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",
"Methods",
"Results",
"Discussion"
] | [] | The Epidemiology and Geographic Distribution of Nontuberculous Mycobacteria Clinical Isolates from Sputum Samples in the Eastern Region of China | journal.pntd.0003623 | null | [
[
"Nontuberculous mycobacteria ( NTM ) were observed soon after Koch’s discovery of Mycobacterium tuberculosis [1] .",
"However , only until the 1950s NTM were defined as ‘atypical’ or ‘anonymous’ mycobacteria [2] .",
"It is well known that more than 100 species of NTM are ubiquitously distributed in th... | [
"Nontuberculous mycobacteria ( NTM ) have been reported to be increasing worldwide and its geographic distribution differs by region .",
"The aim of this study was to describe the epidemiology and distribution of NTM in the eastern part of China .",
"Sputum samples were collected from 30 surveillance sites for ... | [
"Nontuberculous mycobacteria ( NTM ) exist ubiquitously in the environment and cause many kinds of diseases including pulmonary infection .",
"Despite this , NTM does not match compulsory report policy in many countries , such as China .",
"Thus , the epidemiology of NTM is generally unknown .",
"Furthermore ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"chemical compounds",
"dna-binding proteins",
"carbohydrates",
"galactose",
"organic compounds",
"dna damage",
"fungi",
"polymerases",
"dna replication",
"dna",
"mammalian genomics",
"molecular biology techniques",
"research and analysis methods",
"proteins",
"chemistry",
"molecular bi... | DNA replication stress restricts ribosomal DNA copy number | journal.pgen.1007006 | null | [
[
"Ribosomal RNAs ( rRNAs ) in budding yeast are encoded by ~100–200 repeats of a 9 . 1kb sequence arranged in tandem on the long arm of chromosome XII , the ribosomal DNA ( rDNA ) locus .",
"Each 9 . 1kb unit is composed of a region encoding a pre-35S rRNA that gives rise to 25S , 18S and 5 . 8S rRNAs ( tr... | [
"Ribosomal RNAs ( rRNAs ) in budding yeast are encoded by ~100–200 repeats of a 9 . 1kb sequence arranged in tandem on chromosome XII , the ribosomal DNA ( rDNA ) locus .",
"Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis .",
"Despite t... | [
"Eukaryotic genomes contain many copies of ribosomal DNA ( rDNA ) genes , usually far in excess of the requirement for cellular ribosome biogenesis .",
"rDNA array size is highly variable , both within and across species .",
"Although it is becoming increasingly evident that the rDNA locus serves extra-coding f... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Mycobacterial Metabolic Syndrome: LprG and Rv1410 Regulate Triacylglyceride Levels, Growth Rate and Virulence in Mycobacterium tuberculosis | journal.ppat.1005351 | null | [
[
"Tuberculosis continues to be a major global health threat .",
"Mycobacterium tuberculosis ( Mtb ) is estimated to infect 2 billion people worldwide , or one-third of the world’s population [1] .",
"Despite its clinical importance , key aspects of tuberculosis ( TB ) pathogenesis are still not underst... | [
"Mycobacterium tuberculosis ( Mtb ) mutants lacking rv1411c , which encodes the lipoprotein LprG , and rv1410c , which encodes a putative efflux pump , are dramatically attenuated for growth in mice .",
"Here we show that loss of LprG-Rv1410 in Mtb leads to intracellular triacylglyceride ( TAG ) accumulation , an... | [
"Of the estimated 2 billion people worldwide currently infected with Mycobacterium tuberculosis ( Mtb ) , surprisingly few go on to develop active tuberculosis ( TB ) disease .",
"The vast majority , 95 percent , of infected individuals develop latent TB , remaining infected but without disease .",
"Despite its... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"cryptococcus gattii",
"medicine and health sciences",
"cryptococcus",
"pathology and laboratory medicine",
"pathogens",
"population genetics",
"geographical locations",
"microbiology",
"north america",
"fungi",
"phylogenetic analysis",
"molecular biology techniques"... | Population Genetic Analysis Reveals a High Genetic Diversity in the Brazilian Cryptococcus gattii VGII Population and Shifts the Global Origin from the Amazon Rainforest to the Semi-arid Desert in the Northeast of Brazil | journal.pntd.0004885 | null | [
[
"Cryptococcosis is a life-threatening mycosis with high lethality rates , especially in underdeveloped countries [1] .",
"Infection occurs via the respiratory route by inhalation of infectious propagules ( desiccated yeast cells or basidiospores ) of Cryptococcus neoformans and C . gattii , frequently spr... | [
"Cryptococcus neoformans and Cryptococcus gattii are responsible globally for almost one million cryptococcosis cases yearly , mostly in immunocompromised patients , such as those living with HIV .",
"Infections due to C . gattii have mainly been described in tropical and subtropical regions , but its adaptation ... | [
"Cryptococcus neoformans and Cryptococcus gattii are fungal agents responsible globally for almost one million cryptococcosis cases yearly , mostly in immunocompromised patients , such as those living with HIV .",
"Cryptococcosis is a life-threatening mycosis , frequently causing meningoencephalitis .",
"Infect... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"tropical diseases",
"geographical locations",
"surgical and invasive medical procedures",
"bacterial diseases",
"signs and symptoms",
"ulcers",
"neglected tropical diseases",
"molecular biology techniques",
"bacteria",
"afri... | Laboratory confirmation of Buruli ulcer cases in Ghana, 2008-2016 | journal.pntd.0006560 | null | [
[
"Buruli ulcer ( BU ) , a necrotizing skin and soft tissue disease , is caused by the environmental pathogen Mycobacterium ulcerans .",
"BU is the third most important mycobacterial disease after tuberculosis and leprosy in immunocompetent individuals [1] .",
"Currently , BU has been reported in 33 cou... | [
"Buruli ulcer ( BU ) , a necrotizing skin infection caused by Mycobacterium ulcerans is the third most important mycobacterial disease globally after tuberculosis and leprosy in immune competent individuals .",
"This study reports on the retrospective analyses of microbiologically confirmed Buruli ulcer ( BU ) ca... | [
"Buruli ulcer ( BU ) , a necrotizing skin disease caused by Mycobacterium ulcerans , is currently reported in 33 countries , with the greatest disease burden mostly in West African countries along the gulf of Guinea .",
"The lack of pain associated with BU disease enhances delay in seeking medical treatment that ... | 2018 |
[
"Introduction",
"Material and Methods",
"Results",
"Discussion"
] | [] | Altered Protein Expression in the Ileum of Mice Associated with the Development of Chronic Infections with Echinostoma caproni (Trematoda) | journal.pntd.0004082 | null | [
[
"Intestinal helminth infections are among the most prevalent parasitic diseases .",
"Recent studies have estimated that about 1 billion people are currently infected with at least one species of intestinal helminth mainly in developing regions of Asia , Africa and Latin-America [1] .",
"Although intes... | [
"Echinostoma caproni ( Trematoda: Echinostomatidae ) is an intestinal trematode that has been extensively used as experimental model to investigate the factors determining the expulsion of intestinal helminths or , in contrast , the development of chronic infections .",
"Herein , we analyze the changes in protein... | [
"Intestinal helminth infections are among the most prevalent parasitic diseases and about 1 billion people are currently infected with intestinal helminths .",
"Incidence of intestinal helminth infections is high due to both socio-economic factors that facilitates continuous re-infections and the lack of effectiv... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/hiv infection and aids"
] | Structural Basis of HIV-1 Neutralization by Affinity Matured Fabs Directed against the Internal Trimeric Coiled-Coil of gp41 | journal.ppat.1001182 | null | [
[
"The initial steps of fusion of HIV-1 virus to host cells involve binding of the HIV-1 surface envelope ( Env ) glycoprotein gp120 to the primary receptor CD4 and the chemokine co-receptor CXCR4 or CCR5 [1] , [2] .",
"These binding events trigger a series of conformational changes in both gp120 and the as... | [
"The conserved internal trimeric coiled-coil of the N-heptad repeat ( N-HR ) of HIV-1 gp41 is transiently exposed during the fusion process by forming a pre-hairpin intermediate , thus representing an attractive target for the design of fusion inhibitors and neutralizing antibodies .",
"In previous studies we rep... | [
"Membrane fusion of HIV-1 with its target cells represents the first step in viral infection .",
"This process involves a series of conformational changes in two viral envelope glycoproteins , gp120 and gp41 , subsequent to binding of gp120 to the CD4 receptor and the chemokine coreceptor on the target cell membr... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/alternative splicing",
"computational biology/genomics"
] | Genome-Wide Association between Branch Point Properties and Alternative Splicing | journal.pcbi.1001016 | null | [
[
"Pre-mRNA splicing , which is essential for the production of functional mRNAs , is a co-transcriptional set of reactions catalyzed by a large ribonucleoprotein complex – the spliceosome – composed by five small nuclear RNAs ( snRNAs ) and more than hundred proteins [1] , [2] .",
"In addition to these cor... | [
"The branch point ( BP ) is one of the three obligatory signals required for pre-mRNA splicing .",
"In mammals , the degeneracy of the motif combined with the lack of a large set of experimentally verified BPs complicates the task of modeling it in silico , and therefore of predicting the location of natural BPs ... | [
"From transcription to translation , the events underlying protein production from DNA sequence are paramount to all aspects of cellular function .",
"Pre-mRNAs in eukaryotes undergo several processing steps prior to their export to the cytoplasm .",
"Among these , splicing – the process of intron removal and e... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"leptospirosis",
"bacterial diseases",
"infectious diseases",
"veterinary diseases",
"zoonoses",
"medicine and health sciences",
"environmental epidemiology",
"epidemiology",
"infectious disease epidemiology",
"neglected tropical diseases",
"biology and life sciences",
"population biology",
... | Prospective Study of Leptospirosis Transmission in an Urban Slum Community: Role of Poor Environment in Repeated Exposures to the Leptospira Agent | journal.pntd.0002927 | null | [
[
"Leptospirosis is a bacterial disease that has emerged as a major health problem in the developing world [1] .",
"The disease is caused by a spirochete from the genus Leptospira , which colonizes the kidney of a wide range of mammals [2] .",
"Human infection occurs after direct contact with an infecte... | [
"Leptospirosis has emerged as an urban health problem as slum settlements have rapidly spread worldwide and created conditions for rat-borne transmission .",
"Prospective studies have not been performed to determine the disease burden , identify risk factors for infection and provide information needed to guide i... | [
"Leptospirosis is a disease that is transmitted by human contact with an environment contaminated with urine from animals , such as rodents , infected by the Leptospira bacteria .",
"Human illness due to these bacteria can be mild , or can have very severe complications .",
"Residents of urban slum settlements ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"crystal structure",
"pathology and laboratory medicine",
"protein interactions",
"chemical compounds",
"enzymes",
"pathogens",
"condensed matter physics",
"enzymology",
"microbiology",
"organic compounds",
"retroviruses",
"viruses",
"immunodeficiency viruse... | MFPred: Rapid and accurate prediction of protein-peptide recognition multispecificity using self-consistent mean field theory | journal.pcbi.1005614 | null | [
[
"Many natural proteins , including signal transduction hubs and enzymes that process biological information , have evolved to be multispecific–they participate in specific interactions with several interaction partners [1 , 2] .",
"Evolution of multispecificity includes selection for both positive and neg... | [
"Multispecificity–the ability of a single receptor protein molecule to interact with multiple substrates–is a hallmark of molecular recognition at protein-protein and protein-peptide interfaces , including enzyme-substrate complexes .",
"The ability to perform structure-based prediction of multispecificity would ... | [
"Across biology , many proteins that recognize peptides are multispecific; they interact with multiple binding partners of disparate sequence .",
"Computational prediction of these multiple peptide partners would enable greater understanding of individual protein-recognition domains .",
"Additionally , the abil... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genomics",
"biology",
"computational biology"
] | Genomic Hypomethylation in the Human Germline Associates with Selective Structural Mutability in the Human Genome | journal.pgen.1002692 | null | [
[
"Array comparative genomic hybridization ( aCGH ) studies [1] and massively parallel sequencing [2] revealed that approximately 10% of the human genome is structurally polymorphic at the submicroscopic scale ( <4 Mb ) , a much larger fraction than affected by single nucleotide polymorphisms ( SNPs ) .",
"... | [
"The hotspots of structural polymorphisms and structural mutability in the human genome remain to be explained mechanistically .",
"We examine associations of structural mutability with germline DNA methylation and with non-allelic homologous recombination ( NAHR ) mediated by low-copy repeats ( LCRs ) .",
"Com... | [
"The human genome contains many loci with high incidence of structural mutations , including insertions and deletions of chromosomal segments .",
"This excessive mutability has accelerated evolution and contributed to human disease but has yet to be explained .",
"Segments of DNA repeated in low-copy numbers ( ... | 2012 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"blood cells",
"phosphorylation",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"cytokines",
"immunology",
"parasitic diseases",
"parasitic protozoans",
"physiological processes",
"developmental biology",
"protozoans",
"leishmania",
"molecul... | Sphingosine-1-phosphate signaling in Leishmania donovani infection in macrophages | journal.pntd.0006647 | null | [
[
"Leishmaniasis is a neglected tropical disease that affects about 12 million people worldwide [1] It is caused by intracellular protozoa parasite Leishmania that invades macrophages and selectively impairs host’s critical signaling pathways for its successful intracellular growth and proliferation [2] .",
... | [
"Sphingosine-1-phosphate ( S1P ) is a crucial regulator of a wide array of cellular processes , such as apoptosis , cell proliferation , migration , and differentiation , but its role in Leishmania donovani infection is unknown .",
"In the present study , we observed that L . donovani infection in THP-1 derived m... | [
"Leishmania donovani is an intracellular parasite which is internalized by host macrophages by subverting several intracellular signaling events .",
"During infection suppression of p38 MAPK and activation of ERK1/2 MAPK have been acclaimed for survival and proliferation of these protozoan parasites .",
"In thi... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/cell growth and division",
"cell biology",
"cell biology/cytoskeleton"
] | Fission Yeast Cells Undergo Nuclear Division in the Absence of Spindle Microtubules | journal.pbio.1000512 | Through a previously undescribed mechanism, fission yeast cells can undergo nuclear division and enter the next cell cycle, even in the absence of spindle microtubules. | [
[
"Mitosis is a feature of all known eukaryotic cells , essential for the generation of viable progeny .",
"Upon entry into mitosis the duplicated centrosomes that serve as microtubule organizing centers separate and organize a bipolar array of spindle microtubules .",
"Microtubules are essential for ch... | [
"Mitosis in eukaryotic cells employs spindle microtubules to drive accurate chromosome segregation at cell division .",
"Cells lacking spindle microtubules arrest in mitosis due to a spindle checkpoint that delays mitotic progression until all chromosomes have achieved stable bipolar attachment to spindle microtu... | [
