivariate regression of the phenotype .",
"We begin with a method that assumes each variant is equa... | [
"Pathway analyses of genome-wide association studies aggregate information over sets of related genes , such as genes in common pathways , to identify gene sets that are enriched for variants associated with disease .",
"We develop a model-based approach to pathway analysis , and apply this approach to data from ... | [
"Genome-wide association studies have helped locate gene variants that affect our susceptibility to diseases .",
"The analysis of these studies is typically straightforward: test each genetic variant whether it is correlated with predisposition to disease .",
"This approach often works well for identifying comm... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant anatomy",
"plant growth and development",
"enzymes",
"lateral roots",
"enzymology",
"phosphatases",
"developmental biology",
"guanine nucleotide exchange factors",
"plant science",
"seedlings",
"plants",
"cellular structures and organelles",
"proteins",
"subcellular localization",
... | Release of GTP Exchange Factor Mediated Down-Regulation of Abscisic Acid Signal Transduction through ABA-Induced Rapid Degradation of RopGEFs | journal.pbio.1002461 | The hormone abscisic acid causes rapid re-localization and degradation of a guanine nucleotide exchange-factor, RopGEF1, suggesting a control-loop model that inhibits “leaky” signaling and facilitates the abscisic acid response. | [
[
"Abscisic acid ( ABA ) is a phytohormone that protects plants against abiotic stress and is involved in seedling development .",
"In response to abiotic stress conditions , ABA concentrations rise in plant cells [1–3] .",
"ABA can be perceived by a group of soluble “PYL/RCAR” ABA receptor proteins , w... | [
"The phytohormone abscisic acid ( ABA ) is critical to plant development and stress responses .",
"Abiotic stress triggers an ABA signal transduction cascade , which is comprised of the core components PYL/RCAR ABA receptors , PP2C-type protein phosphatases , and protein kinases .",
"Small GTPases of the ROP/RA... | [
"The plant hormone abscisic acid ( ABA ) is critical to plant development and stress responses .",
"The ABA signaling cascade is comprised of ABA receptors , negatively regulating PP2C protein phosphatases and transducing protein kinases .",
"Biochemical assays have indicated that certain ABA receptors constitu... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"renal transplantation",
"virology",
"biology",
"microbiology",
"nephrology"
] | Neutralization Serotyping of BK Polyomavirus Infection in Kidney Transplant Recipients | journal.ppat.1002650 | null | [
[
"The process of kidney transplantation has been revolutionized since the first successful case in identical twins more than 5 decades ago [1] , [2] .",
"Since then , the use of immunosuppressants such as cyclosporine has made renal allografts a viable clinical option [3] , but the process still has many c... | [
"BK polyomavirus ( BKV or BKPyV ) associated nephropathy affects up to 10% of kidney transplant recipients ( KTRs ) .",
"BKV isolates are categorized into four genotypes .",
"It is currently unclear whether the four genotypes are also serotypes .",
"To address this issue , we developed high-throughput serolog... | [
"Serological studies have shown that nearly all humans are chronically infected with BK polyomavirus ( BKV ) .",
"The infection isn't usually associated with noticeable symptoms .",
"However , opportunistic replication of BKV in therapeutically immunosuppressed kidney transplant recipients ( KTRs ) can lead to ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"microbiology",
"host-pathogen interaction",
"escherichia coli",
"animal models",
"model organisms",
"bacterial pathogens",
"biology",
"zebrafish",
"bacterial biofilms",
"gram negative",
"immunity",
"innate immunity",
"microbial control"
] | A New Zebrafish Model of Oro-Intestinal Pathogen Colonization Reveals a Key Role for Adhesion in Protection by Probiotic Bacteria | journal.ppat.1002815 | null | [
[
"Non-pathogenic bacteria associated with animal mucosa contribute to host health and homeostasis by promoting key physiological functions and by providing protection against pathogen infections [1] , [2] , [3] , [4] .",
"This protection , induced upon stimulation of the host immune defenses or by direct b... | [
"The beneficial contribution of commensal bacteria to host health and homeostasis led to the concept that exogenous non-pathogenic bacteria called probiotics could be used to limit disease caused by pathogens .",
"However , despite recent progress using gnotobiotic mammal and invertebrate models , mechanisms unde... | [
"The beneficial contribution of commensal bacteria to host health led to the concept that exogenous and non-pathogenic bacteria ( probiotics ) could be used to prevent infectious disease .",
"However , the absence of relevant experimentally tractable in vivo models severely limits our understanding of the molecul... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methodology"
] | [
"cell motility",
"medicine and health sciences",
"actin filaments",
"myofibrils",
"muscle tissue",
"simulation and modeling",
"molecular motors",
"actin motors",
"myofilaments",
"motor proteins",
"research and analysis methods",
"contractile proteins",
"animal cells",
"proteins",
"biolog... | A stochastic simulation of skeletal muscle calcium transients in a structurally realistic sarcomere model using MCell | journal.pcbi.1006712 | null | [
[
"The rise and fall of free [Ca2+] within individual muscle cells , or the calcium transient , is measured experimentally using a Ca2+ sensitive fluorescent indicator such as furaptra or mag-fluo-4 [1] .",
"The measured fluorescence is then used to estimate changes in [Ca2+] using a spatial averaging techn... | [
"Skeletal muscle contraction is initiated when an action potential triggers the release of Ca2+ into the sarcomere in a process referred to as excitation-contraction coupling .",
"The speed and scale of this process makes direct observation very challenging and invasive .",
"To determine how the concentration o... | [
"In this study we develop a structural stochastic diffusion model , to study how calcium ions diffuse and interact within a skeletal muscle sarcomere following a simulated muscle activation .",
"This type of model allows us to explore how structural elements , namely the actin and myosin filaments , within the sa... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dengue virus",
"medicine and health sciences",
"immune physiology",
"microcephaly",
"pathology and laboratory medicine",
"enzyme-linked immunoassays",
"pathogens",
"immunology",
"microbiology",
"viruses",
"research design",
"developmental biology",
"rna viruses",
"antibodies",
"immunolo... | Perinatal analyses of Zika- and dengue virus-specific neutralizing antibodies: A microcephaly case-control study in an area of high dengue endemicity in Brazil | journal.pntd.0007246 | null | [
[
"Zika virus ( ZIKV ) is an arthropod-borne flavivirus closely related to several human pathogens of public health significance , including dengue viruses ( DENV1-4 ) , yellow fever virus ( YFV ) , Japanese encephalitis virus ( JEV ) and West Nile virus ( WNV ) [1 , 2] .",
"The emergence of ZIKV in the Pac... | [
"Laboratory confirmation of Zika virus ( ZIKV ) infection during pregnancy is challenging due to cross-reactivity with dengue virus ( DENV ) and limited knowledge about the kinetics of anti-Zika antibody responses during pregnancy .",
"We described ZIKV and DENV serological markers and the maternal-fetal transfer... | [
"The epicenter of the ZIKV epidemic was located in Northeast Brazil ( 2015/16 ) and was followed by a space and time cluster of congenital microcephaly cases .",
"This region is also a dengue hyperendemic setting .",
"Laboratory confirmation of ZIKV infection during pregnancy is challenging due to cross-reactiv... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular cell biology",
"genetics",
"developmental biology",
"biology"
] | Notch Controls Cell Adhesion in the Drosophila Eye | journal.pgen.1004087 | null | [
[
"Pattern formation in developing tissues requires cell signaling .",
"A small number of signaling pathways are repeatedly utilized for cell fate decisions in developing tissues ( reviewed in [1] ) .",
"In addition , cell signaling is also known to play a role in controlling cell sorting .",
"For e... | [
"Sporadic evidence suggests Notch is involved in cell adhesion .",
"However , the underlying mechanism is unknown .",
"Here I have investigated an epithelial remodeling process in the Drosophila eye in which two primary pigment cells ( PPCs ) with a characteristic ‘kidney’ shape enwrap and eventually isolate a ... | [
"In developing tissues , one way to isolate a group of cells from the rest of the tissue is to induce a few neighboring cells to surround them .",
"How centrally localized cells communicate with neighboring cells and how neighboring cells respond to signaling is not well understood .",
"This work describes a me... | 2014 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"gut bacteria",
"medical personnel",
"sociology",
"social sciences",
"health care",
"simulation and modeling",
"health care providers",
"systems science",
"mathematics",
"network analysis",
"social networks",
"nosocomial infections",
"bacteria",
"allied he... | Fast and near-optimal monitoring for healthcare acquired infection outbreaks | journal.pcbi.1007284 | null | [
[
"Since the time of Hippocrates , the “father of western medicine” , a central tenet of medical care has been to “do no harm . ”",
"Unfortunately , the scourge of healthcare acquired infections ( HAI ) challenges the medical system to honor this tenet .",
"When patients are hospitalized they are seekin... | [
"According to the Centers for Disease Control and Prevention ( CDC ) , one in twenty five hospital patients are infected with at least one healthcare acquired infection ( HAI ) on any given day .",
"Early detection of possible HAI outbreaks help practitioners implement countermeasures before the infection spreads... | [
"Healthcare acquired infections ( HAIs ) lead to significant losses of lives and result in heavy economic burden on healthcare providers worldwide .",
"Timely detection of HAI outbreaks will have a significant impact on the health infrastructure .",
"Here , we propose an efficient and effective approach to dete... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"public health and epidemiology/epidemiology",
"public health and epidemiology/social and behavioral determinants of health",
"public health and epidemiology/infectious diseases",
"public health and epidemiology/environmental health"
] | Contrasting Spatial Distribution and Risk Factors for Past Infection with Scrub Typhus and Murine Typhus in Vientiane City, Lao PDR | journal.pntd.0000909 | null | [
[
"Scrub typhus and murine typhus are important but under-recognized treatable causes of fever , morbidity and mortality in South-East Asia [1] , [2] , [3] , [4] .",
"There has been a recent resurgence of interest in these diseases , which both cause undifferentiated fever , headache and myalgia progressing... | [
