headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/mechanisms of resistance and susceptibility, including host genetics",
"virology/immunodeficiency viruses",
"virology/host antiviral responses"
] | APOBEC3G Inhibits Elongation of HIV-1 Reverse Transcripts | journal.ppat.1000231 | null | [
[
"APOBEC3G ( A3G ) is a potent anti-viral polynucleotide cytidine deaminase , initially identified as the cellular target of the HIV-1 viral infectivity factor ( Vif ) protein [1] .",
"Since this discovery , many APOBEC proteins from various species have been shown to inhibit the replication of a diverse r... | [
"APOBEC3G ( A3G ) is a host cytidine deaminase that , in the absence of Vif , restricts HIV-1 replication and reduces the amount of viral DNA that accumulates in cells .",
"Initial studies determined that A3G induces extensive mutation of nascent HIV-1 cDNA during reverse transcription .",
"It has been proposed... | [
"APOBEC proteins are cell-encoded factors that inhibit the replication of numerous retroviruses , such as HIV-1 , and retrotransposons .",
"In many cases , inhibition is clearly associated with cytidine-to-uridine editing of viral or transposon DNA .",
"On the other hand , a number of studies with particular AP... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"microbiology/applied microbiology",
"microbiology/microbial physiology and metabolism",
"microbiology/medical microbiology"
] | A Novel Small Acid Soluble Protein Variant Is Important for Spore Resistance of Most Clostridium perfringens Food Poisoning Isolates | journal.ppat.1000056 | null | [
[
"Clostridium perfringens is the 2nd most commonly-identified agent of bacterial food poisoning ( FP ) in the USA and UK , where ( respectively ) 250 , 000 or 85 , 000 cases of C . perfringens FP occur annually [1] , [2] , [3] .",
"C . perfringens FP also currently ranks as the second or third leading caus... | [
"Clostridium perfringens is a major cause of food poisoning ( FP ) in developed countries .",
"C . perfringens isolates usually induce the gastrointestinal symptoms of this FP by producing an enterotoxin that is encoded by a chromosomal ( cpe ) gene .",
"Those typical FP strains also produce spores that are ext... | [
"Spores made by pathogenic Bacillus and Clostridium spp .",
"contribute to disease transmission .",
"Clostridium perfringens food poisoning ( FP ) isolates typically produce spores with exceptional resistance to heat and sodium nitrite .",
"This spore resistance probably facilitates FP strain survival in impr... | 2008 |
[
"Introduction",
"General Methods",
"Experiments and Results",
"Discussion"
] | [
"medicine",
"biology"
] | A Neglected Aspect of the Epidemiology of Sleeping Sickness: The Propensity of the Tsetse Fly Vector to Enter Houses | journal.pntd.0002086 | null | [
[
"Sleeping sickness , or human African trypanosomiasis , is caused by two species of trypanosome , i . e . , Trypanosoma brucei gambiense and T . b .",
"rhodesiense , that are transmitted by tsetse flies ( Glossina spp . ) when taking blood from hosts [1] .",
"It seems to have been assumed that the ris... | [
"When taking a bloodmeal from humans , tsetse flies can transmit the trypanosomes responsible for sleeping sickness , or human African trypanosomiasis .",
"While it is commonly assumed that humans must enter the normal woodland habitat of the tsetse in order to have much chance of contacting the flies , recent st... | [
"To explore the nature of houses as venues for the contact between humans and tsetse flies , and hence for the transmission of sleeping sickness , we studied the sex and species composition and physiological condition of samples of tsetse caught in various types of house throughout the day and at different seasons ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"gene regulation",
"regulatory proteins",
"brassica",
"dna-binding proteins",
"hormones",
"regulator genes",
"plant science",
"model organisms",
"plant hormones",
"membrane receptor signaling",
"hormone receptor signaling",
"transcription factors",
"experimental organism systems",
"gene ty... | A dynamic genetic-hormonal regulatory network model explains multiple cellular behaviors of the root apical meristem of Arabidopsis thaliana | journal.pcbi.1005488 | null | [
[
"The root apical meristem ( RAM ) of A . thaliana is an important model for understanding the complex mechanisms underlying cell differentiation and morphogenesis during organ development of multicellular organisms [1–8] .",
"The RAM of A . thaliana has a relatively simple cellular organization while it s... | [
"The study of the concerted action of hormones and transcription factors is fundamental to understand cell differentiation and pattern formation during organ development .",
"The root apical meristem of Arabidopsis thaliana is a useful model to address this .",