"The process of cell division , mitosis , ensures that chromosomes are accurately segregated to generate two daughter cells , each with a complete genome .",
"Eukaryotic cells use a microtubule-based mitotic spindle to ensure proper chromosome segregation .",
"In the fission yeast Schizosaccharomyces pombe , mi... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology",
"eukaryotes",
"molecular biology",
"genetics and genomics",
"saccharomyces"
] | Alternative 3′ Pre-mRNA Processing in Saccharomyces cerevisiae Is Modulated by Nab4/Hrp1 In Vivo | journal.pbio.0050006 | The authors show that alternative 3′ pre-mRNA processing helps control gene expression as part of a physiological response inS. cerevisiae. | [
[
"3′ pre-mRNA processing severs the nascent transcript from the elongating polymerase to liberate a new polyadenylated mRNP particle [1 , 2] .",
"Since the placement of the cleavage site can include or remove RNA sequences that influence transcript stability , transcript localization , protein expression ,... | [
"The Saccharomyces cerevisiae RNA-binding protein Nab4/Hrp1 is a component of the cleavage factor complex required for 3′ pre-mRNA processing .",
"Although the precise role of Nab4/Hrp1 remains unclear , it has been implicated in correct positioning of the cleavage site in vitro .",
"Here , we show that mutatio... | [
"A fundamental step in gene expression is the generation of the terminal edge ( 3′ end ) of the mRNA transcript by appropriate cleavage of the longer pre-mRNA .",
"In general , the processing site that emerges first is used , but there are interesting examples where alternative sites are used .",
"Because the c... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis",
"infectious diseases/respiratory infections"
] | PerR Confers Phagocytic Killing Resistance and Allows Pharyngeal Colonization by Group A Streptococcus | journal.ppat.1000145 | null | [
[
"Group A Streptococcus ( Streptococcus pyogenes or GAS ) is a strictly human pathogen that causes a spectrum of disease ranging from superficial infection of the pharyngeal mucosa and the skin to invasive infection of deep tissues and the bloodstream .",
"Like other lactic acid bacteria , GAS lacks oxidat... | [
"The peroxide response transcriptional regulator , PerR , is thought to contribute to virulence of group A Streptococcus ( GAS ) ; however , the specific mechanism through which it enhances adaptation for survival in the human host remains unknown .",
"Here , we identify a critical role of PerR-regulated gene exp... | [
"Group A Streptococcus ( GAS ) is the leading cause of bacterial pharyngitis ( strep throat ) in children .",
"It is also associated with the life-threatening conditions of necrotizing fasciitis , streptococcal toxic shock , and the post-streptococcal autoimmune syndrome of rheumatic fever and heart disease .",
... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results and Discussions"
] | [
"viruses",
"infectious diseases",
"infectious diseases of the nervous system",
"medicine and health sciences",
"japanese encephalitis",
"rna viruses",
"viral classification",
"virology",
"dengue fever",
"neglected tropical diseases",
"biology and life sciences",
"tropical diseases",
"microbi... | The Interface between Methyltransferase and Polymerase of NS5 Is Essential for Flavivirus Replication | journal.pntd.0002891 | null | [
[
"The genus of Flavivirus within the family Flaviviridae contains large amounts of arthropod-borne viruses , which includes Japanese encephalitis virus ( JEV ) , West Nile virus ( WNV ) , Dengue virus ( DENV ) , Tick-borne encephalitis virus ( TBEV ) and yellow fever virus ( YFV ) [1] .",
"Most of these vi... | [
"The flavivirus NS5 harbors both a methyltransferase ( MTase ) and an RNA-dependent RNA polymerase ( RdRP ) .",
"Both enzyme activities of NS5 are critical for viral replication .",
"Recently , the full-length NS5 crystal structure of Japanese encephalitis virus reveals a conserved MTase-RdRP interface that fea... | [
"Flaviviruses , such as Japanese encephalitis virus ( JEV ) and dengue virus 1-4 ( DENV1-4 ) , are important arthropod-borne pathogens causing major public health threats worldwide .",
"For example , JEV is the most common cause of viral encephalitis in eastern and southern Asia , affecting over 50 , 000 patients... | 2014 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"kala-azar",
"medicine and health sciences",
"pathology and laboratory medicine",
"tropical diseases",
"geographical locations",
"india",
"parasitic diseases",
"signs and symptoms",
"neglected tropical diseases",
"public and occupational health",
"infectious diseases",
"zoonoses",
"epidemiol... | Active surveillance identified a neglected burden of macular cases of Post Kala-azar Dermal Leishmaniasis in West Bengal | journal.pntd.0007249 | null | [
[
"Leishmaniasis are a group of neglected tropical diseases caused by the parasite Leishmania and demonstrates clinical pleomorphism with regard to the causative species , disease reservoirs , vectors as also host-immune responses .",
"It can manifest as life-threatening and/or disfiguring lesions ranging f... | [
"Post Kala-azar Dermal Leishmaniasis ( PKDL ) develops in patients apparently cured of Visceral Leishmaniasis ( VL ) , and is the strongest contender for being the disease reservoir .",
"Therefore , existence of a few cases is sufficient to trigger an epidemic of VL in a given community , emphasizing the need for... | [
"Post Kala-azar Dermal Leishmaniasis ( PKDL ) is a dermal condition that occurs in South Asia in 10–20% of patients after apparent cure from Visceral Leishmaniasis ( VL ) .",
"It presents with macular or papulonodular lesions that harbor Leishmania parasites , thus playing a major role in the transmission cycle .... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"zoology",
"genetics",
"biology",
"microbiology"
] | Wolbachia-Associated Bacterial Protection in the Mosquito Aedes aegypti | journal.pntd.0002362 | null | [
[
"Wolbachia pipientis is a maternally inherited intracellular bacterium that is found in a wide range of arthropod species and filarial nematodes , with approximately 40% of insect species infected [1] .",
"Wolbachia spreads rapidly through populations and to high frequencies by inducing a range of manipul... | [
"Wolbachia infections confer protection for their insect hosts against a range of pathogens including bacteria , viruses , nematodes and the malaria parasite .",
"A single mechanism that might explain this broad-based pathogen protection is immune priming , in which the presence of the symbiont upregulates the ba... | [
"Wolbachia is a commonly occurring bacterium or symbiont that lives inside the cells of insects .",
"Recently , Wolbachia was artificially introduced into the mosquito vector dengue virus that was naturally Wolbachia-free .",
"Wolbachia limits the growth of a range of pathogens transmitted to humans , including... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology",
"signaling in selected disciplines",
"histone modification",
"plant science",
"model organisms",
"developmental signaling",
"plant ecology",
"chromatin",
"arabidopsis thaliana",
"plant signaling",
"gene expression",
"plant genetics",
"biology",
"molecular biology",
"sign... | Histone H2B Monoubiquitination Facilitates the Rapid Modulation of Gene Expression during Arabidopsis Photomorphogenesis | journal.pgen.1002825 | null | [
[
"To assess the contribution of chromatin state variations to development and phenotypic plasticity , evaluation of the role of histone post-translational modifications in the regulation of genome expression dynamics represents an important objective .",
"A first step requires the establishment of a refere... | [
"Profiling of DNA and histone modifications has recently allowed the establishment of reference epigenomes from several model organisms .",
"This identified a major chromatin state for active genes that contains monoubiquitinated H2B ( H2Bub ) , a mark linked to transcription elongation .",
"However , assessmen... | [
"In eukaryotes , chromatin-based mechanisms overlay with DNA sequence information to determine the transcriptional output of the genome .",
"Evaluating the role of chromatin state variations in the regulation of gene expression is therefore key to understanding their contribution to development .",
"Several tra... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology",
"infectious diseases",
"plasmodium"
] | Plasmodium falciparum Uses gC1qR/HABP1/p32 as a Receptor to Bind to Vascular Endothelium and for Platelet-Mediated Clumping | journal.ppat.0030130 | null | [
[
"Malaria continues to be a major public health problem in many parts of the tropical world , with approximately 500 million malaria cases reported annually that result in 1–2 million deaths every year [1 , 2] .",
"Deaths from malaria mainly occur in young children living in sub-Saharan Africa and are caus... | [
"The ability of Plasmodium falciparum–infected red blood cells ( IRBCs ) to bind to vascular endothelium , thus enabling sequestration in vital host organs , is an important pathogenic mechanism in malaria .",
"Adhesion of P . falciparum IRBCs to platelets , which results in the formation of IRBC clumps , is anot... | [
"Adhesion of Plasmodium falciparum–infected red blood cells ( IRBCs ) to the endothelium lining the capillaries of vital host organs can obstruct blood circulation and is an important pathogenic mechanism in malaria .",
"Adhesion of P . falciparum IRBCs to platelets results in the formation of IRBC clumps that ca... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"public health and epidemiology",
"microbiology",
"bacterial diseases",
"emerging infectious diseases",
"neglected tropical diseases",
"applied microbiology",
"infectious diseases",
"buruli ulcer",
"mycobacterium",
"epidemiology",
"biology",
"microbial ecology",
"protozoology"
... | Amoebae as Potential Environmental Hosts for Mycobacterium ulcerans and Other Mycobacteria, but Doubtful Actors in Buruli Ulcer Epidemiology | journal.pntd.0001764 | null | [
[
"Most mycobacteria are environmental opportunistic species that only occasionally infect humans [1] .",
"Only few mycobacterial species are known to be obligate parasites , such as Mycobacterium tuberculosis and M . leprae , the causative agents of tuberculosis and leprosy respectively .",
"The third ... | [
"The reservoir and mode of transmission of Mycobacterium ulcerans , the causative agent of Buruli ulcer , remain unknown .",
"Ecological , genetic and epidemiological information nonetheless suggests that M . ulcerans may reside in aquatic protozoa .",
"We experimentally infected Acanthamoeba polyphaga with M .... | [
"Buruli ulcer ( BU ) is a devastating skin disease caused by Mycobacterium ulcerans , an environmental bacterium that is probably linked to slow-running water .",
"It is unlikely to occur free-living , but even though M . ulcerans DNA has been detected in quite a few different organisms ( with most studies focusi... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunopathology",
"medicine",
"pulmonology",
"virology",
"immunology",
"biology",
"microbiology",
"host-pathogen interaction",
"immunomodulation",
"respiratory medicine",
"hematology"
] | Plasminogen Controls Inflammation and Pathogenesis of Influenza Virus Infections via Fibrinolysis | journal.ppat.1003229 | null | [
[
"Influenza A viruses ( IAV ) are an important cause of outbreaks of respiratory tract infections and are responsible for significant morbidity and mortality in the human population [1] .",
"Upon infection with IAV , innate and adaptive immune responses are induced that restrict viral replication and that ... | [
"Detrimental inflammation of the lungs is a hallmark of severe influenza virus infections .",
"Endothelial cells are the source of cytokine amplification , although mechanisms underlying this process are unknown .",
"Here , using combined pharmacological and gene-deletion approaches , we show that plasminogen c... | [
"Influenza viruses , including H5N1 bird influenza viruses continue to form a major threat for public health .",
"Available antiviral drugs for the treatment of influenza are effective to a limited extent and the emergence of resistant viruses may further undermine their use .",
"The symptoms associated with in... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell motility",
"parasite groups",
"medicine and health sciences",
"viral transmission and infection",
"enzymes",
"microbiology",
"enzymology",
"parasitic diseases",
"parasitic protozoans",
"in vivo imaging",
"parasitology",
"apicomplexa",
"tachyzoites",
"protozoans",
"toxoplasma",
"r... | Protein kinase A negatively regulates Ca2+ signalling in Toxoplasma gondii | journal.pbio.2005642 | null | [
[
"The phylum Apicomplexa comprises a large group of obligate intracellular parasites that cause many important human and livestock diseases and includes Plasmodium spp .",
"( malaria ) , Cryptosporidium spp .",
"( severe diarrhoea ) , and Toxoplasma gondii ( toxoplasmosis ) .",
"Toxoplasma is trans... | [
"The phylum Apicomplexa comprises a group of obligate intracellular parasites that alternate between intracellular replicating stages and actively motile extracellular forms that move through tissue .",
"Parasite cytosolic Ca2+ signalling activates motility , but how this is switched off after invasion is complet... | [
"Central to pathogenesis and infectivity of Toxoplasma and related parasites is their ability to move through tissue , invade host cells , and establish a replicative niche .",
"Ca2+-dependent signalling pathways are important for activating motility , host cell invasion , and egress , yet how this signalling is ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bioengineering",
"systems biology",
"biomedical engineering",
"medicine",
"oncology",
"forms of evolution",
"microevolution",
"immune evasion",
"immunotherapy",
"basic cancer research",
"cancer treatment",
"biology",
"computational biology",
"evolutionary biology",
"engineering"
] | Induction of Wnt-Inducible Signaling Protein-1 Correlates with Invasive Breast Cancer Oncogenesis and Reduced Type 1 Cell-Mediated Cytotoxic Immunity: A Retrospective Study | journal.pcbi.1003409 | null | [
[
"The discovery of molecular targeted therapies revolutionized the treatment of breast cancer .",
"Tamoxifen , a small molecule inhibitor of the estrogen receptor , was the first drug to inhibit the growth of breast cancer cells that depend on female sex hormones .",
"More recently , trastuzumab was de... | [
"Innate and type 1 cell-mediated cytotoxic immunity function as important extracellular control mechanisms that maintain cellular homeostasis .",
"Interleukin-12 ( IL12 ) is an important cytokine that links innate immunity with type 1 cell-mediated cytotoxic immunity .",
"We recently observed in vitro that tumo... | [
"Effective anti-tumor immunity is proportional to the number and to the cytotoxic activity of immune cells that enter the tumor microenvironment .",
"Recent advances in cancer immunotherapy stem from increasing the number of tumor-infiltrating immune cells by inhibiting immune checkpoints or adoptive T cell thera... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine",
"infectious diseases",
"immune cells",
"nk cells",
"immunology",
"cytomegalovirus infection",
"biology",
"viral diseases"
] | MicroRNA Editing Facilitates Immune Elimination of HCMV Infected Cells | journal.ppat.1003963 | null | [
[
"HCMV is a dsDNA herpesvirus , which is highly prevalent in the human population .",
"It establishes its life long latency by using a diverse panel of sophisticated immune evasion strategies , and specifically by manipulating the expression of Human Leukocyte Antigen ( HLA ) class I molecules [1]–[4] .",
... | [
"The human cytomegalovirus ( HCMV ) is extremely prevalent in the human population .",
"Infection by HCMV is life threatening in immune compromised individuals and in immune competent individuals it can cause severe birth defects , developmental retardation and is even associated with tumor development .",
"Whi... | [
"The human cytomegalovirus ( HCMV ) infects a high percentage of the human population .",
"HCMV infection is life threatening to immune-compromised individuals and when transmitted to the fetus can cause severe birth defects .",
"Thus , it is crucial to understand the anti-viral strategies that are induced in r... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"computational biology/macromolecular structure analysis",