"The aetiological diagnostic of fevers in Laos remains difficult due to limited laboratory diagnostic facilities .",
"However , it has recently become apparent that both scrub and murine typhus are common causes of previous undiagnosed fever .",
"Epidemiological data suggests that scrub typhus would be more com... | [
"Scrub typhus and murine typhus are neglected but important treatable causes of fever , morbidity and mortality in South-East Asia .",
"Epidemiological data suggests that scrub typhus would be more common in rural areas and murine typhus in urban areas but there are very few comparative data from places where bot... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"immunology/cellular microbiology and pathogenesis",
"infectious diseases/protozoal infections"
] | Increased Asymmetric Dimethylarginine in Severe Falciparum Malaria: Association with Impaired Nitric Oxide Bioavailability and Fatal Outcome | journal.ppat.1000868 | null | [
[
"Plasmodium falciparum causes ∼1 million deaths annually [1] , [2] .",
"Despite rapid parasite clearance with the anti-parasitic drug artesunate , the mortality rate in severe malaria remains high [3] , [4] .",
"Endothelial activation , parasite sequestration , impaired microvascular perfusion and dys... | [
"Asymmetrical dimethylarginine ( ADMA ) , an endogenous inhibitor of nitric oxide synthase ( NOS ) , is a predictor of mortality in critical illness .",
"Severe malaria ( SM ) is associated with decreased NO bioavailability , but the contribution of ADMA to the pathogenesis of impaired NO bioavailability and adve... | [
"Severe falciparum malaria is associated with impaired microvascular perfusion , lung injury and decreased bioavailability of nitric oxide ( NO ) , but the causes of these processes are not fully understood .",
"Asymmetrical dimethylarginine ( ADMA ) , a competitive endogenous inhibitor of nitric oxide synthase (... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"vero cells",
"medicine and health sciences",
"vesicles",
"pathology and laboratory medicine",
"pathogens",
"biological cultures",
"microbiology",
"membrane fusion",
"cellular structures and organelles",
"bacterial pathogens",
"endosomes",
"research and analysis methods",
"coxiella burnetii"... | Actin polymerization in the endosomal pathway, but not on the Coxiella-containing vacuole, is essential for pathogen growth | journal.ppat.1007005 | null | [
[
"Coxiella burnetii is an intracellular Gram-negative bacterium that causes a severe flu-like disease called Q fever .",
"Q fever is a zoonosis , and transmission to humans typically occurs by inhalation of contaminated aerosols generated by infected ruminant livestock [1] .",
"Following deposition in ... | [
"Coxiella burnetii is an intracellular bacterium that replicates within an expansive phagolysosome-like vacuole .",
"Fusion between the Coxiella-containing vacuole ( CCV ) and late endosomes/multivesicular bodies requires Rab7 , the HOPS tethering complex , and SNARE proteins , with actin also speculated to play ... | [
"Coxiella burnetii , the human Q fever bacterium , replicates in a harsh , lysosome-like compartment termed the Coxiella-containing vacuole ( CCV ) .",
"Here , the pathogen directs formation of the CCV through the activities of secreted type 4B ( T4B ) effector proteins .",
"Questions remain concerning how the ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"mechanisms of signal transduction",
"endothelial cells",
"microbiology",
"host-pathogen interaction",
"cancers and neoplasms",
"feeback regulation",
"dna transcription",
"oncology",
"bone and soft tissue sarcomas",
"gene expression",
"biology",
"kaposi sarcoma",
"molecular bio... | Opposing Regulation of PROX1 by Interleukin-3 Receptor and NOTCH Directs Differential Host Cell Fate Reprogramming by Kaposi Sarcoma Herpes Virus | journal.ppat.1002770 | null | [
[
"Kaposi sarcoma ( KS ) was originally described by a Hungarian doctor Morris Kaposi in 1872 , but did not attract much scientific , clinical and public attention until 1980s when acquired immunodeficiency syndrome ( AIDS ) became an epidemic and KS was subsequently found to be the most common cancer among HIV... | [
"Lymphatic endothelial cells ( LECs ) are differentiated from blood vascular endothelial cells ( BECs ) during embryogenesis and this physiological cell fate specification is controlled by PROX1 , the master regulator for lymphatic development .",
"When Kaposi sarcoma herpes virus ( KSHV ) infects host cells , it... | [
"Kaposi's sarcoma ( KS ) is one of the most common neoplasms in HIV-positive individuals and organ transplant recipients .",
"KS-associated herpes virus ( KSHV ) , also known as human herpes virus ( HHV ) -8 , has been identified as the causative agent and infects endothelial cells to form KS .",
"Importantly ,... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"fish",
"vertebrates",
"animals",
"animal models",
"osteichthyes",
"mutation",
"developmental biology",
"model organisms",
"nonsense mutation",
"experimental organism systems",
"sequence motif analysis",
"molecular biology techniques",
"research and analysis methods",
"sequence analysis",
... | mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay | journal.pgen.1007105 | null | [
[
"The recent increased use of reverse genetic approaches has been largely driven by the ease , affordability of construction , and implementation of the CRISPR/Cas9 and TALEN systems .",
"Recent communications recount numerous cases of generated mutations in genes of interest lacking an expected effect on ... | [
"As model organism-based research shifts from forward to reverse genetics approaches , largely due to the ease of genome editing technology , a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein .",
"In zebrafish , this lo... | [
"The recent rise of reverse genetic , gene targeting methods has allowed researchers to readily generate mutations in any gene of interest with relative ease .",
"Should these mutations have the predicted effect on the mRNA and encoded protein , we would expect many more abnormal phenotypes than are typically bei... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Single Strand Annealing Plays a Major Role in RecA-Independent Recombination between Repeated Sequences in the Radioresistant Deinococcus radiodurans Bacterium | journal.pgen.1005636 | null | [
[
"The extreme resistance of the bacterium D . radiodurans to DNA-fragmenting treatments , such as ionizing radiation or desiccation , is correlated with the ability to reconstruct a functional genome from hundreds of chromosomal fragments .",
"The rapid reconstitution of an intact genome is thought to occu... | [
"The bacterium Deinococcus radiodurans is one of the most radioresistant organisms known .",
"It is able to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments .",
"Our work aims to highlight the genes involved in recombination between 438 bp direct repeats separated by inte... | [
"Deinococcus radiodurans is known for its exceptional ability to tolerate exposure to DNA damaging agents and , in particular , to very high doses of ionizing radiation .",
"This exceptional radioresistance results from many features including efficient DNA double strand break repair .",
"Here , we examine geno... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"public health and epidemiology/epidemiology",
"infectious diseases/viral infections",
"public health and epidemiology/global health",
"public health and epidemiology/infectious diseases",
"ecology/spatial and landscape ecology",
"mathematics/statistics... | Local and Global Effects of Climate on Dengue Transmission in Puerto Rico | journal.pntd.0000382 | null | [
[
"The dengue viruses are the most widely distributed and damaging arthropod-borne viruses ( arboviruses ) affecting humans .",
"The viruses and their predominant mosquito vector , Aedes aegypti , are endemic to most of the tropical and subtropical regions of the world , where they cause seasonal epidemics ... | [
"The four dengue viruses , the agents of dengue fever and dengue hemorrhagic fever in humans , are transmitted predominantly by the mosquito Aedes aegypti .",
"The abundance and the transmission potential of Ae .",
"aegypti are influenced by temperature and precipitation .",
"While there is strong biological ... | [
"Dengue viruses are a major health problem throughout the tropical and subtropical regions of the world .",
"Because they are transmitted by mosquitoes that are sensitive to changes in rainfall and temperature , transmission intensity may be regulated by weather and climate .",
"Laboratory studies have shown th... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"veterinary diseases",
"clinical laboratory sciences",
"diagnostic medicine",
"veterinary parasitology",
"veterinary diagnostics",
"zoonotic diseases",
"livestock care",
"proteomics",
"biology",
"trypanosomiasis",
"veterinary science",
"veterinary medicine"
] | Identification of Tsetse (Glossina spp.) Using Matrix-Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry | journal.pntd.0002305 | null | [
[
"The trypanosomiasis infection risk of a particular area is determined by several factors , including tsetse species abundance and the sex distribution of a fly population [1] .",
"While the sex is easily distinguishable with the bare eye , species identification can be challenging because there are 32 re... | [
"Glossina ( G . ) spp .",
"( Diptera: Glossinidae ) , known as tsetse flies , are vectors of African trypanosomes that cause sleeping sickness in humans and nagana in domestic livestock .",
"Knowledge on tsetse distribution and accurate species identification help identify potential vector intervention sites ."... | [
"Tsetse flies are confined to tropical Africa and are carriers for trypanosomes , single-celled blood parasites .",
"Through the bite of an infective tsetse , people and animals may contract trypanosomiasis , a degenerative disease leading to death if left untreated .",
"Tsetse control proved effective for dise... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"immunity to infections",
"immunology",
"microbiology",
"immune defense",
"infectious disease control",
"animal models of infection",
"infectious diseases",
"biology",
"immune response",
"west nile fever",
"immunity",
"virology",
"innate immunity",
"microbial control",
"vir... | IRF-3, IRF-5, and IRF-7 Coordinately Regulate the Type I IFN Response in Myeloid Dendritic Cells Downstream of MAVS Signaling | journal.ppat.1003118 | null | [
[
"The type I interferon ( IFN ) signaling network is an essential component of the innate immune response against viral infections , and also functions to shape adaptive immunity [1]–[4] .",
"Infected cells initiate an antiviral response upon recognition of non-self pathogen-associated molecular patterns (... | [
"Although the transcription factors IRF-3 and IRF-7 are considered master regulators of type I interferon ( IFN ) induction and IFN stimulated gene ( ISG ) expression , Irf3−/−×Irf7−/− double knockout ( DKO ) myeloid dendritic cells ( mDC ) produce relatively normal levels of IFN-β after viral infection .",
"We g... | [