"It has a stem cell niche near its tip conformed o... | [
"In multicellular development , signaling molecules are essential for the organization of cells into complex differentiated tissues .",
"It is widely acknowledged that tissue or cell context is instructive for the specificity of cell behavior responses , but the underlying system-level mechanisms remain unresolve... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology",
"molecular cell biology"
] | CD81 Is Essential for the Re-entry of Hematopoietic Stem Cells to Quiescence following Stress-Induced Proliferation Via Deactivation of the Akt Pathway | journal.pbio.1001148 | A protein that is thought to orchestrate the distribution of other signaling molecules on the cell membrane, CD81, is critical to maintaining the functional integrity of hematopoietic stem cells during their regeneration. | [
[
"Hematopoietic stem cells ( HSCs ) , which represent around 1/104 to 1/105 bone marrow cells , can proliferate to replenish the hematopoietic system after its exposure to environmental stresses such as infection , ablative chemotherapy , or irradiation .",
"The stem cell compartment is maintained by self-... | [
"The regulatory mechanisms governing the cell cycle progression of hematopoietic stem cells ( HSCs ) are well characterized , but those responsible for the return of proliferating HSCs to a quiescent state remain largely unknown .",
"Here , we present evidence that CD81 , a tetraspanin molecule acutely responsive... | [
"Hematopoietic stem cells ( HSCs ) remain dormant in the bone marrow until needed to replenish the hematopoietic system , at which point they are stimulated to proliferate extensively , undergoing both regeneration ( self-renewal ) and differentiation .",
"Self-renewal is key to maintaining an adequate HSC reserv... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Models"
] | [
"antimicrobials",
"cell physiology",
"medicine and health sciences",
"evolutionary biology",
"cell cycle and cell division",
"plasmids",
"cell processes",
"drugs",
"microbiology",
"applied mathematics",
"cell metabolism",
"plasmid construction",
"simulation and modeling",
"algorithms",
"... | Evolutionary model for the unequal segregation of high copy plasmids | journal.pcbi.1006724 | null | [
[
"Plasmids are circular or linear pieces of DNA of different size ( several 1000 to 100 , 000 bp ) encoding beneficial genetic information for their microbial hosts replicated independently from the chromosome ( s ) [4] .",
"In some cases , plasmids are essential for the growth and survival of the microorg... | [
"Plasmids are extrachromosomal DNA elements of microorganisms encoding beneficial genetic information .",
"They were thought to be equally distributed to daughter cells during cell division .",
"Here we use mathematical modeling to investigate the evolutionary stability of plasmid segregation for high-copy plas... | [
"In the last years , it becomes more and more clear that heterogeneity in isogenic bacterial populations is rather the rule than the exception .",
"This observation is interesting as it reveals the complex social life of bacteria , and also because of tremendous practical implications in medicine , biotechnology ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Anaplastic Lymphoma Kinase Acts in the Drosophila Mushroom Body to Negatively Regulate Sleep | journal.pgen.1005611 | null | [
[
"Sleep behavior is conserved from worms and insects to fish and mammals [1] .",
"Why animals spend a large amount of time seemingly doing nothing , passing on opportunities to forage , hunt or mate , and remaining vulnerable to dangers , is still a mystery .",
"It is hypothesized that a major function... | [
"Though evidence is mounting that a major function of sleep is to maintain brain plasticity and consolidate memory , little is known about the molecular pathways by which learning and sleep processes intercept .",
"Anaplastic lymphoma kinase ( Alk ) , the gene encoding a tyrosine receptor kinase whose inadvertent... | [
"Animal and human studies suggest that sleep has a profound impact on learning and memory .",
"However , little is known about the molecular pathways linking these phenomena .",
"We report that mutations in the Drosophila Anaplastic lymphoma kinase ( Alk ) gene , an ortholog of a human oncogene ALK , cause incr... | 2015 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"molecular biology/bioinformatics",
"computational biology/macromolecular structure analysis",
"molecular biology/rna-protein interactions"
] | Classifying RNA-Binding Proteins Based on Electrostatic Properties | journal.pcbi.1000146 | null | [
[
"In recent years , there has been a growing appreciation for the importance of RNA and its interacting proteins .",