"molecular biology/molecular evolution",
"computational biology/evolutionary modeling",
"molecular biology/bioinformatics",
"computational biology/macromolecular sequence analysis",
"evolutionary biology/bioinformatics"
] | Joint Evolutionary Trees: A Large-Scale Method To Predict Protein
Interfaces Based on Sequence Sampling | journal.pcbi.1000267 | null | [
[
"Interface residues are essential for understanding interaction mechanisms and are",
"often potential drug targets .",
"Reliable identification of residues that belong to a",
"protein-protein interface typically requires information on protein structures [1] and",
"knowledge of both partners .... | [
"The Joint Evolutionary Trees ( JET ) method detects protein interfaces , the core",
"residues involved in the folding process , and residues susceptible to",
"site-directed mutagenesis and relevant to molecular recognition .",
"The approach ,",
"based on the Evolutionary Trace ( ET ) method , introduces a ... | [
"Information obtained on the structure of macromolecular complexes is important",
"for identifying functionally important partners but also for determining how",
"such interactions will be perturbed by natural or engineered site mutations .",
"Hence , to fully understand or control biological processes we nee... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"dermatology",
"urology",
"medicine and health sciences",
"pathology and laboratory medicine",
"ultraviolet radiation",
"ears",
"immunology",
"immune suppression",
"cancers and neoplasms",
"light",
"electromagnetic radiation",
"oncology",
"animal models",
"otology",
"model organisms",
... | Role of Ultraviolet Radiation in Papillomavirus-Induced Disease | journal.ppat.1005664 | null | [
[
"Papillomaviruses are species-specific , epitheliotropic , double-stranded DNA viruses .",
"There are over 200 strains or genotypes of human papillomaviruses ( HPVs ) [1] .",
"Mucosotropic HPVs are the most common sexually transmitted pathogens , and a subset of these viruses cause 5% of human cancers... | [
"Human papillomaviruses are causally associated with 5% of human cancers .",
"The recent discovery of a papillomavirus ( MmuPV1 ) that infects laboratory mice provides unique opportunities to study the life cycle and pathogenesis of papillomaviruses in the context of a genetically manipulatable host organism .",
... | [
"Epidemiological studies have implicated that ultraviolet radiation ( UVR ) from sunlight drive papillomavirus-induced disease in healthy as well as immunocompromised humans .",
"In this report we demonstrate that treatment of immunocompetent mice with UVR renders them susceptible to papillomas and associated squ... | 2016 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"learning",
"organismal evolution",
"ecology and environmental sciences",
"hominin evolution",
"sociology",
"human evolution",
"social sciences",
"vertebrates",
"neuroscience",
"learning and memory",
"animals",
"mammals",
"primates",
"cultural evolution",
"cognitive psychology",
"anima... | The Cultural Brain Hypothesis: How culture drives brain expansion, sociality, and life history | journal.pcbi.1006504 | null | [
[
"In the last few million years , the cranial capacity of the human lineage dramatically increased , more than tripling in size [1–3] .",
"This rapid expansion may be part of a gradual and longer-term trend toward larger , more complex brains in many taxa [3–7] .",
"These patterns of increasing brain s... | [
"In the last few million years , the hominin brain more than tripled in size .",
"Comparisons across evolutionary lineages suggest that this expansion may be part of a broader trend toward larger , more complex brains in many taxa .",
"Efforts to understand the evolutionary forces driving brain expansion have f... | [
"Humans have extraordinarily large brains , which tripled in size in the last few million years .",
"Other animals also experienced a significant , though smaller , increase in brain size .",
"These increases are puzzling , because brain tissue is energetically expensive—a smaller brain is easier to maintain in... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"systems biology",
"biochemistry",
"genetics",
"biology",
"proteomics",
"molecular cell biology",
"genetics and genomics"
] | A Systematic Approach to Pair Secretory Cargo Receptors with Their Cargo Suggests a Mechanism for Cargo Selection by Erv14 | journal.pbio.1001329 | A systematic approach to visualize proteins exiting the endoplasmic reticulum paired with their cargo receptors identifies novel cargo for known receptors and reveals the mechanism of one conserved receptor, Erv14. | [
[
"The endoplasmic reticulum ( ER ) is the entry site into the secretory pathway , responsible for the folding , maturation , and trafficking of all secreted , membrane-bound , and secretory pathway resident proteins .",
"Once folded , the proteins exit the ER as cargo within COPII-coated vesicles that bud ... | [
"The endoplasmic reticulum ( ER ) is the site of synthesis of secreted and membrane proteins .",
"To exit the ER , proteins are packaged into COPII vesicles through direct interaction with the COPII coat or aided by specific cargo receptors .",
"Despite the fundamental role of such cargo receptors in protein tr... | [
"All cells sense their environment , respond to it , and communicate with neighboring cells .",
"To perform these functions , cells use an impressive array of proteins that they display on their surface membranes and secrete into their external environment .",
"Newly synthesized proteins destined for the surfac... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cardiomyopathies",
"medicine and health sciences",
"variant genotypes",
"tropical diseases",
"parasitic diseases",
"parasitic protozoans",
"genetic mapping",
"protozoans",
"neglected tropical diseases",
"cardiology",
"proteins",
"protozoan infections",
"trypanosoma cruzi",
"biochemistry",... | Human collectin-11 (COLEC11) and its synergic genetic interaction with MASP2 are associated with the pathophysiology of Chagas Disease | journal.pntd.0007324 | null | [
[
"Chagas Disease ( CD ) is a neglected anthropozoonosis in which classically the primary infection with the protozoan Trypanosoma cruzi , transmitted by blood-sucking bugs , can occur during early childhood and may continue clinically silent for decades [1 , 2] .",
"Approximately 30% of chronically infecte... | [
"Chagas Disease ( CD ) is an anthropozoonosis caused by Trypanosoma cruzi .",
"With complex pathophysiology and variable clinical presentation , CD outcome can be influenced by parasite persistence and the host immune response .",
"Complement activation is one of the primary defense mechanisms against pathogens... | [
"The heterogeneity of clinical progression during chronic Trypanosoma cruzi infection and the mechanisms determining why some individuals develop symptoms whereas others remain asymptomatic are still poorly understood .",
"The pathogenesis of chronic Chagas Disease ( CD ) has been attributed mainly to the persist... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [
"invertebrates",
"medicine and health sciences",
"pruritus",
"tropical diseases",
"geographical locations",
"social sciences",
"parasitic diseases",
"animals",
"neuroscience",
"parasitology",
"nematode infections",
"pharmaceutics",
"drug administration",
"neglected tropical diseases",
"e... | Comparison of different drug regimens for the treatment of loiasis—A TropNet retrospective study | journal.pntd.0006917 | null | [
[
"Loa loa is a filarial worm transmitted to the human hosts by the tabanid flies of the genus Chrysops .",
"Human loiasis occurs only in Africa , where the transmission is confined to the rainforests areas from south-eastern Benin in the west , South Sudan and Uganda in the east , North Angola in the south... | [
"Loa loa infection is endemic in limited areas of West-Central Africa .",
"Loiasis has been associated with excess mortality , but clinical studies on its treatment are scant , particularly outside endemic areas , due to the rarity of cases diagnosed .",
"With this retrospective TropNet ( European Network for T... | [
"Loa loa is a worm which infects millions of people living in wide forested areas of central Africa .",
"The infection is rarely diagnosed outside Africa , and cases are mainly referred to referral centers on tropical medicine .",
"Aim of this study was to describe the treatment and management of patients diagn... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Human Neutrophil Peptide-1 (HNP-1): A New Anti-Leishmanial Drug Candidate | journal.pntd.0002491 | null | [
[
"AMPs are small , cationic proteins which are found in a wide variety of organisms and function as key components of the innate immune system [1] , [2] .",
"They exhibit broad-spectrum anti-bacterial , anti-viral , anti-fungal and anti-parasitic activities and have low cytotoxicity to mammalian cells at c... | [
"The toxicity of available drugs for treatment of leishmaniasis , coupled with emerging drug resistance , make it urgent to find new therapies .",
"Antimicrobial peptides ( AMPs ) have a strong broad-spectrum antimicrobial activity with distinctive modes of action and are considered as promising therapeutic agent... | [
"In Iran , cutaneous leishmaniasis ( CL ) is a widespread and highly endemic disease in young individuals .",
"To date , treatment strategy is based on chemotherapy accompanied with high incidence of toxicity and drug resistance .",
"Distinctive mode of action of defensins ( members of antimicrobial peptides ) ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics"
] | Age- and Temperature-Dependent Somatic Mutation Accumulation in Drosophila melanogaster | journal.pgen.1000950 | null | [
[
"Aging is a complex process with an as yet unclear etiology and a - for most species - poorly described phenotype [1] .",
"Accumulation of somatic mutations , due to imperfect repair and maintenance , has since long been implicated as a universal , major cause of aging [2] , [3] , but proved difficult to ... | [
"Using a transgenic mouse model harboring a mutation reporter gene that can be efficiently recovered from genomic DNA , we previously demonstrated that mutations accumulate in aging mice in a tissue-specific manner .",
"Applying a recently developed , similar reporter-based assay in Drosophila melanogaster , we n... | [
"DNA mutations are changes in the DNA sequence , including basepair substitutions and genome rearrangements .",
"Mutations are inevitable and are a consequence of errors made in replicating DNA during cell division or repairing damage .",
"Aging is a complex process of functional decline and increased disease r... | 2010 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"taxonomy",
"invertebrates",
"parasite groups",
"medicine and health sciences",
"evolutionary biology",
"plasmodium",
"tropical diseases",
"parasitic diseases",
"animals",
"parasitic protozoans",
"parasitology",
"apicomplexa",
"phylogenetics",
"data management",
"protozoans",
"phylogen... | Phylogenetic analysis of simian Plasmodium spp. infecting Anopheles balabacensis Baisas in Sabah, Malaysia | journal.pntd.0005991 | null | [
[
"Anopheles species of the Leucosphyrus group have been identified as medically important vectors in Southeast Asia region [1 , 2] .",
"The Leucosphyrus group has three main subgroups; Hackeri , Leucosphyrus and Riparis subgroups [3] , with the Leucosphyrus subgroup further divided into Dirus complex and L... | [
"Anopheles balabacensis of the Leucospyrus group has been confirmed as the primary knowlesi malaria vector in Sabah , Malaysian Borneo for some time now .",
"Presently , knowlesi malaria is the only zoonotic simian malaria in Malaysia with a high prevalence recorded in the states of Sabah and Sarawak .",
"Anoph... | [
"Anopheles balabacensis has been incriminated as the primary vector of zoonotic simian malaria , P . knowlesi in Malaysian Borneo with a high prevalence recorded in the states of Sabah and Sarawak .",
"In this study , Anopheles spp .",
"were sampled using human landing catch ( HLC ) method at Paradason village ... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"classical mechanics",
"nervous system",
"electrophysiology",
"neuroscience",
"simulation and modeling",
"membrane proteins",
"mathematics",
"statistics (mathematics)",
"reflection",
"cellular structures and organelles",
"research and analysis methods",
"prote... | Self-crowding of AMPA receptors in the excitatory postsynaptic density can effectuate anomalous receptor sub-diffusion | journal.pcbi.1005984 | null | [
[
"Glutamate-binding transmembrane alpha-amino-3-hydroxy-5-methyl-4-isoxazole-propionic acid ( AMPA ) -type receptors ( AMPARs ) are the pivotal element of fast synaptic transmission at excitatory synapses in the central nervous system [1 , 2] .",
"At the site of synaptic contact , these receptors are prese... | [
"AMPA receptors ( AMPARs ) and their associations with auxiliary transmembrane proteins are bulky structures with large steric-exclusion volumes .",
"Hence , self-crowding of AMPARs , depending on the local density , may affect their lateral diffusion in the postsynaptic membrane as well as in the highly crowded ... | [
"The transmembrane AMPA receptors ( AMPARs ) prominently exhibit lateral diffusion in the postsynaptic membrane at excitatory synapses .",
"Steric obstructions to AMPAR diffusion due to the crowd of other relatively static transmembrane proteins and binding of AMPARs to the submembranous scaffold proteins in the ... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public and occupational health",
"infectious diseases",
"geography",
"medicine and health sciences",
"global health",
"earth sciences",
"social sciences"
] | Strengths and Weaknesses of Global Positioning System (GPS) Data-Loggers and Semi-structured Interviews for Capturing Fine-scale Human Mobility: Findings from Iquitos, Peru | journal.pntd.0002888 | null | [
[
"Knowledge of daily and routine individual human mobility patterns within urban settings are important for urban planning [1]–[3] , developing transportation models [3] , promoting healthy lifestyles [4] , and understanding infectious disease dynamics [5]–[13] .",
"Measuring mobility at fine spatial and t... | [
"Quantifying human mobility has significant consequences for studying physical activity , exposure to pathogens , and generating more realistic infectious disease models .",
"Location-aware technologies such as Global Positioning System ( GPS ) -enabled devices are used increasingly as a gold standard for mobilit... | [
"Being able to quantify human movement is important for studying activity patterns , exposure to pathogens and developing realistic infectious disease models .",
"We compared fine-scale human mobility data obtained by Global Positioning System ( GPS ) -enabled devices and semi-structured interviews ( SSI ) from 1... | 2014 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"homo sapiens",
"genetics and genomics",
"computational biology"
] | A First Look at ARFome: Dual-Coding Genes in Mammalian Genomes | journal.pcbi.0030091 | null | [
[
"Any stretch of DNA contains six reading frames and can potentially code for multiple proteins .",
"Situations when two partially overlapping reading frames code for functional polypeptides ( dual coding ) are quite common in bacteriophages and viruses ( e . g . , φX174 , HIV-1 , hepatitis C , or influenz... | [
"Coding of multiple proteins by overlapping reading frames is not a feature one would associate with eukaryotic genes .",
"Indeed , codependency between codons of overlapping protein-coding regions imposes a unique set of evolutionary constraints , making it a costly arrangement .",
"Yet in cases of tightly coe... | [
"A textbook human gene encodes a protein using a single reading frame .",
"Alternative splicing brings some variation to that picture , but the notion of a single reading frame remains .",
"Although this is true for most of our genes , there are exceptions .",
"Like viral counterparts , some eukaryotic genes ... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"immune cells",
"viral transmission and infection",
"immunology",
"microbiology",
"gene expression",
"t cells",
"biology",
"jurkat cells",
"molecular biology",
"host cells",
"cell biology",
"clinical immunology",
"virology",
"protein translation",
"genetics",
"cellular ty... | Granzyme B Inhibits Vaccinia Virus Production through Proteolytic Cleavage of Eukaryotic Initiation Factor 4 Gamma 3 | journal.ppat.1002447 | null | [