"Host pathogen sensors , including those of the Toll-like receptor and RIG-I like receptor ( RLR ) families , detect viral infection in cells .",
"Signaling through these receptors triggers expression of type I interferon ( IFN ) and IFN-stimulated genes ( ISGs ) , in part through the IRF family of transcription ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience/behavioral neuroscience",
"neuroscience",
"neuroscience/animal cognition"
] | Behavioral Sequence Analysis Reveals a Novel Role for
ß2* Nicotinic Receptors in Exploration | journal.pcbi.1000229 | null | [
[
"nAChRs are well-characterized transmembrane allosteric oligomers composed of five",
"identical ( homopentamers ) or different ( heteropentamers ) subunits [1] .",
"Nine",
"different subunits are widely expressed in the mammalian brain , modulating",
"neurotransmitter release , neuronal excita... | [
"Nicotinic acetylcholine receptors ( nAChRs ) are widely expressed throughout the",
"central nervous system and modulate neuronal function in most mammalian brain",
"structures .",
"The contribution of defined nAChR subunits to a specific behavior is",
"thus difficult to assess .",
"Mice deleted for ß2-co... | [
"Understanding mechanisms underlying complex behaviors and the abnormalities that",
"accompany most neuropathologies is a current challenge in biomedical research .",
"A",
"number of approaches is primarily based on the identification of genes and their",
"associated molecular pathways implicated in complex... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"sequencing techniques",
"medicine and health sciences",
"pathology and laboratory medicine",
"nucleases",
"enzymes",
"pathogens",
"messenger rna",
"dna-binding proteins",
"operons",
"enzymology",
"microbiology",
"bacterial diseases",
"enterobacteriaceae",
"genome analysis",
"dna",
"mo... | Extensive reshaping of bacterial operons by programmed mRNA decay | journal.pgen.1007354 | null | [
[
"One of the defining features of bacterial gene expression is the co-transcription of multiple genes within polycistronic mRNAs [1] .",
"Co-transcribed genes often encode proteins that participate in the same biological process or interact in a protein complex , allowing these genes to share the rate limi... | [
"Bacterial operons synchronize the expression of multiple genes by placing them under the control of a shared promoter .",
"It was previously shown that polycistronic transcripts can undergo differential RNA decay , leaving some genes within the polycistron more stable than others , but the extent of regulation b... | [
"Bacteria utilize operonic transcription to synchronize the expression of multiple consecutive genes .",
"However , this strategy lacks the ability to fine-tune the expression of specific operon members , which is often biologically important .",
"In this report , we integrate multiple transcriptome-wide RNA-se... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Beyond the E-Value: Stratified Statistics for Protein Domain Prediction | journal.pcbi.1004509 | null | [
[
"The evaluation of statistical significance is crucial in genome-wide studies , such as detecting differentially-expressed genes in microarray or proteomic studies , performing genome-wide association studies , and uncovering homologous sequences .",
"Different biological applications have settled for dif... | [
"E-values have been the dominant statistic for protein sequence analysis for the past two decades: from identifying statistically significant local sequence alignments to evaluating matches to hidden Markov models describing protein domain families .",
"Here we formally show that for “stratified” multiple hypothe... | [
"Despite decades of research , it remains a challenge to distinguish homologous relationships between proteins from sequence similarities arising due to chance alone .",
"This is an increasingly important problem as sequence database sizes continue to grow , and even today many computational analyses require that... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology",
"genetics and genomics/animal genetics",
"genetics and genomics/gene discovery",
"genetics and genomics/disease models",
"genetics and genomics/genetics of disease",
"genetics and genomics/gene function",
"genetics and genomics/cancer genetics"
] | Genetic Deletion of the Desmosomal Component Desmoplakin Promotes Tumor Microinvasion in a Mouse Model of Pancreatic Neuroendocrine Carcinogenesis | journal.pgen.1001120 | null | [
[
"The ability of a tumor to invade into the surrounding normal tissue marks a critical step in the transition from benign to malignant tumor growth .",
"The acquisition of this hallmark of cancer is associated with poor prognosis for many human cancers and is often considered a precursor to the development... | [
"We used the RIP1-Tag2 ( RT2 ) mouse model of islet cell carcinogenesis to profile the transcriptome of pancreatic neuroendocrine tumors ( PNET ) that were either non-invasive or highly invasive , seeking to identify pro- and anti-invasive molecules .",
"Expression of multiple components of desmosomes , structure... | [
"The ability of a tumor to invade into the surrounding normal tissue is one hallmark of a malignant cancer .",
"We sought to identify factors that either restrict or promote tumor invasion in a genetically engineered mouse model of pancreatic neuroendocrine cancer by characterizing the transcriptional profiles of... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"chromosome structure and function",
"centromeres",
"microbiology",
"model organisms",
"dna replication",
"molecular genetics",
"dna",
"chromosome biology",
"biology",
"molecular biology",
"cell biology",
"nucleic acids",
"genetics",
"yeast and fungal models",
"saccharomyces cerevisiae",... | Functional Centromeres Determine the Activation Time of Pericentric Origins of DNA Replication in Saccharomyces cerevisiae | journal.pgen.1002677 | null | [
[
"Centromere function , the ability to assemble a kinetochore and mediate chromosome segregation during meiosis and mitosis , is critical for the survival and propagation of eukaryotic organisms .",
"Defects in centromere/kinetochore complexes lead to genome instability and susceptibility to cancer and cel... | [
"The centromeric regions of all Saccharomyces cerevisiae chromosomes are found in early replicating domains , a property conserved among centromeres in fungi and some higher eukaryotes .",
"Surprisingly , little is known about the biological significance or the mechanism of early centromere replication; however ,... | [
"Genome duplication requires the orderly initiation of DNA synthesis at sites called origins of replication .",
"It has long been known that different origins become active at different times in S-phase ( the period during which cells duplicate their chromosomes ) .",
"Although such temporal regulation of repli... | 2012 |
[
"Introduction",
"Results",
"Discussion"
] | [
"computational biology/systems biology",
"computational biology/transcriptional regulation",
"cell biology/morphogenesis and cell biology",
"computational biology/molecular genetics",
"biophysics/theory and simulation",
"cell biology/developmental molecular mechanisms",
"biophysics/transcription and tra... | Stable, Precise, and Reproducible Patterning of Bicoid and Hunchback Molecules in the Early Drosophila Embryo | journal.pcbi.1000486 | null | [
[
"Pattern formation of multicellular organisms requires the accurate spatial regulation of gene expression .",
"Such regulation has been attributed to the position dependent distribution of signaling molecules called morphogens [1] , [2] .",
"One of the best studied morphogens is Bicoid ( Bcd ) in embr... | [
"Precise patterning of morphogen molecules and their accurate reading out are of key importance in embryonic development .",
"Recent experiments have visualized distributions of proteins in developing embryos and shown that the gradient of concentration of Bicoid morphogen in Drosophila embryos is established rap... | [
"For developing embryos , the precise , position-specific regulation of molecular processes is of fatal importance .",
"As the mechanism of such regulation , widely accepted has been the notion of the intraembryonic distribution of regulatory molecules called “morphogens” .",
"One of the best-studied morphogens... | 2009 |
[
"Introduction",
"Models and methods",
"Results",
"Discussion"
] | [
"taxonomy",
"medicine and health sciences",
"pathology and laboratory medicine",
"infectious disease epidemiology",
"pathogens",
"geographical locations",
"epidemiological methods and statistics",
"simulation and modeling",
"phylogenetics",
"data management",
"phylogenetic analysis",
"research... | Phylodynamics on local sexual contact networks | journal.pcbi.1005448 | null | [
[
"From the viewpoint of an infectious pathogen , host populations are highly structured by the physical contacts necessary for disease transmission to occur .",
"For pathogens whose transmission does not require intimate or sustained physical contact , random mixing models assuming contacts form instantane... | [
"Phylodynamic models are widely used in infectious disease epidemiology to infer the dynamics and structure of pathogen populations .",
"However , these models generally assume that individual hosts contact one another at random , ignoring the fact that many pathogens spread through highly structured contact netw... | [
"Phylodynamic models relate the branching pattern of a pathogen’s phylogenetic tree to the tree-like growth of an epidemic as it spreads through a host population .",
"Such models are increasingly used to learn about the epidemiology of different pathogens .",
"We extend current models to consider the structure... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"evolutionary biology/human evolution",
"mathematics"
] | Population Structure Induces a Symmetry Breaking Favoring the Emergence of Cooperation | journal.pcbi.1000596 | null | [
[
"Portuguese is no exception: Like any other language , it has many proverbs and popular sayings .",
"One of them states something like: I have already contributed to that charity [1] , concerning originally situations in which individuals are faced with the decision of offering ( or not ) a contribution t... | [
"The evolution of cooperation described in terms of simple two-person interactions has received considerable attention in recent years , where several key results were obtained .",
"Among those , it is now well established that the web of social interaction networks promotes the emergence of cooperation when mode... | [
"Humans contribute to a broad range of cooperative endeavors .",
"In many of them , the amount or effort contributed often depends on the social context of each individual .",
"Recent evidence has shown how modern societies are grounded in complex and heterogeneous networks of exchange and cooperation , in whic... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"anaphase",
"cell cycle and cell division",
"cell processes",
"chromatids",
"mutation",
"immunoprecipitation",
"nonsense mutation",
"research and analysis methods",
"missense mutation",
"chromosome biology",
"chromosomal disorders",