"RNA-binding proteins ( RBPs ) function both in basic cellular processes and as key regulators of gene expression .",
"Genome sequencing and analysis has identified many highly conserved... | [
"Protein structure can provide new insight into the biological function of a protein and can enable the design of better experiments to learn its biological roles .",
"Moreover , deciphering the interactions of a protein with other molecules can contribute to the understanding of the protein's function within cel... | [
"Gene expression in all living organisms is regulated by a complex set of events at both transcriptional and posttranscriptional levels .",
"RNA-binding proteins play a key role in posttranscriptional events including splicing , stability , transport , and translation .",
"Nowadays , there is increasing evidenc... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Unraveling Adaptation in Eukaryotic Pathways: Lessons from Protocells | journal.pcbi.1003300 | null | [
[
"The ability to adapt to different environmental conditions is a hallmark of any living organism , allowing sensory systems to adjust their sensitivity to changes in nutrient availability , stress , and other stimuli [1] , [2] .",
"Adaptation mechanisms generally rely on biochemical feedback pathways , sp... | [
"Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation .",
"Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes , all require energy consumption .",
"Here , we present two minimal models showing that expenditure ... | [
"Adaptation is a common feature in sensory systems , well familiar to us from light and dark adaptation of our visual system .",
"Biological cells , ranging from bacteria to complex eukaryotes , including single-cell organisms and human sensory receptors , adopt different strategies to fulfill this property .",
... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"liver",
"respiratory infections",
"gene regulation",
"immunology",
"rna extraction",
"microbiology",
"pulmonology",
"micrornas",
"extraction techniques",
"research and analysis methods",
"animal cells",
"gene expression",
"hepatocytes",
"viral replication... | MicroRNA and cellular targets profiling reveal miR-217 and miR-576-3p as proviral factors during Oropouche infection | journal.pntd.0006508 | null | [
[
"Oropouche Virus ( OROV ) is the etiological agent of Oropouche fever , an arthropod-borne viral disease characterized by symptoms like fever , headache , myalgia , arthralgia , malaise , photophobia , nausea , vomiting , dizziness , skin rash , and in few cases encephalitis and meningitis [1–7] .",
"It w... | [
"Oropouche Virus is the etiological agent of an arbovirus febrile disease that affects thousands of people and is widespread throughout Central and South American countries .",
"Although isolated in 1950’s , still there is scarce information regarding the virus biology and its prevalence is likely underestimated ... | [
"Oropouche Virus causes typical arboviral febrile illness and is widely distributed in tropical region of Americas , mainly Amazon region , associated with cases of encephalitis .",
"500 , 000 people are estimated to be infected with Oropouche worldwide and some states in Brazil detected higher number of cases am... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"parasitology",
"biology and life sciences",
"immunology"
] | MIF Contributes to Trypanosoma brucei Associated Immunopathogenicity Development | journal.ppat.1004414 | null | [
[
"African trypanosomiasis is a parasitic disease of medical and veterinary importance that adversely affects the public health and economic development of sub-Saharan Africa .",
"The causative agents , trypanosomes transmitted by the tsetse fly ( Glossina spp ) , are extracellular hemoflagellated protozoan... | [
"African trypanosomiasis is a chronic debilitating disease affecting the health and economic well-being of many people in developing countries .",
"The pathogenicity associated with this disease involves a persistent inflammatory response , whereby M1-type myeloid cells , including Ly6Chigh inflammatory monocytes... | [
"Uncontrolled inflammation is a major contributor to pathogenicity development during many chronic parasitic infections , including African trypanosome infections .",
"Hence , therapies should aim at re-establishing the balance between pro- and anti-inflammatory responses to reduce tissue damage .",
"Our experi... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"infectious disease epidemiology",
"pathogens",
"spatial epidemiology",
"microbiology",
"geographical locations",
"tropical diseases",
"ebola hemorrhagic fever",
"viruses",
"filoviruses",
"mathematics",
"rn... | Potential Impact of Sexual Transmission on Ebola Virus Epidemiology: Sierra Leone as a Case Study | journal.pntd.0004676 | null | [