[
"One major strategy of the host to survive the attack of viruses is to induce apoptosis in infected host cells .",
"Cytotoxic T-lymphocytes ( CTLs ) play an important role in the apoptosis pathway , which activates a family of cytosolic proteins called caspases in target cells .",
"When caspases are a... | [
"Cytotoxic T lymphocytes ( CTLs ) are the major killer of virus-infected cells .",
"Granzyme B ( GrB ) from CTLs induces apoptosis in target cells by cleavage and activation of substrates like caspase-3 and Bid .",
"However , while undergoing apoptosis , cells are still capable of producing infectious viruses u... | [
"Lymphocytes , a type of white blood cell , are the major killer of virus-infected cells .",
"Lymphocytes secrete proteins like granzyme B that are responsible for the destruction of the virus-infected host cell .",
"However , killing an infected cell through this pathway may take several hours , thus allowing ... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"animal types",
"medicine and health sciences",
"infectious disease epidemiology",
"binomials",
"domestic animals",
"tropical diseases",
"geographical locations",
"vertebrates",
"dogs",
"animals",
"mammals",
"rabies",
"mathematics",
"algebra",
"network analysis",
"neglected tropical di... | High-resolution contact networks of free-ranging domestic dogs Canis familiaris and implications for transmission of infection | journal.pntd.0007565 | null | [
[
"Heterogeneity in contact rates is influential in the epidemiology of both human and non-human animal diseases .",
"In principle , variation in the contact rates among individuals affects their risk of acquiring and/or transmitting infections [1 , 2] .",
"Relationships between host social behaviour an... | [
"Contact patterns strongly influence the dynamics of disease transmission in both human and non-human animal populations .",
"Domestic dogs Canis familiaris are a social species and are a reservoir for several zoonotic infections , yet few studies have empirically determined contact patterns within dog population... | [
"For communicable infections , variations in contact rates determine the flow of disease through populations .",
"Therefore , describing contact patterns within populations could help to better predict and prevent disease outbreaks .",
"Free-ranging domestic dogs are susceptible to a number of zoonotic infectio... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"preclinical models",
"hiv diagnosis and management",
"clinical research design",
"immunity",
"hiv",
"drugs and devices",
"hiv clinical manifestations",
"immunology",
"drug distribution",
"biology",
"viral diseases",
"infectious disease modeling",
"phar... | Targeted Cytotoxic Therapy Kills Persisting HIV Infected Cells During ART | journal.ppat.1003872 | null | [
[
"ART is a lifesaving and effective means to control HIV infection [1] .",
"However , the persistent nature of this infection requires lifelong adherence to daily ART dosing [2]–[4] .",
"This viral persistence , the cumulative costs of ART , adverse events associated with long-term ART and the constant... | [
"Antiretroviral therapy ( ART ) can reduce HIV levels in plasma to undetectable levels , but rather little is known about the effects of ART outside of the peripheral blood regarding persistent virus production in tissue reservoirs .",
"Understanding the dynamics of ART-induced reductions in viral RNA ( vRNA ) le... | [
"Antiretroviral therapy ( ART ) improves the quality of life for HIV infected individuals .",
"However , ART is currently a lifelong commitment because HIV persists during treatment despite being suppressed below detection .",
"If therapy is stopped , the HIV reappears .",
"A concerted effort is ongoing to de... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"epidemiological statistics",
"public and occupational health",
"bacterial diseases",
"infectious diseases",
"medicine and health sciences",
"disabilities",
"epidemiology",
"leprosy",
"neglected tropical diseases",
"tropical diseases",
"epidemiological methods and statistics"
] | The Cultural Validation of Two Scales to Assess Social Stigma in Leprosy | journal.pntd.0003274 | null | [
[
"The framework for cross-cultural equivalence testing used in this study , draws entirely on the work of Herdman et al [25] , [30] , Terwee et al [26] and Stevelink & van Brakel [29] .",
"Five equivalences and the universalist approach are important for this study .",
"Herdman et al note that a univer... | [
"Stigma plays in an important role in the lives of persons affected by neglected tropical diseases , and assessment of stigma is important to document this .",
"The aim of this study is to test the cross-cultural validity of the Community Stigma Scale ( EMIC-CSS ) and the Social Distance Scale ( SDS ) in the fiel... | [
"Persons affected by neglected tropical diseases , such as , Buruli ulcer , lymphatic filariasis , onchocerciasis , leishmaniasis and leprosy , can experience stigma .",
"One important source of stigma are members in the community .",
"Neighbours , religious leaders , and community leaders can exclude , reject ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"plant anatomy",
"protein interactions",
"molecular probe techniques",
"microbiology",
"fluorophotometry",
"northern blot",
"fungi",
"plant science",
"model organisms",
"experimental organism systems",
"molecular biology techniques",
"gel electrophoresis",
"research and analysis methods",
... | Co-opting ATP-generating glycolytic enzyme PGK1 phosphoglycerate kinase facilitates the assembly of viral replicase complexes | journal.ppat.1006689 | null | [
[
"Positive-strand ( + ) RNA viruses build robust viral replication machineries , called replication organelles , with the help of many co-opted cellular factors .",
"In addition , viruses also obtain metabolites and energy from the infected cells .",
"Overall , ( + ) RNA viruses induce major metabolic ... | [
"The intricate interactions between viruses and hosts include exploitation of host cells for viral replication by using many cellular resources , metabolites and energy .",
"Tomato bushy stunt virus ( TBSV ) , similar to other ( + ) RNA viruses , induces major changes in infected cells that lead to the formation ... | [
"Positive-strand ( + ) RNA viruses build replication organelles with the help of many co-opted cellular factors and by usurping cellular metabolites and energy , which frequently lead to disease states in plants , animals and humans .",
"The authors discovered that tomato bushy stunt virus ( TBSV ) co-opts the gl... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods",
"Availability of supporting materials"
] | [
"chemical compounds",
"neural networks",
"neuroscience",
"optimization",
"mathematics",
"mapk signaling cascades",
"discrete mathematics",
"combinatorics",
"computer and information sciences",
"cluster compounds",
"gene expression",
"chemistry",
"signal transduction",
"permutation",
"dat... | Representing high throughput expression profiles via perturbation barcodes reveals compound targets | journal.pcbi.1005335 | null | [
[
"Pharmacology is generally explored in a linear and iterative manner , starting from the observation of an activity , that is then optimized for selectivity and potency via various methods , and subsequently tested in preclinical and randomized controlled clinical studies for safety and efficacy .",
"In g... | [
"High throughput mRNA expression profiling can be used to characterize the response of cell culture models to perturbations such as pharmacologic modulators and genetic perturbations .",
"As profiling campaigns expand in scope , it is important to homogenize , summarize , and analyze the resulting data in a manne... | [
"The effects of small molecules or biologics can be measured via their effect on cells’ gene expression profiles .",
"Such experiments have been performed with small , focused sample sets for decades .",
"Technological advances now permit this approach to be used on the scale of tens of thousands of samples per... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"cell motility",
"caenorhabditis",
"neuroscience",
"animals",
"gene function",
"animal models",
"developmental biology",
"mutation",
"caenorhabditis elegans",
"model organisms",
"organism development",
"molecular development",
"molecular genetics",
"body plan organizatio... | Netrins and Wnts Function Redundantly to Regulate Antero-Posterior and Dorso-Ventral Guidance in C. elegans | journal.pgen.1004381 | null | [
[
"Migrating cells and axons respond to a multitude of extracellular cues encountered along their migratory paths .",
"These include secreted cues such as Netrins , which are known to guide migrating cells and axons along the D/V axis of invertebrates and the vertebrate spinal cord [1]–[3] , and Wnts , whic... | [
"Guided migrations of cells and developing axons along the dorso-ventral ( D/V ) and antero-posterior ( A/P ) body axes govern tissue patterning and neuronal connections .",
"In C . elegans , as in vertebrates , D/V and A/P graded distributions of UNC-6/Netrin and Wnts , respectively , provide instructive polarit... | [
"While ample information was gathered in past decades on identifying guidance cues and their downstream mediators , very little is known about how the information from multiple extracellular cues is integrated within the cell to generate normal patterning .",
"Netrin and Wnt signaling pathways are both critical t... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"demography",
"computational biology",
"vertebrates",
"animals",
"mammals",
"primates",
"substitution mutation",
"mutation",
"genome analysis",
"mammalian genomics",
"epigenetics",
"dna",
"chromatin",
"dna methylation",
"research and analysis methods",
"chromosome biology",
"gene exp... | Mutation Rate Variation is a Primary Determinant of the Distribution of Allele Frequencies in Humans | journal.pgen.1006489 | null | [
[
"The distribution of allele frequencies across segregating sites , commonly referred to as the Site Frequency Spectrum ( SFS ) , is a central focus of population genetics research as it can reflect a wide range of evolutionary processes , including demographic history as well as positive and purifying selecti... | [
"The site frequency spectrum ( SFS ) has long been used to study demographic history and natural selection .",
"Here , we extend this summary by examining the SFS conditional on the alleles found at the same site in other species .",
"We refer to this extension as the “phylogenetically-conditioned SFS” or cSFS ... | [
"The site frequency spectrum ( SFS , i . e . , the distribution of allele frequencies ) is a summary of natural variation , used to study demographic history and natural selection .",
"Here , we extended the SFS by conditioning on phylogenetic divergence patterns .",
"We refer to this extension as the “phylogen... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"open science",
"open access publishing",
"research funding",
"publication practices",
"replication studies",
"research design",
"research and analysis methods",
"sequence analysis",
"meta-research article",
"bioinformatics",
"government funding of science",
"biological databases",
"research... | Reproducible research practices, transparency, and open access data in the biomedical literature, 2015–2017 | journal.pbio.2006930 | null | [
[
"There is a growing interest in evaluating and ensuring the transparency and reproducibility of the published scientific literature .",
"According to an internet-based survey of 1 , 576 researchers in Nature , 90% of respondents believe that there is either a slight or significant crisis of reproducibilit... | [
"Currently , there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature .",
"According to a previous evaluation of 441 biomedical journals articles published in 2000–2014 , the biomedical literature largely lacked transparency in important dimensions .",
... | [
"Currently , there is a growing interest in ensuring the transparency and reproducibility of the published scientific literature .",
"According to a previous evaluation of 441 biomedical articles published from 2000–2014 , the majority of studies did not share protocols and raw data or disclose funding or potenti... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"x chromosome inactivation",
"genetics",
"epigenetics",
"biology"
] | Chromosome X-Wide Association Study Identifies Loci for Fasting Insulin and Height and Evidence for Incomplete Dosage Compensation | journal.pgen.1004127 | null | [
[
"Genome-wide association studies ( GWAS ) have discovered a wealth of loci associated with complex phenotypes with almost 5 , 800 significant associations for more than 500 different phenotypes reported in the NHGRI GWAS catalog [1] ( accessed August 13 , 2013 ) .",
"These GWAS discoveries are , however ,... | [
"The X chromosome ( chrX ) represents one potential source for the “missing heritability” for complex phenotypes , which thus far has remained underanalyzed in genome-wide association studies ( GWAS ) .",
"Here we demonstrate the benefits of including chrX in GWAS by assessing the contribution of 404 , 862 chrX S... | [
"The X chromosome ( chrX ) analyses have often been neglected in large-scale genome-wide association studies .",
"Given that chrX contains a considerable proportion of DNA , we wanted to examine how the variation in the chromosome contributes to commonly studied phenotypes .",
"To this end , we studied the asso... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"taxonomy",
"plastids",
"parasite groups",
"plant cell biology",
"light microscopy",
"parasitology",
"apicomplexa",
"plant science",
"phylogenetics",
"data management",
"microscopy",
"sequence motif analysis",
"research and analysis methods",
"oxidation-reduction reactions",
"sequence an... | Two essential Thioredoxins mediate apicoplast biogenesis, protein import, and gene expression in Toxoplasma gondii | journal.ppat.1006836 | null | [
[
"Apicomplexan parasites are global killers of animals and humans .",
"Most apicomplexans possess a plastid , the apicoplast .",
"The apicoplast is essential for parasite survival [1] throughout their complex life cycles and has no equivalent in humans .",
"Accordingly , apicoplast functions and pa... | [
"Apicomplexan parasites are global killers , being the causative agents of diseases like toxoplasmosis and malaria .",
"These parasites are known to be hypersensitive to redox imbalance , yet little is understood about the cellular roles of their various redox regulators .",
"The apicoplast , an essential plast... | [
"To survive , apicomplexan parasites must adjust to the redox insults they experience .",
"These parasites undergo redox stresses induced by the host cell within which they live , by the host immune system , and by their own metabolic activities .",
"Yet the myriad of cellular processes that are affected by red... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"genetics and genomics/population genetics",
"genetics and genomics",
"evolutionary biology/evolutionary and comparative genetics"
] | Did Genetic Drift Drive Increases in Genome Complexity? | journal.pgen.1001080 | null | [
[
"The vast array of genome sizes is a pattern that begs for explanation [1] , [2] .",
"Haploid ( 1C ) genome size ( measured either in base pairs or mass , where 106 Kb ≈1 picogram ) spans eight orders of magnitude: the known eukaryotic range is ≈2 , 249–978 , 000 , 000 Kb [3] , while Archaea and Bacteria ... | [
"Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious .",
"Effective population size ( Ne ) has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with larg... | [
"Genome size ( the amount of nuclear DNA ) varies tremendously across organisms but is not necessarily correlated with organismal complexity .",
"For example , genome sizes just within the grasses vary nearly 20-fold , but large-genomed grass species are not obviously more complex in terms of morphology or physio... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | The Alternative Sigma Factor SigX Controls Bacteriocin Synthesis and Competence, the Two Quorum Sensing Regulated Traits in Streptococcus mutans | journal.pgen.1005353 | null | [
[
"Horizontal gene transfer in prokaryotes is mediated via three distinct mechanisms comprising conjugation , transduction , and transformation [1 , 2] .",