"precipitation techniques",... | Intact Cohesion, Anaphase, and Chromosome Segregation in Human Cells Harboring Tumor-Derived Mutations in STAG2 | journal.pgen.1005865 | null | [
[
"Cohesin is a multiprotein complex comprised of four primary subunits ( SMC1A , SMC3 , RAD21 , and either STAG1 or STAG2 ) and four regulatory subunits ( WAPL , CDCA5 , and PDS5A or PDS5B ) that is responsible for sister chromatid cohesion , regulation of gene expression , DNA repair , and other phenotypes [1... | [
"Somatic mutations of the cohesin complex subunit STAG2 are present in diverse tumor types .",
"We and others have shown that STAG2 inactivation can lead to loss of sister chromatid cohesion and alterations in chromosome copy number in experimental systems .",
"However , studies of naturally occurring human tum... | [
"Mutations of the STAG2 gene are common in several types of adult and pediatric cancers .",
"In fact , STAG2 is one of only 12 genes known to be significantly mutated in four of more types of cancer .",
"The STAG2 gene encodes a protein component of the “cohesin complex , ” a ring-like structure that binds chro... | 2016 |
[
"Introduction",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"maternal health",
"obstetrics and gynecology",
"cell cycle and cell division",
"cell processes",
"immunology",
"bone marrow cells",
"oncology",
"physiological processes",
"mutation",
"women's health",
"granulocytes",
"stem c... | Mutation, drift and selection in single-driver hematologic malignancy: Example of secondary myelodysplastic syndrome following treatment of inherited neutropenia | journal.pcbi.1006664 | null | [
[
"Cancer development is driven by series of mutational events , which may become fixed in a hematologic or non-hematologic tumor via genetic drift .",
"This process usually includes a limited number of driver ( advantageous ) mutations , and a greater number of passenger ( neutral or mildly deleterious ) m... | [
"Cancer development is driven by series of events involving mutations , which may become fixed in a tumor via genetic drift and selection .",
"This process usually includes a limited number of driver ( advantageous ) mutations and a greater number of passenger ( neutral or mildly deleterious ) mutations .",
"We... | [
"Cancer develops by multistep acquisition of mutations in a progenitor cell and its daughter cells .",
"Severe congenital neutropenia ( SCN ) manifests itself through an inability to produce enough granulocytes to prevent infections .",
"SCN commonly results from a germline ELANE mutation .",
"Large doses of ... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"ionizing radiation",
"dose prediction methods",
"cell cycle and cell division",
"cell processes",
"dna-binding proteins",
"radiation",
"simulation and modeling",
"dna damage",
"pharmaceutics",
"dna",
"research and analysis methods",
"proteins",
"physics",
... | Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair | journal.pcbi.1005131 | null | [
[
"Double-strand breaks ( DSBs ) are lesions in DNA that occur naturally by oxidative stress , DNA replication and exogenous sources [1 , 2] .",
"When left unprocessed or during erroneous repair , they cause changes to DNA structure creating mutations and potential genomic instability [3–8] .",
"To repa... | [
"DNA double-strand breaks are lesions that form during metabolism , DNA replication and exposure to mutagens .",
"When a double-strand break occurs one of a number of repair mechanisms is recruited , all of which have differing propensities for mutational events .",
"Despite DNA repair being of crucial importan... | [
"DNA double-strand breaks occur during metabolism , DNA replication and by exposure to exogenous sources such as ionising radiation .",
"When the genome is inflicted with this type of damage , DNA repair machinery is promoted to restore genome structure .",
"The efficient interplay between DNA damage and repair... | 2016 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [] | Generalization and Dilution of Association Results from European GWAS in Populations of Non-European Ancestry: The PAGE Study | journal.pbio.1001661 | A multi-ethnic study demonstrates that the extrapolation of genetic disease risk models from European populations to other ethnicities is compromised more strongly by genetic structure than by environmental or global genetic background in differential genetic risk associations across ethnicities. | [
[
"In the past six years , genome-wide association studies ( GWAS ) have revealed thousands of common polymorphisms ( tagSNPs ) associated with a wide variety of traits and diseases , particularly as study sample sizes have increased from thousands to hundreds of thousands of subjects .",
"Typically GWAS an... | [
"The vast majority of genome-wide association study ( GWAS ) findings reported to date are from populations with European Ancestry ( EA ) , and it is not yet clear how broadly the genetic associations described will generalize to populations of diverse ancestry .",
"The Population Architecture Using Genomics and ... | [
"The number of known associations between human diseases and common genetic variants has grown dramatically in the past decade , most being identified in large-scale genetic studies of people of Western European origin .",
"But because the frequencies of genetic variants can differ substantially between continent... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell physiology",
"medicine and health sciences",
"neurochemistry",
"nervous system",
"astrocytes",
"junctional complexes",
"vertebrates",
"electrophysiology",
"neuroscience",
"macroglial cells",
"mammals",
"animals",
"gap junctions",
"synaptic plasticity",
"neurotransmitters",
"neuro... | The influence of astrocytes on the width of orientation hypercolumns in visual cortex: A computational perspective | journal.pcbi.1005785 | null | [
[
"The cortex is the outermost layer of cerebral tissue , composed of neuronal cell bodies and protoplasmic astroytes .",
"The neurons in the cortex are arranged in columns , and the neurons in each column usually respond to similar features .",
"In the macaque these columns , known as microcolumns or m... | [
"Orientation preference maps ( OPMs ) are present in carnivores ( such as cats and ferrets ) and primates but are absent in rodents .",
"In this study we investigate the possible link between astrocyte arbors and presence of OPMs .",
"We simulate the development of orientation maps with varying hypercolumn widt... | [
"Columns of neurons in the primary visual cortex ( V1 ) are known to be tuned to visual stimuli containing edges of a particular orientation .",
"The arrangement of these cortical columns varies across species .",
"In many species such as in ferrets , cats , and monkeys a topology preserving map is observed , w... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"statistics",
"metaanalysis",
"drugs",
"experimental design",
"social sciences",
"biological locomotion",
"chemotherapeutic agents",
"animal models",
"oncology",
"research design",
"animal behavior",
"mathematics",
"experimental organism systems",
"oncolog... | Animal models of chemotherapy-induced peripheral neuropathy: A machine-assisted systematic review and meta-analysis | journal.pbio.3000243 | This systematic review assesses limitations in the experimental design of studies modelling peripheral neuropathy induced by chemotherapy. The data allow the authors to provide guidance on experimental design to improve the robustness and validity of future studies. | [
[
"Chemotherapy-induced peripheral neuropathy ( CIPN ) is a disabling side effect of many frequently used and effective cancer chemotherapeutic agents and is known to impair daily function and diminish quality of life [1] .",
"Frequently used chemotherapeutic agents reported to cause neurotoxic effects incl... | [
"We report a systematic review and meta-analysis of research using animal models of chemotherapy-induced peripheral neuropathy ( CIPN ) .",
"We systematically searched 5 online databases in September 2012 and updated the search in November 2015 using machine learning and text mining to reduce the screening for in... | [
"Many frequently used and effective cancer chemotherapies can cause a disabling side effect that features pain , numbness , tingling , and sensitivity to cold and heat in the extremities known as chemotherapy-induced peripheral neuropathy ( CIPN ) .",
"There are currently no effective therapies to treat or preven... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"teleost fishes",
"chicken",
"vertebrates",
"evolutionary biology",
"homo (human)",
"genetics and genomics",
"mus (mouse)"
] | Rapid Birth–Death Evolution Specific to Xenobiotic Cytochrome P450 Genes in Vertebrates | journal.pgen.0030067 | null | [
[
"Genes in animal and plant gene families vary greatly in their phylogenetic stability .",
"Some genes persist as a single copy over a wide phylogenetic range of species , with few or no gene duplications or losses on different evolving lineages .",
"Other genes undergo frequent duplication and loss in... | [
"Genes vary greatly in their long-term phylogenetic stability and there exists no general explanation for these differences .",
"The cytochrome P450 ( CYP450 ) gene superfamily is well suited to investigating this problem because it is large and well studied , and it includes both stable and unstable genes .",
... | [
"Genes vary greatly in their long-term phylogenetic stability , and there exists no general explanation for these differences .",
"Stable genes persist as a single copy over a wide range of distantly related species , whereas unstable genes undergo frequent duplication and loss in a process called birth-death evo... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Integration of Posttranscriptional Gene Networks into Metabolic Adaptation and Biofilm Maturation in Candida albicans | journal.pgen.1005590 | null | [
[
"Metabolism is a key driver of cell growth and division , and has a widespread influence on cell function .",
"For example , metabolites can regulate gene expression [1] , metabolic enzymes can double as RNA binding proteins and regulate mRNA expression [2] , and the “power house of eukaryotic cells”–the ... | [
"The yeast Candida albicans is a human commensal and opportunistic pathogen .",
"Although both commensalism and pathogenesis depend on metabolic adaptation , the regulatory pathways that mediate metabolic processes in C . albicans are incompletely defined .",
"For example , metabolic change is a major feature t... | [
"Metabolism is a master regulator of cell biology , including gene regulation , developmental switches and cellular life-death decisions , with the mitochondrion playing a central role in eukaryotes .",
"For the yeast Candida albicans mitochondrial functions have been implicated in host-pathogen interactions , bu... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics and genomics/genetics of disease",
"genetics and genomics/complex traits",
"mathematics/statistics"
] | A New Testing Strategy to Identify Rare Variants with Either Risk or Protective Effect on Disease | journal.pgen.1001289 | null | [
[
"Common diseases such as diabetes , heart disease , schizophrenia , etc . , are likely caused by a complex interplay among many genes and environmental factors .",