[
"Recent reports suggesting the potential for sexual transmission of Ebola virus from convalescent survivors have raised a number of important questions regarding its impact on the final phase of the epidemic in West Africa [1 , 2] .",
"Even once the worst hit countries of Guinea , Liberia , and Sierra Leo... | [
"Sexual transmission of Ebola virus disease ( EVD ) 6 months after onset of symptoms has been recently documented , and Ebola virus RNA has been detected in semen of survivors up to 9 months after onset of symptoms .",
"As countries affected by the 2013–2015 epidemic in West Africa , by far the largest to date , ... | [
"Researchers have recently raised suspicion that the Ebola virus can be transmitted sexually from survivors after recovering from the life-threatening acute phase characteristic of Ebola virus disease ( EVD ) .",
"However , the nature of the impact sexual transmission from convalescent survivors may have on disea... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"statistical mechanics",
"applied mathematics",
"bayes theorem",
"probability distribution",
"animal behavior",
"mathematics",
"theoretical ecology",
"stochastic processes",
"zoology",
"complex systems",
"theoretical biology",
"probability density",
"biology",
"probability theory",
"beha... | Multi-scale Inference of Interaction Rules in Animal Groups Using Bayesian Model Selection | journal.pcbi.1002308 | null | [
[
"The most striking features of the collective motion of animal groups are the large-scale patterns produced by flocks , schools and other groups .",
"These patterns can extend over scales that exceed the interaction ranges of the individuals within the group [1]–[4] .",
"For most flocking animals , th... | [
"Inference of interaction rules of animals moving in groups usually relies on an analysis of large scale system behaviour .",
"Models are tuned through repeated simulation until they match the observed behaviour .",
"More recent work has used the fine scale motions of animals to validate and fit the rules of in... | [
"The collective movement of animals in a group is an impressive phenomenon whereby large scale spatio-temporal patterns emerge from simple interactions between individuals .",
"Theoretically , much of our understanding of animal group motion comes from models inspired by statistical physics .",
"In these models... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"taxonomy",
"livestock",
"medicine and health sciences",
"body fluids",
"pathology and laboratory medicine",
"pathogens",
"geographical locations",
"microbiology",
"vertebrates",
"diet",
"animals",
"animal products",
"bacterial diseases",
"phylogenetics",
"data management",
"nutrition"... | Emergence of phylogenetically diverse and fluoroquinolone resistant Salmonella Enteritidis as a cause of invasive nontyphoidal Salmonella disease in Ghana | journal.pntd.0007485 | null | [
[
"Nontyphoidal Salmonella ( NTS ) are a leading cause of bloodstream infection in sub-Saharan Africa ( sSA ) , a clinical syndrome referred to as invasive nontyphoidal Salmonella ( iNTS ) disease .",
"iNTS disease in sSA is most commonly caused by Salmonella enterica serovars Salmonella Typhimurium or Salm... | [
"Salmonella enterica serovar Enteritidis is a cause of both poultry- and egg-associated enterocolitis globally and bloodstream-invasive nontyphoidal Salmonella ( iNTS ) disease in sub-Saharan Africa ( sSA ) .",
"Distinct , multi-drug resistant genotypes associated with iNTS disease in sSA have recently been descr... | [
"Salmonella enterica serovar Enteritidis is both a prominent global cause of zoonotic gastroenteritis , in association with the industrial production of eggs and poultry , and of bloodstream-invasive infection in sub-Saharan Africa , a clinical syndrome referred to as invasive nontyphoidal Salmonella ( iNTS ) disea... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | New Players in the Same Old Game: Disturbance of Group 2 Innate Lymphoid Cells in HIV-1 and Mycobacterium leprae Co-infected Patients | journal.pntd.0004030 | null | [
[
"Leprosy is a chronic infectious disease caused by the intracellular bacillus Mycobacterium leprae .",
"Although usually asymptomatic , some subjects develop the clinical form of disease , exhibiting skin and peripheral nerves lesions [1] .",
"In 2013 , the Brazilian Healthy Department , registered 31... | [
"Leprosy control is achieved through a fine-tuning of TH1 and TH2 immune response pattern balance .",
"Given the increasing epidemiological overlay of HIV and M . leprae infections , immune response in co-infected patients consists in an important contemporary issue .",
"Here we describe for the first time the ... | [
"Mycobacterium leprae is a clinical relevant pathogen that can lead to leprosy upon infection .",