"Studying those mechanisms in detail is needed because they are among the reasons for the spread of antibiotic resistance and virulence determinants bet... | [
"Two small quorum sensing ( QS ) peptides regulate competence in S . mutans in a cell density dependent manner: XIP ( sigX inducing peptide ) and CSP ( competence stimulating peptide ) .",
"Depending on the environmental conditions isogenic S . mutans cells can split into a competent and non-competent subpopulati... | [
"Streptococcus mutans is a bacterium of the human dental plaque that contributes to caries development .",
"It controls two important survival mechanisms via a cell-density dependent communication system ( quorum sensing ) : The synthesis of peptide antibiotics , and of a membrane apparatus for genetic competence... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"smell",
"medicine and health sciences",
"pathology and laboratory medicine",
"tropical diseases",
"geographical locations",
"social sciences",
"neuroscience",
"bacterial diseases",
"research design",
"mathematics",
"signs and symptoms",
"forecasting",
"statistics (mathematics)",
"neglecte... | The “Buruli Score”: Development of a Multivariable Prediction Model for Diagnosis of Mycobacterium ulcerans Infection in Individuals with Ulcerative Skin Lesions, Akonolinga, Cameroon | journal.pntd.0004593 | null | [
[
"Buruli ulcer ( BU ) is a skin infection due to Mycobaterium ulcerans .",
"Classical cases with painless ulcerated plaques and undermined edges are believed to be relatively easy to diagnose clinically in endemic regions [1] .",
"Nevertheless , without laboratory testing to confirm the findings , diag... | [
"Access to laboratory diagnosis can be a challenge for individuals suspected of Buruli Ulcer ( BU ) .",
"Our objective was to develop a clinical score to assist clinicians working in resource-limited settings for BU diagnosis .",
"Between 2011 and 2013 , individuals presenting at Akonolinga District Hospital , ... | [
"In most Buruli ulcer ( BU ) endemic areas , laboratory diagnosis is hard to access and comes at a high cost .",
"Clinicians are in need of new tools to assist them in identifying which patients truly require additional work-up and which can be treated directly .",
"We analyzed the clinical data of all patients... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"sequence analysis",
"protein structure",
"biology",
"computational biology",
"macromolecular structure analysis"
] | Analysis of Physicochemical and Structural Properties Determining HIV-1 Coreceptor Usage | journal.pcbi.1002977 | null | [
[
"The entry of the human immunodeficiency virus ( HIV ) into human cells is initiated by binding of the viral envelope glycoprotein gp120 to the cellular CD4 receptor [1] , [2] .",
"This primary interaction induces conformational changes in gp120 [3] that enable viral binding to one of the cell-surface cor... | [
"The relationship of HIV tropism with disease progression and the recent development of CCR5-blocking drugs underscore the importance of monitoring virus coreceptor usage .",
"As an alternative to costly phenotypic assays , computational methods aim at predicting virus tropism based on the sequence and structure ... | [
"Human Immunodeficiency Virus ( HIV ) requires one of the chemokine coreceptors CCR5 or CXCR4 for entry into the host cell .",
"The capacity of the virus to use one or both of these coreceptors is termed tropism .",
"Monitoring HIV tropism is of high importance due to the relationship of the emergence of CXCR4-... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"immunology/antigen processing and recognition",
"infectious diseases",
"immunology/immune response",
"infectious diseases/viral infections",
"infectious diseases/respiratory infections",
"immunology/immunity to infections",
"biochemistry/drug discovery"
] | Protection from the 2009 H1N1 Pandemic Influenza by an Antibody from Combinatorial Survivor-Based Libraries | journal.ppat.1000990 | null | [
[
"Controlling the spread of influenza remains a major challenge due to the unpredictable nature of the virus .",
"Recently , a novel human adapted H1N1 virus has emerged and progressed globally such that the World Health Organization ( WHO ) has declared the first influenza pandemic in 40 years [1] , [2] .... | [
"Influenza viruses elude immune responses and antiviral chemotherapeutics through genetic drift and reassortment .",
"As a result , the development of new strategies that attack a highly conserved viral function to prevent and/or treat influenza infection is being pursued .",
"Such novel broadly acting antivira... | [
"Influenza viruses constantly challenge our ability to prevent and treat their resulting infection .",
"From a survivor of the H5N1 influenza we have discovered an antibody that is effective against both H5N1 and seasonal H1N1 influenza viruses .",
"Here we show the antibody is effective against 2009 pandemic i... | 2010 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"microbiology",
"computational biology",
"molecular biology",
"genetics and genomics",
"eubacteria"
] | Identification of DNA Motifs Implicated in Maintenance of Bacterial Core Genomes by Predictive Modeling | journal.pgen.0030153 | null | [
[
"Analyses of bacterial pan genomes reveal a high level of genetic diversity , even within a short evolutionary scale [1 , 2] .",
"This raises the question of how bacterial chromosomes remain organized yet allow recombination events to occur .",
"Noncoding functional DNA motifs have been implicated in ... | [
"Bacterial biodiversity at the species level , in terms of gene acquisition or loss , is so immense that it raises the question of how essential chromosomal regions are spared from uncontrolled rearrangements .",
"Protection of the genome likely depends on specific DNA motifs that impose limits on the regions tha... | [
"Availability of bacterial “pan genomes , ” based on multiple genome sequences of a given species , has revealed the existence of core genomes , but also of high levels of variable , nonconserved regions .",
"The nature of bacterial strategies that assure genome organization while permitting biodiversity remains ... | 2007 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"reverse transcriptase-polymerase chain reaction",
"geomorphology",
"taxonomy",
"dengue virus",
"medicine and health sciences",
"pathology and laboratory medicine",
"landforms",
"engineering and technology",
"pathogens",
"topography",
"geographical locations",
"microbiology",
"australia",
... | Hyperendemic dengue transmission and identification of a locally evolved DENV-3 lineage, Papua New Guinea 2007-2010 | journal.pntd.0006254 | null | [
[
"The dengue viruses ( DENV ) are the most important arboviral pathogens of humans causing an estimated 390 million infections annually , of which approximately one quarter are symptomatic [1] .",
"Infection with DENV causes a spectrum of clinical outcomes ranging from self-limiting febrile illness ( dengu... | [
"Dengue is endemic in the Western Pacific and Oceania and the region reports more than 200 , 000 cases annually .",
"Outbreaks of dengue and severe dengue occur regularly and movement of virus throughout the region has been reported .",
"Disease surveillance systems , however , in many areas are not fully estab... | [
"Dengue virus ( DENV ) was first identified in Papua New Guinea ( PNG ) in 1944 .",
"Dengue is currently assumed to be an endemic disease in PNG although there is little incidence or prevalence data , and the evidence consensus for dengue presence is low .",
"Routine surveillance is not undertaken and dengue is... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Should Symbionts Be Nice or Selfish? Antiviral Effects of Wolbachia Are Costly but Reproductive Parasitism Is Not | journal.ppat.1005021 | null | [
[
"Heritable symbionts are frequent in insects and their evolutionary success relies on various strategies .",
"By sharing a common route of transmission with their host’s genes , they benefit from increasing host fitness .",
"Consequently , numerous endosymbiotic bacteria evolved towards mutualism , fo... | [
"Symbionts can have mutualistic effects that increase their host’s fitness and/or parasitic effects that reduce it .",
"Which of these strategies evolves depends in part on the balance of their costs and benefits to the symbiont .",
"We have examined these questions in Wolbachia , a vertically transmitted endos... | [
"Arthropods are commonly infected with heritable bacteria , and some of these symbionts can protect their hosts against infection and/or be reproductive parasites .",
"Which of these traits evolves will depend on whether the trait is costly to the symbiont and the host .",
"Using a panel of strains of the symbi... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"systems biology",
"biochemistry",
"enzymes",
"metabolic networks",
"biology",
"computational biology"
] | Biochemical Competition Makes Fatty-Acid β-Oxidation Vulnerable to Substrate Overload | journal.pcbi.1003186 | null | [
[
"Pathophysiological mechanisms underlying acquired and inborn metabolic diseases , such as type-2 diabetes and deficiencies in the fatty-acid oxidation , are largely elusive .",
"Although we know many important molecular factors , yet the complexity of the metabolic and regulatory network hampers elucidat... | [
"Fatty-acid metabolism plays a key role in acquired and inborn metabolic diseases .",
"To obtain insight into the network dynamics of fatty-acid β-oxidation , we constructed a detailed computational model of the pathway and subjected it to a fat overload condition .",
"The model contains reversible and saturabl... | [
"Lipid metabolism plays an important role in the development of metabolic syndrome , a major risk factor for cardiovascular disease and diabetes .",
"Furthermore , inborn errors in lipid oxidation cause rare , but severe diseases in children .",
"To obtain more insight into the response of lipid oxidation to di... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Evidence That Rhesus Macaques Self-Cure from a Schistosoma japonicum Infection by Disrupting Worm Esophageal Function: A New Route to an Effective Vaccine? | journal.pntd.0003925 | null | [
[
"Schistosomiasis is one of the most important parasitic diseases in tropical and sub-tropical regions of the world , with about 800 million people at risk and more than 200 million infected [1 , 2] .",
"With intense efforts over six decades , great progress has been made in combating this disease in China... | [
"Rhesus macaques are unusual among schistosome hosts , self-curing from an established infection and thereafter manifesting solid immunity against a challenge , an ideal model for vaccine development .",
"Previously , the immunological basis of self-cure was confirmed; surviving worms had ceased feeding but how i... | [
"Rhesus macaques can self-cure from a schistosome infection .",
"Antibody is crucial to drive this process and adult worm elimination is preceded by cessation of blood feeding .",
"Recently we have shown that the schistosome esophagus plays a central role in blood processing .",
"We first confirm the self-cur... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | CD39 Expression Identifies Terminally Exhausted CD8+ T Cells | journal.ppat.1005177 | null | [
[
"In acute infections , antigen-specific T cells differentiate into activated effector cells and then into memory T cells which rapidly gain effector functions and re-expand on subsequent encounter with the same pathogen [1] .",
"In contrast , during chronic infections , pathogen-specific T cells gradually... | [
"Exhausted T cells express multiple co-inhibitory molecules that impair their function and limit immunity to chronic viral infection .",
"Defining novel markers of exhaustion is important both for identifying and potentially reversing T cell exhaustion .",
"Herein , we show that the ectonucleotidse CD39 is a ma... | [
"Chronic viral infection induces an acquired state of T cell dysfunction known as exhaustion .",
"Discovering surface markers of exhausted T cells is important for both to identify exhausted T cells as well as to develop potential therapies .",
"We report that the ectonucleotidase CD39 is expressed by T cells s... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"model organisms",
"genetics",
"biology",
"molecular cell biology",
"genetics and genomics"
] | Drosophila Araucan and Caupolican Integrate Intrinsic and Signalling Inputs for the Acquisition by Muscle Progenitors of the Lateral Transverse Fate | journal.pgen.1002186 | null | [
[
"In Drosophila as in vertebrates the proper function of the muscular system relies on the generation of a stereotyped pattern of discrete muscles and their intimate connection with the nervous system , which together control the adequate release of contraction power to fulfil the functional requirements of th... | [
"A central issue of myogenesis is the acquisition of identity by individual muscles .",
"In Drosophila , at the time muscle progenitors are singled out , they already express unique combinations of muscle identity genes .",
"This muscle code results from the integration of positional and temporal signalling inp... | [
"In Drosophila , as in vertebrates , the muscular system consists of different types of muscles that must act in coordination with the nervous system to control the adequate release of contraction power required for the proper functioning of the organism .",
"Therefore , the acquisition of specific identities by ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"biology",
"microbiology",
"molecular cell biology"
] | 2′-O Methylation of Internal Adenosine by Flavivirus NS5 Methyltransferase | journal.ppat.1002642 | null | [
[
"Many members within the Flavivirus genus from Flaviviridae family are important human pathogens , including the four serotypes of Dengue virus ( DENV-1 to -4 ) , yellow fever virus ( YFV ) , West Nile virus ( WNV ) , Japanese encephalitis virus ( JEV ) , and tick-borne encephalitis virus ( TBEV ) .",
"Th... | [
"RNA modification plays an important role in modulating host-pathogen interaction .",
"Flavivirus NS5 protein encodes N-7 and 2′-O methyltransferase activities that are required for the formation of 5′ type I cap ( m7GpppAm ) of viral RNA genome .",
"Here we reported , for the first time , that flavivirus NS5 h... | [
"We report that flavivirus NS5 has a novel internal RNA methylation activity .",
"Recombinant proteins of NS5 and its N-terminal methyltransferase domain of West Nile virus and Dengue virus ( DENV ) specifically methylates polyA , but not polyG , polyC , or polyU .",
"RNAs with internal adenosines substituted w... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"microbial physiology",
"biology",
"microbiology",
"microbial growth and development",
"bacterial pathogens"
] | Protein Complexes and Proteolytic Activation of the Cell Wall Hydrolase RipA Regulate Septal Resolution in Mycobacteria | journal.ppat.1003197 | null | [
[
"Mycobacterium tuberculosis is the causative agent of tuberculosis and accounts for up to 10 million symptomatic infections a year [1] .",
"The spread of multi- , extensively- and now totally- drug resistant strains [2] has created a pressing need to understand essential mycobacterial processes in an effo... | [
"Peptidoglycan hydrolases are a double-edged sword .",
"They are required for normal cell division , but when dysregulated can become autolysins lethal to bacteria .",
"How bacteria ensure that peptidoglycan hydrolases function only in the correct spatial and temporal context remains largely unknown .",
"Here... | [
"Peptidoglycan ( PG ) is a major component of the bacterial cell wall , which forms a flexible , but strong mesh around the cell to oppose osmotic pressure and prevent lysis .",
"PG is also dynamically modified , continually being disassembled and polymerized as the cell elongates and divides .",
"It remains po... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"invertebrates",
"medicine and health sciences",
"immune cells",
"body fluids",
"pathology and laboratory medicine",
"immunology",
"parasitic diseases",
"animals",
"signs and symptoms",
"edema",
"white blood cells",
"wuchereria bancrofti",
"animal cells",
"wuchereria",
"... | Wuchereria bancrofti-infected individuals harbor distinct IL-10-producing regulatory B and T cell subsets which are affected by anti-filarial treatment | journal.pntd.0007436 | null | [
[
"Helminths like filarial nematodes are tropical parasitic worms and the infections that they induce are classified as neglected tropical diseases ( NTDs ) .",