"At any single disease locus allelic heterogeneity is expected , i . e . , there may be multiple , different susceptibility mutations at the l... | [
"Rapid advances in sequencing technologies set the stage for the large-scale medical sequencing efforts to be performed in the near future , with the goal of assessing the importance of rare variants in complex diseases .",
"The discovery of new disease susceptibility genes requires powerful statistical methods f... | [
"Risk to common diseases , such as diabetes , heart disease , etc . , is influenced by a complex interaction among genetic and environmental factors .",
"Most of the disease-association studies conducted so far have focused on common variants , widely available on genotyping platforms .",
"However , recent adva... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer science/applications",
"computational biology/systems biology",
"genetics and genomics/gene expression",
"computational biology/transcriptional regulation",
"genetics and genomics/bioinformatics"
] | Using Network Component Analysis to Dissect Regulatory Networks Mediated by Transcription Factors in Yeast | journal.pcbi.1000311 | null | [
[
"With advances in whole genome high-throughput technologies such as ChIP-Chip , expression , and genotyping arrays , it is now possible to integrate data from these sources together to decipher the complex regulatory networks that govern transcription .",
"In addition to serving as powerful models for how... | [
"Understanding the relationship between genetic variation and gene expression is a central question in genetics .",
"With the availability of data from high-throughput technologies such as ChIP-Chip , expression , and genotyping arrays , we can begin to not only identify associations but to understand how genetic... | [
"One of the fundamental challenges in biology in the post-genomics era is understanding the complex regulatory mechanisms that govern how genes are turned on and off .",
"In a single organism where the functions of individual genes in a population do not differ much , many of the differences between individuals i... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Complex Epidemiology of a Zoonotic Disease in a Culturally Diverse Region: Phylogeography of Rabies Virus in the Middle East | journal.pntd.0003569 | null | [
[
"Rabies is a fatal encephalitis caused by viruses in the genus Lyssavirus [1 , 2] .",
"Although the majority of lyssavirus species are associated with bats , rabies virus ( RABV ) has successfully adapted to terrestrial carnivores on multiple occasions [3 , 4] and causes an estimated 70 , 000 deaths each ... | [
"The Middle East is a culturally and politically diverse region at the gateway between Europe , Africa and Asia .",
"Spatial dynamics of the fatal zoonotic disease rabies among countries of the Middle East and surrounding regions is poorly understood .",
"An improved understanding of virus distribution is neces... | [
"Despite being one of the oldest recognised infectious diseases , rabies continues to cause thousands of preventable human deaths per year .",
"As a zoonotic disease , control of infection in the reservoir has been proven the most efficient route to reduction of human cases .",
"In some regions , the epidemiolo... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"cervical cancer",
"pathogens",
"cell cycle and cell division",
"carcinomas",
"cell processes",
"microbiology",
"social sciences",
"cancers and neoplasms",
"viruses",
"oncology",
"dna replication",
"dna viruses",
"dna",... | KDM6A addiction of cervical carcinoma cell lines is triggered by E7 and mediated by p21CIP1 suppression of replication stress | journal.ppat.1006661 | null | [
[
"Human papillomaviruses ( HPVs ) are a group of small , double-stranded DNA viruses that infect the squamous epithelium .",
"The more than 200 HPV types described to date can be divided into mucosal and cutaneous types based on their tissue tropism .",
"The mucosal HPVs can be clinically designated “l... | [
"Expression of E7 proteins encoded by carcinogenic , high-risk human papillomaviruses ( HPVs ) triggers increased expression of the histone H3 lysine 27 demethylase KDM6A .",
"KDM6A expression is necessary for survival of high-risk HPV E7 expressing cells , including several cervical cancer lines .",
"Here we s... | [
"High-risk human papillomaviruses ( HPVs ) are associated with approximately five percent of all human cancers , including virtually all cervical cancers as well as a large percentage of anal , vaginal , vulvar , penile , and oropharyngeal cancers .",
"The HPV E6 and E7 proteins are the major oncogenic drivers in... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biochemistry",
"gram negative",
"transmembrane proteins",
"protein interactions",
"proteins",
"protein structure",
"macromolecular assemblies",
"microbial pathogens",
"biology",
"transmembrane transport proteins",
"microbiology",
"bacterial pathogens",
"pathogenesis"
] | Structural and Functional Studies on the Interaction of GspC and GspD in the Type II Secretion System | journal.ppat.1002228 | null | [
[
"Many Gram-negative bacteria use a multi-protein type II secretion system ( T2SS ) to secrete a wide variety of exoproteins from the periplasm into the extra-cellular milieu [1] , [2] , [3] , [4] .",
"In Vibrio cholerae and enterotoxigenic Escherichia coli ( ETEC ) , cholera toxin and the closely related ... | [
"Type II secretion systems ( T2SSs ) are critical for secretion of many proteins from Gram-negative bacteria .",
"In the T2SS , the outer membrane secretin GspD forms a multimeric pore for translocation of secreted proteins .",
"GspD and the inner membrane protein GspC interact with each other via periplasmic d... | [
"Many bacterial pathogens affecting humans , animals and plants export diverse proteins across the cell membranes into the medium surrounding the bacteria .",
"Some of these secreted proteins are involved in pathogenesis .",
"One example is cholera toxin secreted by the bacterium Vibrio cholerae , a causative a... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [] | Development of a Fluorescence-based Trypanosoma cruzi CYP51 Inhibition Assay for Effective Compound Triaging in Drug Discovery Programmes for Chagas Disease | journal.pntd.0004014 | null | [
[
"Chagas disease is a tropical parasitic disease caused by the flagellate eukaryotic ( protozoan ) parasite Trypanosoma cruzi ( T . cruzi ) , endemic in Latin America and now emerging in North America and Europe through human migration .",
"It is becoming a severe global health problem with approximately 8... | [
"Chagas disease , caused by the protozoan parasite Trypanosoma cruzi ( T . cruzi ) , is a life threatening global health problem with only two drugs available for treatment ( benznidazole and nifurtimox ) , both having variable efficacy in the chronic stage of the disease and high rates of adverse drug reactions ."... | [
"Chagas disease , caused by the parasite Trypanosoma cruzi ( T . cruzi ) , is endemic in Latin America and emerging in North America and Europe through human migration .",
"It is a severe global health problem with 8–10 million people infected and an estimated 12 , 000 deaths annually .",
"Current treatment opt... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion",
"Conclusions"
] | [] | Effectiveness and Safety of Short Course Liposomal Amphotericin B (AmBisome) as First Line Treatment for Visceral Leishmaniasis in Bangladesh | journal.pntd.0003699 | null | [
[
"Visceral Leishmaniasis ( VL ) , also known as Kala Azar , is a vector borne disease caused by parasites of the genus Leishmania , L . donovani—L .",
"infantum complex , which are transmitted through the bite of an infected sand fly ( mainly genus Phlebotomus , old world , and Lutzomya , new world ) , Lei... | [
"Bangladesh is one of the endemic countries for Visceral Leishmaniasis ( VL ) .",
"Médecins Sans Frontières ( MSF ) ran a VL treatment clinic in the most endemic district ( Fulbaria ) between 2010 and 2013 using a semi-ambulatory regimen for primary VL of 15mg/kg Liposomal Amphotericin-B ( AmBisome ) in three equ... | [
"Visceral Leishmaniasis ( VL ) is a parasitic disease which is endemic in more than 80 countries , although 90% of cases occur in India , Bangladesh , Sudan , South Sudan , Ethiopia and Brazil .",
"Most treatments are complex , expensive and require long application periods .",
"AmBisome is one of the newest tr... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary biology/human evolution",
"evolutionary biology/evolutionary and comparative genetics"
] | A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions | journal.pcbi.1000734 | null | [
[
"Many mechanisms for the origination of new genes are known , such as tandem gene duplication , retrotransposition , exon shuffling and gene fusion [1]–[5] .",
"By these mechanisms , the origination of new protein coding genes involved “mother” genes that served as blueprints for the new genes .",
"Ho... | [
"To understand whether any human-specific new genes may be associated with human brain functions , we computationally screened the genetic vulnerable factors identified through Genome-Wide Association Studies and linkage analyses of nicotine addiction and found one human-specific de novo protein-coding gene , FLJ33... | [
"For decades , gene duplication , retrotranspositions and gene fusions were believed to be major ways to increase gene number .",
"All involve “mother” genes as the “building blocks” for new genes .",
"However , several recently identified “motherless” genes challenged the idea in that some proteins might have ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal models of infection",
"infectious diseases",
"medicine and health sciences",
"cell biology",
"viral immune evasion",
"pathology and laboratory medicine",
"virulence factors",
"virology",
"pathogens",
"biology and life sciences",
"immunology",
"microbiology",
"viral diseases",
"path... | EVM005: An Ectromelia-Encoded Protein with Dual Roles in NF-κB Inhibition and Virulence | journal.ppat.1004326 | null | [
[
"The NF-κB family of transcription factors activate potent pro-inflammatory and anti-viral immune responses that are activated by a variety of signalling pathways [1] , [2] .",
"The family consists of five members , p50 , p52 , p65 ( RelA ) , RelB , and c-Rel , which function as homo- or heterodimers to a... | [
"Poxviruses contain large dsDNA genomes encoding numerous open reading frames that manipulate cellular signalling pathways and interfere with the host immune response .",
"The NF-κB signalling cascade is an important mediator of innate immunity and inflammation , and is tightly regulated by ubiquitination at seve... | [
"Poxviruses are large dsDNA viruses that are renowned for regulating cellular pathways and manipulating the host immune response , including the NF-κB pathway .",
"NF-κB inhibition by poxviruses is a growing area of interest and this family of viruses has developed multiple mechanisms to manipulate the pathway ."... | 2014 |
[
"Introduction",
"Results",
"Discussion"
] | [
"carbohydrate metabolism",
"medicine and health sciences",
"liver",
"body fluids",
"chemical compounds",
"enzymology",
"carbohydrates",
"glucose metabolism",
"organic compounds",
"glucose",
"glycobiology",
"enzyme metabolism",
"enzyme chemistry",
"research and analysis methods",
"mathema... | A multiscale modelling approach to assess the impact of metabolic zonation and microperfusion on the hepatic carbohydrate metabolism | journal.pcbi.1006005 | null | [
[
"In mammals , the liver is the central organ for the control of plasma glucose .",
"To restrict variations of plasma glucose to the range between 3 mM ( after exercise or moderate fast [1] ) and 10 mM ( after meal ingestion , [2] ) , liver metabolism may switch between glucose production ( gluconeogenesis... | [
"The capacity of the liver to convert the metabolic input received from the incoming portal and arterial blood into the metabolic output of the outgoing venous blood has three major determinants: The intra-hepatic blood flow , the transport of metabolites between blood vessels ( sinusoids ) and hepatocytes and the ... | [
"Glucose homeostasis is one of the central liver functions .",
"The liver extracts glucose from the blood when plasma glucose levels are high and produces glucose when plasma glucose levels are low .",
"To fulfill this function the liver is organized in smallest functional units , the sinusoidal tissue units ( ... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"death rates",
"medicine and health sciences",
"clinical laboratory sciences",
"aminotransferases",
"pathology and laboratory medicine",
"viral transmission and infection",
"enzymes",
"enzymology",
"microbiology",
"biomarkers",
"signs and symptoms",
"population biology",
"viral load",
"thr... | A scoring model for predicting prognosis of patients with severe fever with thrombocytopenia syndrome | journal.pntd.0005909 | null | [
[
"Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease caused by a novel bunyavirus , which first emerged in China in 2005[1] .",
"In 2009 , the novel bunyavirus , designated as SFTS virus ( SFTSV ) or Huaiyangshan virus , was first isolated from patients with SFTS in Chin... | [
"Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging epidemic infectious disease caused by the SFTS bunyavirus ( SFTSV ) with an estimated high case-fatality rate of 12 . 7% to 32 . 6% .",
"Currently , the disease has been reported in mainland China , Japan , Korea , and the United States .",
"A... | [
"Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging infectious disease caused by a novel SFTS bunyavirus ( SFTSV ) with an estimated high case-fatality rate .",
"However , there is no specific antiviral therapy for SFTSV infection .",
"Symptomatic treatment and supportive therapy are the most e... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"virology/vaccines",
"infectious diseases/neglected tropical diseases",
"immunology/immune response",
"infectious diseases/viral infections"
] | Vaccination with DNA Plasmids Expressing Gn Coupled to C3d or Alphavirus Replicons Expressing Gn Protects Mice against Rift Valley Fever Virus | journal.pntd.0000725 | null | [
[
"Rift Valley fever ( RVF ) is an arthropod-borne viral zoonosis .",
"The causative agent Rift Valley fever virus ( RVFV ) belongs to the genus Phlebovirus of the family Bunyaviridae and was first discovered in the Rift Valley of Kenya in 1931 [1] .",
"RVFV infections in livestock are characterized by ... | [
"Rift Valley fever ( RVF ) is an arthropod-borne viral zoonosis .",
"Rift Valley fever virus ( RVFV ) is an important biological threat with the potential to spread to new susceptible areas .",
"In addition , it is a potential biowarfare agent .",
"We developed two potential vaccines , DNA plasmids and alphav... | [
"Rift Valley fever virus ( RVFV ) is an arthropod-borne phlebovirus associated with abortion storms , neonatal mortality in livestock and hemorrhagic fever or fatal encephalitis in a proportion of infected humans .",
"Requirement of multiple booster immunizations to maintain the level of protective immunity with ... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"viral hemorrhagic fevers",
"infectious diseases",
"infectious disease immunology",
"medicine and health sciences",
"clinical immunology",
"dengue fever",
"biology and life sciences",
"immunology",
"viral diseases",
"vector-borne diseases"
] | Dengue Virus Neutralizing Antibody Levels Associated with Protection from Infection in Thai Cluster Studies | journal.pntd.0003230 | null | [
[
"Dengue is caused by four closely related , but antigenically distinct dengue virus serotypes ( DENV-1 , -2 , -3 , -4 ) from the genus Flavivirus in the family Flaviviridae [1] , [2] .",
"In recent decades , dengue has expanded in tropical and subtropical regions and become one of the most prevalent vecto... | [
"Long-term homologous and temporary heterologous protection from dengue virus ( DENV ) infection may be mediated by neutralizing antibodies .",
"However , neutralizing antibody titers ( NTs ) have not been clearly associated with protection from infection .",
"Data from two geographic cluster studies conducted ... | [
"Dengue is caused by four different dengue virus serotypes ( DENV-1 , -2 , -3 , -4 ) .",
"Infection induces long-term protection against the same serotype , but only short-term protection , and possible enhancement , from different serotypes .",
"DENV neutralizing antibody titers ( NTs ) are thought to mediate ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide association studies",
"aneuploidy",
"x-linked",
"chromosomal disorders",
"genetics",
"biology",
"human genetics",
"genetics of disease",
"chromosomal deletions and duplications",
"genetics and genomics",
"y-linked"
] | Human Spermatogenic Failure Purges Deleterious Mutation Load from the Autosomes and Both Sex Chromosomes, including the Gene DMRT1 | journal.pgen.1003349 | null | [
[
"Male infertility is a multifaceted disorder affecting nearly 5% of men of reproductive age .",
"In spite of its prevalence and a considerable research effort over the past several decades , the underlying cause of male infertility is uncharacterized in up to half of all cases [1] .",
"Some degree of ... | [
"Gonadal failure , along with early pregnancy loss and perinatal death , may be an important filter that limits the propagation of harmful mutations in the human population .",
"We hypothesized that men with spermatogenic impairment , a disease with unknown genetic architecture and a common cause of male infertil... | [
"Infertility is a disease that prevents the transmission of DNA from one generation to the next , and consequently it has been difficult to study the genetics of infertility using classical human genetics methods .",
"Now , new technologies for screening entire genomes for rare and patient-specific mutations are ... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Polyfunctional T Cell Responses in Children in Early Stages of Chronic Trypanosoma cruzi Infection Contrast with Monofunctional Responses of Long-term Infected Adults | journal.pntd.0002575 | null | [
[
"Chagas disease , a neglected tropical disease affecting approximately 10 million people from south of the United States to Mexico and Central and South America [1] , is caused by the protozoan parasite Trypanosoma cruzi .",
"As a consequence of migration flows , the disease has been also become establish... | [
"Adults with chronic Trypanosoma cruzi exhibit a poorly functional T cell compartment , characterized by monofunctional ( IFN-γ-only secreting ) parasite-specific T cells and increased levels of terminally differentiated T cells .",
"It is possible that persistent infection and/or sustained exposure to parasites ... | [
"Chagas disease is a neglected tropical disease affecting approximately 10 million people in the world .",
"As a consequence of migration flows , the disease has also become established in non-endemic countries .",
"Previous studies have demonstrated that Trypanosoma cruzi-specific T cells inversely correlates ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"ultraviolet radiation",
"experimental design",
"random variables",
"light",
"covariance",
"electromagnetic radiation",
"simulation and modeling",
"research design",
"probability distribution",
"mathematics",
"algebra",
"research and analysis methods",
"gene expression",
"probability theor... | The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments | journal.pcbi.1006365 | null | [
[
"Stochastic gene expression can be modeled as a discrete state , continuous time Markov process , where different states x i = [ η 1 , η 2 , … , η N s ] i T ∈ X ⊂ Z ≥ 0 N s represent the Ns species of interest .",
"In a biological context , the species η often correspond to gene configurations , RNA or pr... | [
"Modern optical imaging experiments not only measure single-cell and single-molecule dynamics with high precision , but they can also perturb the cellular environment in myriad controlled and novel settings .",
"Techniques , such as single-molecule fluorescence in-situ hybridization , microfluidics , and optogene... | [
"A main objective of quantitative modeling is to predict the behaviors of complex systems under varying conditions .",
"In a biological context , stochastic fluctuations in expression levels among isogenic cell populations have required modeling efforts to incorporate and even rely upon stochasticity .",
"At th... | 2019 |
[
"Introduction",
"Materials and methods",
"Results and discussion"
] | [
"chemical compounds",
"aliphatic amino acids",
"organic compounds",
"serine",
"isoleucine",
"amino acids",
"bacteria",
"proteins",
"prokaryotic cells",
"chemistry",
"cyclic amino acids",
"proline",
"biochemistry",
"eukaryota",
"organic chemistry",
"cell biology",
"proteomes",
"prot... | Why do eukaryotic proteins contain more intrinsically disordered regions? | journal.pcbi.1007186 | null | [
[
"Eukaryotic cells are more complex than prokaryotic cells , and therefore , have an increased need for regulation .",
"They also contain organelles , have more complex genes and a more advanced chaperonin system enabling the folding of longer proteins [1] .",
"In response to the increased complexity ,... | [
"Intrinsic disorder is more abundant in eukaryotic than prokaryotic proteins .",
"Methods predicting intrinsic disorder are based on the amino acid sequence of a protein .",
"Therefore , there must exist an underlying difference in the sequences between eukaryotic and prokaryotic proteins causing the ( predicte... | [
"Intrinsic disorder is essential for various functions in eukaryotic cells and is a signature of eukaryotic proteins .",
"Here , we try to understand the origin of the difference in disorder between eukaryotic and prokaryotic proteins .",
"We show that eukaryotic proteins contain more extended linker regions an... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | ALS-Associated FUS Mutations Result in Compromised FUS Alternative Splicing and Autoregulation | journal.pgen.1003895 | null | [
[
"Amyotrophic lateral sclerosis ( ALS ) is a neuronal degenerative disorder caused by progressive loss of motor neurons in brain and spinal cord , leading to paralysis and death [1] .",
"FUS is a frequently mutated gene in ALS ( combining familial and sporadic ALS ) , in addition to C9ORF72 , SOD1 and TDP-... | [