"Filarial infections are vector-borne diseases which are transmitted by blood-feeding insects that are common in tropical and subtropical countries... | [
"Despite worldwide mass drug administration , it is estimated that 68 million individuals are still infected with lymphatic filariasis with 19 million hydrocele and 17 million lymphedema reported cases .",
"Despite the staggering number of pathology cases , the majority of LF-infected individuals do not develop c... | [
"Regulation of the host`s immune system by filarial nematodes is crucial for the fertility and survival of the nematode .",
"Indeed , the majority of W . bancrofti-infected individuals are characterized by a regulated state including increased regulatory T cells ( Treg ) , IL-10 , TGF-β and filarial-specific IgG4... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"organismal evolution",
"gene regulation",
"microbiology",
"developmental biology",
"regulator genes",
"microbial evolution",
"gene types",
"population biology",
"fecundity",
"kin selection",
"gene expression",
"life cycles",
"evolutionary genetics",
"population metrics",
"heredity",
"... | Pleiotropy, cooperation, and the social evolution of genetic architecture | journal.pbio.2006671 | null | [
[
"Recent empirical breakthroughs in microbial genetics have suggested a novel mechanism for maintaining cooperation [1–9] .",
"The problem with cooperation is that noncooperative cheats can avoid the cost of cooperating whilst still gaining the benefits , allowing them to outcompete cooperators [10] .",
... | [
"Pleiotropy has been suggested as a novel mechanism for stabilising cooperation in bacteria and other microbes .",
"The hypothesis is that linking cooperation with a trait that provides a personal ( private ) benefit can outweigh the cost of cooperation in situations when cooperation would not be favoured by mech... | [
"Recent research into microbial communities has revealed that the cooperative secretion of molecules—which are produced by individual cells and benefit neighbouring cells—is linked to the production of privately beneficial intracellular enzymes .",
"This pleiotropic link between commonly and privately beneficial ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"movement disorders",
"biochemistry",
"molecular neuroscience",
"computer and information sciences",
"cellular neuroscience",
"medicine and health sciences",
"computer modeling",
"cell biology",
"neurology",
"neurodegenerative diseases",
"parkinson disease",
"biology and life sciences",
"bio... | Phosphorylation by PINK1 Releases the UBL Domain and Initializes the Conformational Opening of the E3 Ubiquitin Ligase Parkin | journal.pcbi.1003935 | null | [
[
"Mutations in the PTEN-induced putative kinase 1 ( PINK1 ) and PARKIN genes are the most common causes of autosomal recessive Parkinson's disease ( PD ) [1] .",
"Although the molecular mechanism underlying the pathogenesis of PD remain elusive , it has become clear that PINK1 and Parkin protein functional... | [
"Loss-of-function mutations in PINK1 or PARKIN are the most common causes of autosomal recessive Parkinson's disease .",
"Both gene products , the Ser/Thr kinase PINK1 and the E3 Ubiquitin ligase Parkin , functionally cooperate in a mitochondrial quality control pathway .",
"Upon stress , PINK1 activates Parkin... | [
"Parkinson's disease ( PD ) is a devastating neurological condition caused by the selective and progressive degeneration of dopaminergic neurons in the brain .",
"Loss-of-function mutations in the PINK1 or PARKIN genes are the most common causes of recessively inherited PD .",
"Together the encoded proteins coo... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Dissemination of a Highly Virulent Pathogen: Tracking The Early Events That Define Infection | journal.ppat.1004587 | null | [
[
"Dissemination is key for a pathogen to reach sites where the environment favors survival or the probability of being transmitted to other hosts is higher .",
"As the pathogen invades new tissues , however , the host responds by eliciting immune responses in an effort to eliminate infection .",
"These... | [
"The series of events that occurs immediately after pathogen entrance into the body is largely speculative .",
"Key aspects of these events are pathogen dissemination and pathogen interactions with the immune response as the invader moves into deeper tissues .",
"We sought to define major events that occur earl... | [
"The earliest stage of any infection takes place when a pathogen enters the body ( inoculation ) at an initial site of contact .",
"From this point , the pathogen can spread into deeper tissues where the pathogen itself and the immune responses against it cause disease .",
"Very little is known about the events... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"systems biology",
"biochemistry",
"enzymes",
"metabolic pathways",
"biology",
"enzyme kinetics",
"metabolism",
"computational biology"
] | Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism | journal.pcbi.1003483 | null | [
[
"A primary scientific goal of metabolic research is to develop an understanding of the evolutionary , chemical and physical forces that shape the structure of cellular metabolism .",
"Specifically , to what extent are present-day metabolic pathways the result of evolutionary optimization rather than fossi... | [
"In metabolism research , thermodynamics is usually used to determine the directionality of a reaction or the feasibility of a pathway .",
"However , the relationship between thermodynamic potentials and fluxes is not limited to questions of directionality: thermodynamics also affects the kinetics of reactions th... | [
"Given data about enzyme kinetics and reaction thermodynamics , traditional metabolic control analysis ( MCA ) can pinpoint the enzymes whose expression will have the largest effect on steady-state flux through the pathway .",
"These analyses can aid experimentalists in tuning enzyme expression levels along a met... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome evolution",
"gene function",
"genome sequencing",
"plant science",
"plant genomics",
"plants",
"flowering plants",
"plant genetics",
"comparative genomics",
"biology",
"evolutionary genetics",
"flowers",
"angiosperms",
"plant evolution",
"plant phylogenetics",
"genetics",
"ge... | Secondary Evolution of a Self-Incompatibility Locus in the Brassicaceae Genus Leavenworthia | journal.pbio.1001560 | Self-incompatibility enables plants to avoid inbreeding by self-pollination. Here we report that the genetic locus encoding self-pollen recognition has evolved twice in the Brassicaceae family, challenging the notion that loss of self-incompatibility is irreversible. | [
[
"Self-incompatibility ( SI ) is a widespread plant reproductive system that prevents inbreeding by facilitating the rejection of self-pollen .",
"It is a major evolutionary feature of the flowering plants [1] .",
"SI is a complex phenotype whose functioning requires co-evolution among several interact... | [
"Self-incompatibility ( SI ) is the flowering plant reproductive system in which self pollen tube growth is inhibited , thereby preventing self-fertilization .",
"SI has evolved independently in several different flowering plant lineages .",
"In all Brassicaceae species in which the molecular basis of SI has be... | [
"Self-incompatibility ( SI ) is a pollen recognition system that enables plants to avoid the inbreeding caused by self-pollination .",
"It involves a pair of tightly linked genes known as the S locus .",
"The product of one of these genes acts as the receptor and recognizes the pollen protein produced by the sa... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Blimp-1-Dependent IL-10 Production by Tr1 Cells Regulates TNF-Mediated Tissue Pathology | journal.ppat.1005398 | null | [
[
"TNF is a key pro-inflammatory cytokine required to control intracellular pathogens and kill tumours [1] .",
"However , excessive TNF production can cause diseases such as rheumatoid arthritis , inflammatory bowel disease , psoriasis , ankylosing spondylitis , graft-versus-host disease and sepsis [2 , 3] ... | [
"Tumor necrosis factor ( TNF ) is critical for controlling many intracellular infections , but can also contribute to inflammation .",
"It can promote the destruction of important cell populations and trigger dramatic tissue remodeling following establishment of chronic disease .",
"Therefore , a better underst... | [
"Many parasitic diseases are associated with the generation of potent inflammatory responses .",
"These are often needed to control infection , but can also cause tissue damage if not appropriately regulated .",
"IL-10 has emerged as an important immune regulator that protects tissues by dampening inflammation ... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"rna interference",
"cell processes",
"animals",
"nerve regeneration",
"head regeneration",
"developmental biology",
"organism development",
"network analysis",
"molecular development",
"epigenetics",
"morphogenesis",
"tail regeneration",
"planarians",
"computer and info... | Neural control of body-plan axis in regenerating planaria | journal.pcbi.1006904 | null | [
[
"Humanity’s inability to regenerate significant portions of anatomy ( e . g . lost limbs , severed spinal cord , damaged organs ) has prompted decades of intensive study into organisms that can .",
"The planarian flatworm is one such model organism , as it can completely regrow from a piece as small as ~1... | [
"Control of axial polarity during regeneration is a crucial open question .",
"We developed a quantitative model of regenerating planaria , which elucidates self-assembly mechanisms of morphogen gradients required for robust body-plan control .",
"The computational model has been developed to predict the fracti... | [
"Understanding how large-scale anatomy emerges from the activity of cellular pathways is a key goal of evolutionary developmental biology .",
"Elucidating the rules of body-wide morphogenesis is especially essential for transitioning molecular signaling data at the cellular level into advances in regenerative bio... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"epilepsy",
"computer and information sciences",
"medicine and health sciences",
"computer modeling",
"systems science",
"network analysis",
"neurology",
"epileptic seizures"
] | Dynamics on Networks: The Role of Local Dynamics and Global Networks on the Emergence of Hypersynchronous Neural Activity | journal.pcbi.1003947 | null | [
[
"The human brain is perhaps the best example of a multiscale complex network , with organizational hierarchies spanning many spatial and temporal scales .",
"At the microscale , neurons communicate with other neurons through both chemical and electrical coupling , with estimates varying from 1000 to 10000... | [
"Graph theory has evolved into a useful tool for studying complex brain networks inferred from a variety of measures of neural activity , including fMRI , DTI , MEG and EEG .",
"In the study of neurological disorders , recent work has discovered differences in the structure of graphs inferred from patient and con... | [
"In this paper we show that within modular networks ( that is , networks with multiple scales of connections ) , two distinct mechanisms may drive the emergence of synchrony at the global level .",
"We term the first of these mechanisms “network-driven synchrony” , which is characterized by the presence of cycles... | 2014 |
[
"Introduction",
"Methods",
"Results/Discussion",
"Conclusions"
] | [
"education",
"biology",
"computational biology"
] | A First Attempt to Bring Computational Biology into Advanced High School Biology Classrooms | journal.pcbi.1002244 | null | [
[
"The absence of a computational element in secondary biology classrooms is of growing concern to the computational biology community .",
"While computer science is increasingly important in modern biology research [1]–[4] , it plays almost no role in high school and undergraduate biology classes .",
"... | [
"Computer science has become ubiquitous in many areas of biological research , yet most high school and even college students are unaware of this .",
"As a result , many college biology majors graduate without adequate computational skills for contemporary fields of biology .",
"The absence of a computational e... | [
"We have designed and implemented a curriculum to teach basic computational biology to advanced high school students .",
"The curriculum includes an introduction to the concept of algorithms , an overview of the Basic Local Alignment Search Tool ( BLAST ) algorithm used to compare DNA sequences , and methods for ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"animal genetics",
"chromosome structure and function",
"population genetics",
"reproductive physiology",
"germ cells",
"telomeres",
"clutches",
"epigenetics",
"population biology",
"bird genetics",
"sperm",
"telomere length",
"genetic polymorphism",
"chro... | Epigenetic inheritance of telomere length in wild birds | journal.pgen.1007827 | null | [
[
"Telomeres are evolutionarily conserved DNA sequence repeats , which form the ends of chromosomes together with associated proteins and contribute to genome stability [1] .",
"Telomeres shorten due to incomplete replication during cell division , which can be accelerated by DNA and protein damaging factor... | [
"Telomere length ( TL ) predicts health and survival across taxa .",
"Variation in TL between individuals is thought to be largely of genetic origin , but telomere inheritance is unusual , because zygotes already express a TL phenotype , the TL of the parental gametes .",
"Offspring TL changes with paternal age... | [
"Telomeres are DNA-protein structures at chromosome ends and a short telomere length predicts reduced survival in humans , birds and other organisms .",
"Variation in telomere length between individuals is thought to be largely of genetic origin , but telomere inheritance may be unusual because not only genes reg... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"neglected tropical diseases",
"onchocerciasis"
] | Oligonucleotide Based Magnetic Bead Capture of Onchocerca volvulus DNA for PCR Pool Screening of Vector Black Flies | journal.pntd.0001712 | null | [
[
"Onchocerciasis , or river blindness has historically represented one of the most important neglected tropical diseases in the developing world as measured as a cause of socio-economic disruption [1] .",
"It is also considered a candidate for elimination by the international community [2] , [3] .",
"A... | [
"Entomological surveys of Simulium vectors are an important component in the criteria used to determine if Onchocerca volvulus transmission has been interrupted and if focal elimination of the parasite has been achieved .",
"However , because infection in the vector population is quite rare in areas where control... | [
"The absence of infective larvae of Onchocerca volvulus in the black fly vector of this parasite is a major criterion used to certify that transmission has been eliminated in a focus .",
"This process requires screening large numbers of flies .",
"Currently , this is accomplished by screening pools of flies usi... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"evolutionary biology",
"infectious diseases/helminth infections",
"infectious diseases/antimicrobials and drug resistance"
] | Reduced Susceptibility to Praziquantel among Naturally Occurring Kenyan Isolates of Schistosoma mansoni | journal.pntd.0000504 | null | [
[
"Schistosomiasis is one of the most common human parasitic diseases in the world .",
"An estimated total of 207 million persons are infected worldwide , 97% of which are on the African continent [1] .",
"The chronic and debilitating nature of the disease results in high costs in public health and econ... | [
"The near exclusive use of praziquantel ( PZQ ) for treatment of human schistosomiasis has raised concerns about the possible emergence of drug-resistant schistosomes .",
"We measured susceptibility to PZQ of isolates of Schistosoma mansoni obtained from patients from Kisumu , Kenya continuously exposed to infect... | [
"The emergence of drug resistant pathogens is a great challenge to the control of infectious diseases .",
"Schistosomiasis is one of the world's greatest neglected tropical diseases , and it is primarily controlled with the drug praziquantel .",