"The gene encoding a DNA/RNA binding protein FUS/TLS is frequently mutated in amyotrophic lateral sclerosis ( ALS ) .",
"Mutations commonly affect its carboxy-terminal nuclear localization signal , resulting in varying deficiencies of FUS nuclear localization and abnormal cytoplasmic accumulation .",
"Increasin... | [
"FUS/TLS is a frequently mutated gene in amyotrophic lateral sclerosis ( ALS ) .",
"ALS , also known as Lou Gehrig's disease , is characterized by a progressive degeneration of motor neurons .",
"The abnormal cytoplasmic accumulation of mutant FUS protein is a characteristic pathology of ALS; however , recent e... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"geographical locations",
"vertebrates",
"parasitic diseases",
"parasitic protozoans",
"animals",
"mammals",
"protozoans",
"molecular biology techniques",
"cellular structures and organelles",
"research and analysis methods",... | Small subunit ribosomal metabarcoding reveals extraordinary trypanosomatid diversity in Brazilian bats | journal.pntd.0005790 | null | [
[
"Trypanosoma cruzi is the etiological agent of Chagas disease , a complex zoonosis that continues to take dozens of human lives each day [1] .",
"Alongside its close relative Trypanosoma cruzi marinkellei in the Schizotrypanum subgenus , this important protozoan flagellate belongs to a broader , inter-con... | [
"Bats are a highly successful , globally dispersed order of mammals that occupy a wide array of ecological niches .",
"They are also intensely parasitized and implicated in multiple viral , bacterial and parasitic zoonoses .",
"Trypanosomes are thought to be especially abundant and diverse in bats .",
"In thi... | [
"Bats make up a mega-diverse , intensely parasitized order of volant mammals whose unique behavioural and physiological adaptations promote infection by a vast array of microorganisms .",
"Trypanosomes stand out as ancient protozoan parasites of bats .",
"As cryptic morphology , low parasitaemia and selective g... | 2017 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"biophysics/theory and simulation",
"neuroscience/theoretical neuroscience",
"computational biology/computational neuroscience"
] | Instantaneous Non-Linear Processing by Pulse-Coupled Threshold Units | journal.pcbi.1000929 | null | [
[
"Understanding the dynamics of single neurons , recurrent networks of neurons , and spike-timing dependent synaptic plasticity requires the quantification of how a single neuron transfers synaptic input into outgoing spiking activity .",
"If the incoming activity has a slowly varying or constant rate , th... | [
"Contemporary theory of spiking neuronal networks is based on the linear response of the integrate-and-fire neuron model derived in the diffusion limit .",
"We find that for non-zero synaptic weights , the response to transient inputs differs qualitatively from this approximation .",
"The response is instantane... | [
"Our work demonstrates a fast-firing response of nerve cells that remained unconsidered in network analysis , because it is inaccessible by the otherwise successful linear response theory .",
"For the sake of analytic tractability , this theory assumes infinitesimally weak synaptic coupling .",
"However , reali... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"computational neuroscience",
"biology",
"neuroscience",
"learning and memory"
] | Reinforcement Learning Using a Continuous Time Actor-Critic Framework with Spiking Neurons | journal.pcbi.1003024 | null | [
[
"Many instances of animal behavior learning such as path finding in foraging , or – a more artificial example – navigating the Morris water-maze , can be interpreted as exploration and trial-and-error learning .",
"In both examples , the behavior eventually learned by the animal is the one that led to hig... | [
"Animals repeat rewarded behaviors , but the physiological basis of reward-based learning has only been partially elucidated .",
"On one hand , experimental evidence shows that the neuromodulator dopamine carries information about rewards and affects synaptic plasticity .",
"On the other hand , the theory of re... | [
"As every dog owner knows , animals repeat behaviors that earn them rewards .",
"But what is the brain machinery that underlies this reward-based learning ?",
"Experimental research points to plasticity of the synaptic connections between neurons , with an important role played by the neuromodulator dopamine , ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetic networks",
"cell cycle and cell division",
"cell processes",
"fungi",
"model organisms",
"network analysis",
"experimental organism systems",
"tubulins",
"genetic interactions",
"research and analysis methods",
"saccharomyces",
"polymer chemistry",
"computer and information sciences... | Predicting bioprocess targets of chemical compounds through integration of chemical-genetic and genetic interactions | journal.pcbi.1006532 | null | [
[
"The discovery of chemical compounds with desirable and interesting biological activity advances our understanding of how compounds and biological systems interact .",
"Chemical-genetic interaction profiling enables this discovery by measuring the response of defined gene mutants to chemical compounds [1–... | [
"Chemical-genetic interactions–observed when the treatment of mutant cells with chemical compounds reveals unexpected phenotypes–contain rich functional information linking compounds to their cellular modes of action .",
"To systematically identify these interactions , an array of mutants is challenged with a com... | [
"Understanding how chemical compounds affect biological systems is of paramount importance as pharmaceutical companies strive to develop life-saving medicines , governments seek to regulate the safety of consumer products and agrichemicals , and basic scientists continue to study the fundamental inner workings of b... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"sequencing techniques",
"cell physiology",
"cell binding",
"rna-binding proteins",
"medicine and health sciences",
"immune cells",
"gene regulation",
"immunology",
"neuroscience",
"micrornas",
"mathematics",
"forecasting",
"statistics (mathematics)",
"artificial intellige... | Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data | journal.pcbi.1005026 | null | [
[
"Recent high-throughput technologies like AGO CLIP sequencing [1 , 2] and CLASH ( crosslinking , ligation , and sequencing of miRNA-RNA hybrids [3] ) enable direct biochemical identification of AGO binding and miRNA target sites transcriptome-wide .",
"The miRNA field has a strong tradition of computation... | [
"Recent technologies like AGO CLIP sequencing and CLASH enable direct transcriptome-wide identification of AGO binding and miRNA target sites , but the most widely used miRNA target prediction algorithms do not exploit these data .",
"Here we use discriminative learning on AGO CLIP and CLASH interactions to train... | [
"MicroRNAs ( or miRNAs ) are a family of small RNA molecules that guide Argonaute ( AGO ) to specific target sites within mRNAs and regulate numerous biological processes in normal cells and in disease .",
"Despite years of research , the principles of miRNA targeting are incompletely understood , and computation... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"classical mechanics",
"decision making",
"neuroscience",
"health care",
"preventive medicine",
"research design",
"cognition",
"surveys",
"infectious disease control",
"questionnaires",
"research and analysis methods",
"public and occupational health",
"inf... | KAP Surveys and Dengue Control in Colombia: Disentangling the Effect of Sociodemographic Factors Using Multiple Correspondence Analysis | journal.pntd.0005016 | null | [
[
"Dengue is an endemic or epidemic disease in countries located in the tropics [1] , and approximately 40% of the world’s population is at risk of suffering dengue [2] .",
"In Latin America , the number of cases has increased over the last three decades; it has grown from a low dengue-endemic to a hyper-en... | [
"During the last few decades , several studies have analyzed and described knowledge , attitudes , and practices ( KAP ) of populations regarding dengue .",
"However , few studies have applied geometric data analytic techniques to generate indices from KAP domains .",
"Results of such analyses have not been use... | [
"Local vector control programs , as part of their routine activities , often use Knowledge Attitudes and Practices ( KAP ) surveys to guide their dengue control strategies .",
"Usually , these questionnaires are extensive and result in a large amount of data that is difficult to analyze and summarize .",
"This ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | An In-Depth Comparison of Latent HIV-1 Reactivation in Multiple Cell Model Systems and Resting CD4+ T Cells from Aviremic Patients | journal.ppat.1003834 | null | [
[
"The possibility to achieve HIV eradication has been limited , at least in part , by the existence of latently infected cellular reservoirs [1]–[3] .",
"The major known cellular reservoir is established in quiescent memory CD4+ T cells , providing an extremely long-lived set of cells in which the virus ca... | [
"The possibility of HIV-1 eradication has been limited by the existence of latently infected cellular reservoirs .",
"Studies to examine control of HIV latency and potential reactivation have been hindered by the small numbers of latently infected cells found in vivo .",
"Major conceptual leaps have been facili... | [
"HIV establishes a state of latency in vivo and this latent reservoir , although small , is difficult to eradicate .",
"To be able to better understand this state of latency , and to develop strategies to eliminate it , many groups have developed in vitro models of HIV latency .",
"However , notable differences... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/persistence and latency",
"immunology/antigen processing and recognition",
"virology/viral replication and gene regulation",
"virology/vaccines",
"immunology/immunomodulation",
"immunology/immune response",
"immunology/immunity to infections",
"virology/new therapies, including antivirals an... | T Cell Detection of a B-Cell Tropic Virus Infection: Newly-Synthesised versus Mature Viral Proteins as Antigen Sources for CD4 and CD8 Epitope Display | journal.ppat.1000699 | null | [
[
"Many intracellular pathogens , particularly viruses , naturally infect cells of the haemopoietic system that express both MHC I and MHC II molecules .",
"Such infected cells may be rendered visible to the host T cell response through the intracellular processing of virally-encoded proteins , leading to c... | [
"Viruses that naturally infect cells expressing both MHC I and MHC II molecules render themselves potentially visible to both CD8+ and CD4+ T cells through the de novo expression of viral antigens .",
"Here we use one such pathogen , the B-lymphotropic Epstein-Barr virus ( EBV ) , to examine the kinetics of these... | [
"Many viruses infect cells in which both the MHC I and MHC II pathways of antigen presentation are active , and so viral proteins expressed in those cells may be presented as MHC I-peptide complexes to CD8+ T cells and as MHC II-peptide complexes to CD4+ T cells .",