"This drug is often used by repeatedly treating patients to mainta... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Hyper-Acetylation of Histone H3K56 Limits Break-Induced Replication by Inhibiting Extensive Repair Synthesis | journal.pgen.1004990 | null | [
[
"DNA damage drives mutagenesis and chromosomal rearrangements .",
"Homologous recombination ( HR ) removes DNA lesions primarily at S/G2 phase of the cell cycle by pairing broken DNA ends with intact homologous template and copying across DNA breaks [1] .",
"Break-induced replication ( BIR ) is the su... | [
"Break-induced replication ( BIR ) has been implicated in restoring eroded telomeres and collapsed replication forks via single-ended invasion and extensive DNA synthesis on the recipient chromosome .",
"Unlike other recombination subtypes , DNA synthesis in BIR likely relies heavily on mechanisms enabling effici... | [
"Chromatin poses a barrier to the recombination process .",
"Chromatin modification is therefore a prerequisite factor for the efficient execution of the recombination event .",
"Chromatin remodeling and several unique histone modifications at or near DNA double strand breaks ( DSBs ) facilitate early recombina... | 2015 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"bacteriology",
"prokaryotic models",
"model organisms",
"caulobacter crescentus",
"gene expression",
"genetics",
"epigenetics",
"biology",
"dna modification",
"microbiology",
"gene networks",
"dna transcription"
] | DNA Binding of the Cell Cycle Transcriptional Regulator GcrA Depends on N6-Adenosine Methylation in Caulobacter crescentus and Other Alphaproteobacteria | journal.pgen.1003541 | null | [
[
"Epigenetic signals , such as methylation of DNA , play an important role in the regulation of gene expression in eukaryotes .",
"Methylation of adenines in the N6 position ( m6A ) has been described in Bacteria , Archaea , Protists and Fungi .",
"Though known for its protective role in bacterial rest... | [
"Several regulators are involved in the control of cell cycle progression in the bacterial model system Caulobacter crescentus , which divides asymmetrically into a vegetative G1-phase ( swarmer ) cell and a replicative S-phase ( stalked ) cell .",
"Here we report a novel functional interaction between the enigma... | [
"Methylation of genomic DNA at a specific regulatory site can impact a myriad of processes in eukaryotic cells .",
"In bacteria , methylation at the N6 position of adenosine ( m6A ) is known to mediate a non-adaptive immunity response to protect cells from foreign DNA .",
"While m6A marks are not known to gover... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"skin",
"medicine and health sciences",
"integumentary system",
"pathology and laboratory medicine",
"enzymes",
"immunology",
"enzymology",
"animal models",
"developmental biology",
"model organisms",
"signs and symptoms",
"experimental organism systems",
"epidermis",
"embryos",
"researc... | KLK5 and KLK7 Ablation Fully Rescues Lethality of Netherton Syndrome-Like Phenotype | journal.pgen.1006566 | null | [
[
"Netherton syndrome ( NS ) is a life-threatening autosomal recessive disorder that affects approximately one in 200 000 newborn children [1 , 2] .",
"Newborns suffering from NS exhibit congenital ichthyosiform erythroderma with scaly and peeling skin , resulting in severe disruption of epidermal barrier ,... | [
"Netherton syndrome ( NS ) is a severe skin disease caused by the loss of protease inhibitor LEKTI , which leads to the dysregulation of epidermal proteases and severe skin-barrier defects .",
"KLK5 was proposed as a major protease in NS pathology , however its inactivation is not sufficient to rescue the lethal ... | [
"Netherton syndrome ( NS ) is a genetic skin disorder caused by the loss of protease inhibitor LEKTI , which leads to the dysregulation of epidermal proteases and severe skin-barrier defects .",
"In this work , we aimed to explore the molecular mechanisms underlying this disease using a novel mutant mouse model f... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"computer science",
"adaptive immunity",
"computer modeling",
"immune cells",
"immunity",
"gastroenterology and hepatology",
"t cells",
"inflammatory bowel disease",
"immunology",
"biology",
"immunoregulation",
"immunomodulation"
] | Systems Modeling of Molecular Mechanisms Controlling Cytokine-driven CD4+ T Cell Differentiation and Phenotype Plasticity | journal.pcbi.1003027 | null | [
[
"The CD4+ T cell differentiation process activates the transcriptional and secretory cellular machinery that helps orchestrate immune modulation in infectious , allergic and immune-mediated diseases .",
"Upon antigen presentation , naïve CD4+ T cells become activated and undergo a differentiation process ... | [
"Differentiation of CD4+ T cells into effector or regulatory phenotypes is tightly controlled by the cytokine milieu , complex intracellular signaling networks and numerous transcriptional regulators .",
"We combined experimental approaches and computational modeling to investigate the mechanisms controlling diff... | [
"CD4+ T cells can differentiate into different phenotypes depending on the cytokine milieu .",
"Due to the complexity of this process , we have constructed a computational and mathematical model with sixty ordinary differential equations representing a CD4+ T cell differentiating into either Th1 , Th2 , Th17 or i... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"genetic oscillators",
"animal genetics",
"invertebrate genetics",
"gene regulatory networks",
"genetics",
"biology and life sciences",
"gene disruption",
"molecular genetics",
"computational biology",
"evolutionary developmental biology"
] | Caudal Regulates the Spatiotemporal Dynamics of Pair-Rule Waves in Tribolium | journal.pgen.1004677 | null | [
[
"The anterior-posterior ( AP ) axis of arthropods , annelids , and vertebrates is partitioned into segments .",
"The French flag model , in which threshold concentrations of morphogen gradients are interpreted by downstream genes to partition a developing tissue [1] , [2] , provides the main theoretical f... | [
"In the short-germ beetle Tribolium castaneum , waves of pair-rule gene expression propagate from the posterior end of the embryo towards the anterior and eventually freeze into stable stripes , partitioning the anterior-posterior axis into segments .",
"Similar waves in vertebrates are assumed to arise due to th... | [
"One of the most popular problems in development is how the anterior-posterior axis of vertebrates , arthropods and annelids is partitioned into segments .",
"In vertebrates , and recently shown in the beetle Tribolium castaneum , segments are demarcated by means of gene expression waves that propagate from poste... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"microarrays",
"systems biology",
"biology",
"computational biology",
"metabolic networks",
"genetics and genomics"
] | Viral Perturbations of Host Networks Reflect Disease Etiology | journal.pcbi.1002531 | null | [
[
"Functional interactions between cellular targets of viral proteins and disease susceptibility genes [1] , [2] , [3] , [4] , [5] might play key roles in disease etiology .",
"Advances in the mapping of the human interactome network , as well as in the systematic identification of gene-disease associations... | [
"Many human diseases , arising from mutations of disease susceptibility genes ( genetic diseases ) , are also associated with viral infections ( virally implicated diseases ) , either in a directly causal manner or by indirect associations .",
"Here we examine whether viral perturbations of host interactome may u... | [
"Many “virally implicated human diseases” - diseases for which there is scientific consensus of viral involvement - are associated with genetic alterations in particular disease susceptibility genes .",
"We proposed and demonstrated that for two human viruses , Epstein-Barr virus and human papillomavirus , topolo... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics",
"molecular biology",
"biology and life sciences",
"mycology"
] | Comparative Phenotypic Analysis of the Major Fungal Pathogens Candida parapsilosis and Candida albicans | journal.ppat.1004365 | null | [
[
"More than 300 Candida species have been described to date [1] .",
"Although all Candida species are Ascomycetes ( belonging to the Saccharomycetales ) , they are paraphyletic , and do not share a recent common ancestor [2] .",
"As a result , they have few shared characteristics .",
"The term “Can... | [
"Candida parapsilosis and Candida albicans are human fungal pathogens that belong to the CTG clade in the Saccharomycotina .",
"In contrast to C . albicans , relatively little is known about the virulence properties of C . parapsilosis , a pathogen particularly associated with infections of premature neonates .",... | [
"Candida species are among the most common causes of fungal infection worldwide .",
"Infections can be both community-based and hospital-acquired , and are particularly associated with immunocompromised individuals .",
"Candida albicans is the most commonly isolated species and is the best studied .",
"Howeve... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide association studies",
"genomics",
"functional genomics",
"gene regulatory networks",
"genome analysis",
"gene expression",
"genetics",
"biology and life sciences",
"computational biology",
"human genetics"
] | Cis and Trans Effects of Human Genomic Variants on Gene Expression | journal.pgen.1004461 | null | [
[
"Genome-wide association studies ( GWAS ) have discovered a large number of loci implicated in many complex traits and diseases [1] .",
"The vast majority of variants discovered are found in non-coding regions ( 88% ) , which challenges the interpretation of their functional effect [1] .",
"One way to... | [
"Gene expression is a heritable cellular phenotype that defines the function of a cell and can lead to diseases in case of misregulation .",
"In order to detect genetic variations affecting gene expression , we performed association analysis of single nucleotide polymorphisms ( SNPs ) and copy number variants ( C... | [
"Humans differ in their genetic sequences at millions of positions but only a subset of these differences have a functional effect .",
"In order to detect functional genetic differences , we assessed the impact of common genetic variants on gene expression in 869 individuals and discovered that the expression of ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/animal models of infection",
"virology"
] | H5N1 and 1918 Pandemic Influenza Virus Infection Results in Early and Excessive Infiltration of Macrophages and Neutrophils in the Lungs of Mice | journal.ppat.1000115 | null | [
[
"The influenza pandemic from 1918 to 1919 was the most devastating infectious disease pandemic ever documented in such a short period of time , killing nearly 50 million people worldwide [1] .",
"Unlike the epidemiological profiles of most influenza infections , young adults aged 18–35 yrs old had the hig... | [
"Fatal human respiratory disease associated with the 1918 pandemic influenza virus and potentially pandemic H5N1 viruses is characterized by severe lung pathology , including pulmonary edema and extensive inflammatory infiltrate .",
"Here , we quantified the cellular immune response to infection in the mouse lung... | [
"Patients who succumbed to influenza during the 1918 pandemic had severe lung pathology marked by extensive inflammatory infiltrate , indicating a robust immune response in the lung .",
"Similar findings have been reported from H5N1-infected patients , raising the question as to why people expire in the presence ... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"functional genomics",
"genetic mutation",
"microbiology",
"gene function",
"bacterial diseases",
"genome analysis tools",
"enterococcus infection",
"bacterial pathogens",
"infectious diseases",
"microbial pathogens",
"biology",
"gram positive",
"mutagenesis",
"genetic screen... | Genome-Wide Identification of Ampicillin Resistance Determinants in Enterococcus faecium | journal.pgen.1002804 | null | [
[
"Enterococci rank third overall as causative agents of healthcare-associated infections [1] , [2] .",
"Up to the late 1980s , Enterococcus faecalis was responsible for practically all enterococcal infections , but starting from the 1990s nosocomial infections with E . faecium became more frequent .",
... | [
"Enterococcus faecium has become a nosocomial pathogen of major importance , causing infections that are difficult to treat owing to its multi-drug resistance .",
"In particular , resistance to the β-lactam antibiotic ampicillin has become ubiquitous among clinical isolates .",
"Mutations in the low-affinity pe... | [
"Enterococcus faecium has emerged as an important nosocomial pathogen around the world .",
"Clinical E . faecium isolates are often resistant to multiple antibiotics , thereby complicating therapeutic interventions .",
"However , the molecular mechanisms that contribute to the recent emergence of E . faecium as... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"social and behavioral sciences",
"health economics",
"infectious disease epidemiology",
"epidemiology",
"epidemiological methods",
"economics"
] | Optimal Screening Strategies for Healthcare Associated Infections in a Multi-Institutional Setting | journal.pcbi.1003407 | null | [
[
"Hospital associated infections represent a major cause of morbidity and mortality [1] .",
"Disease screening can facilitate efforts to reduce disease prevalence through the treatment of infected patients or reducing transmission within a healthcare setting .",
"Because screening and treatment are exp... | [
"Health institutions may choose to screen newly admitted patients for the presence of disease in order to reduce disease prevalence within the institution .",
"Screening is costly , and institutions must judiciously choose which patients they wish to screen based on the dynamics of disease transmission .",
"Sin... | [
"Healthcare associated infections are a major cause of morbidity and mortality .",
"Screening patients on admission to the hospital may reduce prevalence by identifying infected individuals; infected individuals can then be treated or isolated to prevent further spread .",
"Because screening is costly , institu... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"flow cytometry",
"cell cycle and cell division",
"cell processes",
"enzymology",
"dna-binding proteins",
"organisms",
"dna damage",
"fungi",
"model organisms",
"polymerases",
"dna replication",
"experimental organism systems",
"dna",
"molecular biology techniques",
"synthesis phase",
... | Replication fork slowing and stalling are distinct, checkpoint-independent consequences of replicating damaged DNA | journal.pgen.1006958 | null | [
[
"In response to DNA damage during the G1 or G2 phase of the cell cycle , DNA damage checkpoints block cell cycle progression , giving cells time to repair damage before proceeding to the next phase of the cell cycle [1 , 2] .",
"The response to DNA damage during S phase is more complicated , because repai... | [
"In response to DNA damage during S phase , cells slow DNA replication .",
"This slowing is orchestrated by the intra-S checkpoint and involves inhibition of origin firing and reduction of replication fork speed .",
"Slowing of replication allows for tolerance of DNA damage and suppresses genomic instability ."... | [
"Faithful duplication of the genome is essential for genetic stability of organisms and species .",
"To ensure faithful duplication , cells must be able to replicate damaged DNA .",
"To do so , they employ checkpoints that regulate replication in response to DNA damage .",
"However , the mechanisms by which c... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Qualitative and Quantitative Protein Complex Prediction Through Proteome-Wide Simulations | journal.pcbi.1004424 | null | [
[
"Mass-spectrometry ( MS ) techniques solved many fundamental issues in the identification of protein complexes [1–3] and other high-throughput techniques allowed the identification of Protein-Protein Interactions ( PPI ) and Domain-Domain Interactions ( DDI ) , which paved the way for computational methods to... | [
"Despite recent progress in proteomics most protein complexes are still unknown .",
"Identification of these complexes will help us understand cellular regulatory mechanisms and support development of new drugs .",
"Therefore it is really important to establish detailed information about the composition and the... | [