"Here we study these processes in a model syste... | 2009 |
[
"Introduction",
"Methods",
"Results/Discussion"
] | [
"biomacromolecule-ligand interactions",
"medicine",
"biochemistry",
"infectious diseases",
"fasciolosis",
"enzymes",
"neglected tropical diseases",
"biology",
"enzyme kinetics",
"parasitic diseases"
] | Dissecting the Active Site of the Collagenolytic Cathepsin L3 Protease of the Invasive Stage of Fasciola hepatica | journal.pntd.0002269 | null | [
[
"The common liver fluke F . hepatica , together with F . gigantica , are the causative agents of fascioliasis , a zoonosis causing huge global losses in the agricultural section by infecting more than 700 million ruminants worldwide .",
"The disease is also recognized by the WHO as an important emerging n... | [
"A family of secreted cathepsin L proteases with differential activities is essential for host colonization and survival in the parasitic flatworm Fasciola hepatica .",
"While the blood feeding adult secretes predominantly FheCL1 , an enzyme with a strong preference for Leu at the S2 pocket of the active site , t... | [
"The flatworm Fasciola hepatica is responsible for fasciolosis , one of the most common parasitic diseases of livestock worldwide , with increased incidence of human cases .",
"When contaminated plants are ingested , infective larvae are released and transverse the gut wall before migrating to the bile ducts with... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"embryology",
"evolutionary biology",
"molecular development",
"biology",
"morphogenesis",
"evolutionary developmental biology"
] | Deficient Induction Response in a Xenopus Nucleocytoplasmic Hybrid | journal.pbio.1001197 | Defects in induction signaling and response underlie the nucleocytoplasmic incompatibility between two evolutionarily distant frog species, while specific treatments partially restore this response in explants and whole embryos. | [
[
"Investigation of the mechanisms generating the characters or phenotypes during development has revealed the importance of the nucleus and its DNA content in directing developmental processes [1]–[4] .",
"Nonetheless , the cytoplasm of the egg is responsible for the specification of many early aspects of ... | [
"Incompatibilities between the nucleus and the cytoplasm of sufficiently distant species result in developmental arrest of hybrid and nucleocytoplasmic hybrid ( cybrid ) embryos .",
"Several hypotheses have been proposed to explain their lethality , including problems in embryonic genome activation ( EGA ) and/or... | [
"When two species evolve separately for several million years , their respective genomes accumulate many small changes that together are responsible for the differences in their characters .",
"Some of these affect the way eggs are prepared inside the germline , and/or how embryos develop , such that the egg cyto... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"larvicides",
"invertebrates",
"medicine and health sciences",
"pathology and laboratory medicine",
"togaviruses",
"pathogens",
"microbiology",
"animals",
"alphaviruses",
"reproductive physiology",
"viruses",
"chikungunya virus",
"rna viruses",
"oils",
"pest control",
"insect vectors",... | Targeting a Hidden Enemy: Pyriproxyfen Autodissemination Strategy for the Control of the Container Mosquito Aedes albopictus in Cryptic Habitats | journal.pntd.0005235 | null | [
[
"Aedes albopictus is a highly invasive mosquito species that has originated from South East Asia and now has spread in most part of the world[1] .",
"In the United States , this mosquito species was first reported from Texas in 1985 and has since expanded its range to more than 30 states [2] .",
"Aede... | [
"The Asian tiger mosquito , Aedes albopictus , is a vector of dengue , Chikungunya , and Zika viruses .",
"This mosquito inhabits a wide range of artificial water-holding containers in urban and suburban areas making it difficult to control .",
"We tested the hypothesis that female-driven autodissemination of a... | [
"Aedes albopictus is a highly invasive mosquito species and a competent vector of dengue , Chikungunya , Zika and other arboviruses .",
"In the absence of therapeutics , vector control is the only means of controlling these diseases .",
"Larvicides are important tool to limit mosquito populations .",
"Backpac... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials & methods"
] | [
"insertion mutation",
"cell cycle and cell division",
"cell processes",
"dna-binding proteins",
"mutation",
"fungi",
"model organisms",
"dna replication",
"experimental organism systems",
"sequence motif analysis",
"dna",
"synthesis phase",
"research and analysis methods",
"saccharomyces",... | Recruitment of Fkh1 to replication origins requires precisely positioned Fkh1/2 binding sites and concurrent assembly of the pre-replicative complex | journal.pgen.1006588 | null | [
[
"Replication of genomic DNA in budding yeast ( Saccharomyces cerevisiae ) is initiated from hundreds of origins throughout the S phase .",
"Replication origins can be characterized by their efficiency , which refers to the probability that a particular origin will fire in a given cell cycle , and by the t... | [
"In budding yeast , activation of many DNA replication origins is regulated by their chromatin environment , whereas others fire in early S phase regardless of their chromosomal location .",
"Several location-independent origins contain at least two divergently oriented binding sites for Forkhead ( Fkh ) transcri... | [
"In this study , we explore the mechanisms that determine activation of DNA replication origins in early S phase .",
"It has been shown that a subset of replication origins is regulated by Forkhead family transcription factors that ensure their firing at the beginning of S phase .",
"However , the recruitment o... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"atmospheric science",
"tropical diseases",
"social sciences",
"geoinformatics",
"population modeling",
"neglected tropical diseases",
"veterinary science",
"public and occupational health",
"infectious diseases",
"computer and information sciences",
"veterinary... | El Niño Southern Oscillation and Leptospirosis Outbreaks in New Caledonia | journal.pntd.0002798 | null | [
[
"Leptospirosis is an important zoonotic disease with high incidence in tropical and subtropical regions worldwide , with more than 850 , 000 cases a year , a high incidence in tropical regions worldwide [1] and a case fatality ratio frequently exceeding 10% [2] .",
"It has also been reported as an emergin... | [
"Leptospirosis is an important cause of seasonal outbreaks in New Caledonia and the tropics .",
"Using time series derived from high-quality laboratory-based surveillance from 2000–2012 , we evaluated whether climatic factors , including El Niño Southern Oscillation ( ENSO ) and meteorological conditions allow fo... | [
"The El Niño Southern Oscillation is a major ocean – atmosphere phenomenon that strongly contributes to the timing and intensity of rainfall in the tropical Pacific islands and beyond .",
"As a consequence , it also has a major effect on the number of cases of leptospirosis .",
"By incorporating oceanographic p... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"mathematics",
"plant biology",
"crops",
"genetics",
"statistics",
"biology",
"genomics",
"genetics and genomics",
"agriculture"
] | Lessons from Dwarf8 on the Strengths and Weaknesses of Structured Association Mapping | journal.pgen.1003246 | null | [
[
"Association mapping , which was developed as a necessity for large-scale human studies , is commonly used in conjunction with family ( linkage ) mapping in plant and animal genetic studies .",
"The application of association mapping for plants was originally assessed in Thornsberry J . M . ( 2001 ) [1] w... | [
"The strengths of association mapping lie in its resolution and allelic richness , but spurious associations arising from historical relationships and selection patterns need to be accounted for in statistical analyses .",
"Here we reanalyze one of the first generation structured association mapping studies of th... | [
"Eleven years ago , association mapping was a cutting-edge tool used to identify regions of a genome associated with phenotypic variation .",
"One of the first association studies performed in plants was reported in Thornsberry , et al . ( 2001 ) .",
"Since then , researchers continued to develop new and improv... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular cell biology",
"immunity",
"immunology",
"biology",
"immune response"
] | Mitochondrial Ubiquitin Ligase MARCH5 Promotes TLR7 Signaling by Attenuating TANK Action | journal.ppat.1002057 | null | [
[
"Germline-encoded pattern recognition receptors ( PRRs ) play pivotal roles in sensing a wide range of invading pathogens , via recognizing conserved microbial signature molecules ( PAMPs , pathogen associated molecular patterns ) .",
"As molecular switches that register microbial infection , these recept... | [
"The signaling of Toll-like receptors ( TLRs ) is the host's first line of defense against microbial invasion .",
"The mitochondrion is emerging as a critical platform for antiviral signal transduction .",
"The regulatory role of mitochondria for TLR signaling remains to be explored .",
"Here , we show that t... | [
"In 2005 , MAVS was characterized as the critical adaptor protein for the signal transduction of RIG-I-like receptors ( RLRs ) .",
"This provided the first link between mitochondria and the intracellular antiviral defense system .",
"From then on , exploring the potential functions of novel mitochondrial protei... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"rna transport",
"rna interference",
"evolutionary biology",
"germ cells",
"developmental biology",
"pattern formation",
"gene expression",
"comparative genomics",
"biology",
"molecular biology",
"rna",
"cell biology",
"nucleic acids",
"cellular types",
"genomics",
"molecular cell biol... | The Phylogenetic Origin of oskar Coincided with the
Origin of Maternally Provisioned Germ Plasm and Pole Cells at the Base of the
Holometabola | journal.pgen.1002029 | null | [
[
"Germ cells are essential for the transfer of heritable information and , therefore ,",
"the determination of their fate is a critical event in the development and evolution",
"of sexually reproducing organisms .",
"Two general strategies for generating the",
"germline have evolved in animals:... | [
"The establishment of the germline is a critical , yet surprisingly evolutionarily",
"labile , event in the development of sexually reproducing animals .",
"In the fly",
"Drosophila , germ cells acquire their fate early during",
"development through the inheritance of the germ plasm , a specialized maternal... | [
"The establishment of the germline during embryogenesis is a critical milestone",
"for sexually reproducing organisms , but one that is surprisingly labile in",
"evolution .",
"For example , in the fly Drosophila , the germline is",
"set aside early in embryogenesis due to the localized synthesis of the ger... | 2011 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.