"Most proteins are biologically active only when part of a complex with other proteins of the same or other type .",
"Hence , to unravel biological functions of proteins , it is important to identify the type of complexes they can form .",
"Multiple copies of each protein are present in cells and some of these ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"primates",
"mammals",
"human",
"genetics and genomics"
] | The Diploid Genome Sequence of an Individual Human | journal.pbio.0050254 | Comparison of the DNA sequence of an individual human from the reference sequence reveals a surprising amount of difference. | [
[
"Each of our genomes is typically composed of DNA packaged into two sets of 23 chromosomes; one set inherited from each parent whose own DNA is a mosaic of preceding ancestors .",
"As such , the human genome functions as a diploid entity with phenotypes arising due to the sometimes complex interplay of al... | [
"Presented here is a genome sequence of an individual human .",
"It was produced from ∼32 million random DNA fragments , sequenced by Sanger dideoxy technology and assembled into 4 , 528 scaffolds , comprising 2 , 810 million bases ( Mb ) of contiguous sequence with approximately 7 . 5-fold coverage for any given... | [
"We have generated an independently assembled diploid human genomic DNA sequence from both chromosomes of a single individual ( J . Craig Venter ) .",
"Our approach , based on whole-genome shotgun sequencing and using enhanced genome assembly strategies and software , generated an assembled genome over half of wh... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"fibroblasts",
"cytoplasmic staining",
"viruses",
"stem cells",
"dna viruses",
"connective tissue cells",
"epigenetics",
"dna",
"dna methylation",
"chromatin",
"herpesviruses",
"research a... | Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs | journal.pgen.1005793 | null | [
[
"Research on human subjects is limited by the availability of samples .",
"Practical and ethical considerations dictate that functional molecular studies in humans can generally only make use of frozen post mortem tissues , a small collection of available cell lines , or easily accessible primary cell typ... | [
"The advent of induced pluripotent stem cells ( iPSCs ) revolutionized human genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues .",
"This technology can have immense implications for regenerative medicine , but iPSCs also represent a paradigm shift in the study of complex... | [
"Induced pluripotent stem cells ( iPSCs ) are a new and powerful cell type that provides scientists the ability to model complex human diseases in vitro .",
"These cells can be cryopreserved and later expanded , providing a renewable source of cells from the same individual .",
"iPSCs can be made from a variety... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biophysics/macromolecular assemblies and machines",
"biophysics/membrane proteins and energy transduction",
"computational biology/synthetic biology",
"computational biology/transcriptional regulation",
"biophysics/theory and simulation",
"biophysics/biomacromolecule-ligand interactions",
"pharmacology... | Scalable Rule-Based Modelling of Allosteric Proteins and Biochemical Networks | journal.pcbi.1000975 | null | [
[
"A goal of biology is to understand the structure and function of the biochemical networks that underpin cellular decision-making .",
"One organizing principle is that these networks are inherently modular [1]–[3] , with specific functions ascribed to a subset of proteins in the network .",
"Yet , lik... | [
"Much of the complexity of biochemical networks comes from the information-processing abilities of allosteric proteins , be they receptors , ion-channels , signalling molecules or transcription factors .",
"An allosteric protein can be uniquely regulated by each combination of input molecules that it binds .",
... | [
"The complexity of biochemical networks challenges our ability to create quantitative and predictive models of cellular responses to extracellular changes .",
"In these networks , the regulation of allosteric receptors and proteins by multiple drugs or endogenous ligands introduces “regulatory complexity” because... | 2010 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [] | Parvoviruses Cause Nuclear Envelope Breakdown by Activating Key Enzymes of Mitosis | journal.ppat.1003671 | null | [
[
"The nuclear envelope separates cytoplasm and nucleus requiring shuttling of cargos between the compartments .",
"In non-dividing cells macromolecule exchange occurs via the nuclear pore complexes ( NPC ) , which are composed of ∼30 different proteins ( nucleoporins , Nups ) .",
"NPCs allow the passag... | [
"Disassembly of the nuclear lamina is essential in mitosis and apoptosis requiring multiple coordinated enzymatic activities in nucleus and cytoplasm .",
"Activation and coordination of the different activities is poorly understood and moreover complicated as some factors translocate between cytoplasm and nucleus... | [
"Parvoviruses are small non-enveloped DNA viruses successfully used in gene therapy .",
"Their nuclear replication requires transit of the nuclear envelope .",
"Analyzing the interaction between parvoviruses and the nucleus , we showed that despite their small size , they did not traverse the nuclear pore , but... | 2013 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"sequencing techniques",
"genome sequencing",
"genome expression analysis",
"genomics",
"functional genomics",
"genome analysis",
"gene expression",
"transcriptome analysis",
"genetics",
"biology and life sciences",
"molecular biology techniques",
"computational biology",
"molecular biology"... | Allelic Expression of Deleterious Protein-Coding Variants across Human Tissues | journal.pgen.1004304 | null | [
[
"Recent genome sequencing studies have highlighted that healthy individuals carry multiple loss-of-function and rare deleterious variants whose interpretation is expected to inform individual disease risk and facilitate precision medicine [1]–[3] .",
"However , accurate interpretation of these variants re... | [
"Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden .",
"However , for each allele , accurate interpretation of its effect will depend on both its penetrance and the trait's expres... | [
"Gene expression is a fundamental cellular process that contributes to phenotypic diversity .",
"Gene expression can vary between alleles of an individual through differences in genomic imprinting or cis-acting regulatory variation .",
"Distinguishing allelic activity is important for informing the abundance of... | 2014 |
[
"Introduction",
"Discussion",
"Methods"
] | [
"carbachol",
"medicine and health sciences",
"action potentials",
"neurochemistry",
"acetylcholine",
"drugs",
"membrane potential",
"electrophysiology",
"neuroscience",
"fibroblasts",
"connective tissue cells",
"cardiac pacing",
"pharmacology",
"neurotransmitters",
"cardiology",
"arrhy... | A Mathematical Model of Neonatal Rat Atrial Monolayers with Constitutively Active Acetylcholine-Mediated K+ Current | journal.pcbi.1004946 | null | [
[
"Atrial fibrillation ( AF ) is the most frequent form of arrhythmia occurring in patients with or without the risk for heart failure [1–8] .",
"Each identified form of AF ( paroxysmal , persistent , or chronic ) requires specialized treatment .",
"Therefore , an in-depth understanding of the underlyin... | [
"Atrial fibrillation ( AF ) is the most frequent form of arrhythmia occurring in the industrialized world .",
"Because of its complex nature , each identified form of AF requires specialized treatment .",
"Thus , an in-depth understanding of the bases of these arrhythmias is essential for therapeutic developmen... | [
"A fundamentally important element in cardiac in silico research is a model for the cardiac cell .",
"It provides a link between measurable characteristics at the subcellular level and biological processes at the whole cell level , thereby allowing the researcher to study mechanisms of cardiac arrhythmias from a ... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"medicine",
"public health and epidemiology",
"population genetics",
"parasitic diseases",
"phylogenetics",
"molecular systematics",
"neglected tropical diseases",
"ascariasis",
"infectious diseases",
"soil-transmitted helminths",
"genetic polymorphism",
"molecular epidemiology",... | Phylogeographical Studies of Ascaris spp. Based on Ribosomal and Mitochondrial DNA Sequences | journal.pntd.0002170 | null | [
[
"Ascariasis in pigs and in humans is caused by two of the most socio-economically important nematodes: Ascaris suum Goeze , 1782 and Ascaris lumbricoides Linneaus , 1758 , respectively .",
"Human ascariasis is a soil-transmitted helminthiasis ( STH ) , included in the WHO list of neglected tropical diseas... | [
"The taxonomic distinctiveness of Ascaris lumbricoides and A . suum , two of the world's most significant nematodes , still represents a much-debated scientific issue .",
"Previous studies have described two different scenarios in transmission patterns , explained by two hypotheses: ( 1 ) separated host-specific ... | [
"Ascaris lumbricoides , the world's most common human nematode , and A . suum , the pig roundworm , are two of the most important soil-transmitted helminthes of public health and socio-economic concern .",
"However , previously documented similarities at the morphological and genetic level , coupled with evidence... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/virulence factors and mechanisms",
"virology/immunodeficiency viruses",
"infectious diseases/hiv infection and aids",
"biochemistry/macromolecular assemblies and machines",
"chemical biology/protein chemistry and proteomics",
"cell biology/chemical biology of the cell"
] | Lentiviral Vpx Accessory Factor Targets VprBP/DCAF1 Substrate Adaptor for Cullin 4 E3 Ubiquitin Ligase to Enable Macrophage Infection | journal.ppat.1000059 | null | [
[
"Vpx accessory proteins are virulence factors encoded by viruses of the HIV-2/SIVsm/SIVmac lineage of primate lentiviruses .",
"vpx gene disruption results in greatly reduced rates of virus replication in monocyte-derived cells , such as differentiated macrophages , but has no overt effect in primary T ly... | [
"Vpx is a small virion-associated adaptor protein encoded by viruses of the HIV-2/SIVsm lineage of primate lentiviruses that enables these viruses to transduce monocyte-derived cells .",
"This probably reflects the ability of Vpx to overcome an as yet uncharacterized block to an early event in the virus life cycl... | [
"Monocyte-derived tissue macrophages play crucial roles in infection by primate lentiviruses .",
"Human and simian lentiviruses of the HIV-2 and SIVsm/mac lineages encode a virion-bound virulence factor termed Vpx .",
"Vpx is required to establish infection specifically of monocyte-derived cells , but the under... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"invertebrates",
"innate immune system",
"medicine and health sciences",
"immune physiology",
"immune cells",
"cytokines",
"immunology",
"microbiology",
"animals",
"developmental biology",
"molecular development",
"insect vectors",
"research and analysis methods",
"sequenc... | Viral immunogenicity determines epidemiological fitness in a cohort of DENV-1 infection in Brazil | journal.pntd.0006525 | null | [
[
"The spread of dengue ( DENV ) over the past several decades has made this arbovirus infection a major public health concern of global impact [1 , 2] .",
"The disease has a complex epidemiological pattern and a high economic impact globally and is considered hyperendemic , i .",
"e .",
"dengue fev... | [
"The dynamics of dengue virus ( DENV ) circulation depends on serotype , genotype and lineage replacement and turnover .",
"In São José do Rio Preto , Brazil , we observed that the L6 lineage of DENV-1 ( genotype V ) remained the dominant circulating lineage even after the introduction of the L1 lineage .",
"We... | [
"Since 2008 L6 is the endemic lineage that has circulated in SJRP .",
"In 2010 , the L1 lineage was first identified in the city .",
"For a period , both lineages co-circulated , and then in 2013 , L1 began to diminish until it was no longer detected in the population .",
"Differences in replicative fitness a... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"animal models",
"developmental biology",
"drosophila melanogaster",
"model organisms",
"signaling",
"cell growth",
"molecular development",
"biology",
"molecular cell biology"
] | CDP-Diacylglycerol Synthetase Coordinates Cell Growth and Fat Storage through Phosphatidylinositol Metabolism and the Insulin Pathway | journal.pgen.1004172 | null | [
[
"During development , animals grow rapidly by both cell proliferation and cell growth .",
"Cell growth is a heavily energy-dependent process and requires large amounts of phospholipids for expansion of cellular membranes and other cellular needs .",
"Fat storage on the other hand is an energy-saving p... | [
"During development , animals usually undergo a rapid growth phase followed by a homeostatic stage when growth has ceased .",
"The increase in cell size and number during the growth phase requires a large amount of lipids; while in the static state , excess lipids are usually stored in adipose tissues in preparat... | [
"During development , animals undergo a rapid increase in cell size and number , which requires large amounts of lipids , in the form of phospholipids , for the expansion of cell membranes .",
"Once the growth phase ends , excess lipids are usually stored as body fat , in the form of triacylglycerol ( TAG ) , for... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"invertebrates",
"gene regulation",
"regulatory proteins",
"dna-binding proteins",
"animals",
"circadian oscillators",
"animal models",
"drosophila melanogaster",
"model organisms",
"immunoprecipitation",
"experimental organism systems",
"transcription factors",
"chronob... | O-GlcNAcylation of PERIOD regulates its interaction with CLOCK and timing of circadian transcriptional repression | journal.pgen.1007953 | null | [
[
"Circadian clocks are endogenous protein machines that integrate external time cues and internal metabolic states to impose temporal organization on physiology , metabolism , and behavior ( reviewed in [1–2] ) .",
"They allow organisms from all kingdoms of life , which experience perpetual 24-hour day-nig... | [
"Circadian clocks coordinate time-of-day-specific metabolic and physiological processes to maximize organismal performance and fitness .",
"In addition to light and temperature , which are regarded as strong zeitgebers for circadian clock entrainment , metabolic input has now emerged as an important signal for cl... | [
"Circadian clocks are self-sustained , endogenous pacemakers that enable organisms to anticipate daily environmental changes and resource abundance to perform specific time-of-day activities and achieve optimal survival .",
"Multiple time cues are interpreted by circadian clocks to facilitate synchrony between or... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"t helper cells",
"invertebrates",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"cytokines",
"helminths",
"immunology",
"tropical diseases",
"parasitic diseases",
"animals",
"bacterial diseases",
"developmental biology",
"m... | Mixed Th1 and Th2 Mycobacterium tuberculosis-specific CD4 T cell responses in patients with active pulmonary tuberculosis from Tanzania | journal.pntd.0005817 | null | [
[
"Helminth infections are endemic in many African countries with different prevalence depending on the geographic region helminth species and age of population [1] .",
"Soil transmitted helminth infections are among the most common infections , transmitted via soil contaminated by eggs excreted from human ... | [
"Mycobacterium tuberculosis ( Mtb ) and helminth infections elicit antagonistic immune effector functions and are co-endemic in several regions of the world .",
"We therefore hypothesized that helminth infection may influence Mtb-specific T-cell immune responses .",
"We evaluated the cytokine profile of Mtb-spe... | [
"Mycobacterium tuberculosis ( Mtb ) and helminth infections are co-endemic in several regions of the world and their immune responses may be mutually antagonistic .",
"We therefore hypothesized that helminth infection would impact and potentially shape Mtb-specific T-cell responses and systemic inflammation in pa... | 2017 |
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