"This chronic infectious disease is characterized by the appearance of skin and peripheral nerve lesions .",
"Normally , a healthy immune system is able to control the infection and impede the generation of lesions... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Polymorphism in the Processing Body Component Ge-1 Controls Resistance to a Naturally Occurring Rhabdovirus in Drosophila | journal.ppat.1005387 | null | [
[
"Hosts and their pathogens are engaged in a never-ending arms race , where the evolution of new defences in turn selects for pathogens that can overcome those defences .",
"In order to understand how hosts are evolving resistance , it is necessary to investigate the genes that cause variation in the susce... | [
"Hosts encounter an ever-changing array of pathogens , so there is continual selection for novel ways to resist infection .",
"A powerful way to understand how hosts evolve resistance is to identify the genes that cause variation in susceptibility to infection .",
"Using high-resolution genetic mapping we have ... | [
"Hosts and their pathogens are engaged in a never-ending arms race , and hosts must continually evolve new defences to protect themselves from infection .",
"In the fruit fly Drosophila melanogaster we show that virus resistance can evolve through a single mutation .",
"In flies that are highly resistant to a n... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"microbiology",
"vertebrates",
"cloning",
"parasitic diseases",
"animals",
"protozoan life cycles",
"mammals",
"dogs",
"parasitic protozoans",
"developmental biology",
"protozoans",
"leishmania",
"genome analysis",
"molecular biology techniques",
"promas... | Induction of allopurinol resistance in Leishmania infantum isolated from dogs | journal.pntd.0005910 | null | [
[
"Visceral leishmaniasis caused by Leishmania infantum is a life threatening disease , affecting humans in Europe , Asia , North Africa and Latin America , as well as domestic dogs which are the main reservoir for this infection [1 , 2] .",
"We recently reported the detection of disease relapse in infected... | [
"Resistance to allopurinol in zoonotic canine leishmaniasis has been recently shown to be associated with disease relapse in naturally-infected dogs .",
"However , information regarding the formation of resistance and its dynamics is lacking .",
"This study describes the successful in-vitro induction of allopur... | [
"Visceral leishmaniasis caused by the parasite Leishmania infantum is a neglected tropical disease transmitted from animal hosts to humans by sand fly bites .",
"This potentially fatal disease affects thousands of people annually and threatens millions who live in disease risk areas .",
"Domestic dogs are consi... | 2017 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [] | Improved estimates for extinction probabilities and times to extinction for populations of tsetse (Glossina spp) | journal.pntd.0006973 | null | [
[
"Both sexes of tsetse ( Glossina spp . ) feed only on blood and are vectors of human and animal trypanosomiasis in Africa .",
"They are also very unusual biologically .",
"During each reproductive event , the mature adult female tsetse ovulates a single egg that is retained in the uterus until it hatc... | [
"A published study used a stochastic branching process to derive equations for the mean and variance of the probability of , and time to , extinction in population of tsetse flies ( Glossina spp ) as a function of adult and pupal mortality , and the probabilities that a female is inseminated by a fertile male .",
... | [
"We derive equations for the mean and variance of the probability of , and time to , extinction in population of tsetse flies ( Glossina spp ) , the vectors of trypanosomiasis in sub-Saharan Africa .",
"In so doing we provide the complete proofs for all results , which were not provided in a previously published ... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"heme",
"b vitamins",
"medicine and health sciences",
"pathology and laboratory medicine",
"chemical compounds",
"gene regulation",
"pathogens",
"bacillus",
"microbiology",
"organic compounds",
"toxicology",
"toxicity",
"prokaryotic models",
"experimental organism systems",
"bacteria",
... | Intracellular Zn(II) Intoxication Leads to Dysregulation of the PerR Regulon Resulting in Heme Toxicity in Bacillus subtilis | journal.pgen.1006515 | null | [
[
"Approximately 30% of proteins require a metal cofactor .",
"Unlike iron ( Fe ( II ) ) , which can generate cell damaging hydroxyl radicals in the presence of hydrogen peroxide ( Fenton reaction ) , Zn ( II ) is not redox reactive .",
"As a result , Zn ( II ) is favored as a structural cofactor that f... | [
"Transition metal ions ( Zn ( II ) , Cu ( II ) / ( I ) , Fe ( III ) / ( II ) , Mn ( II ) ) are essential for life and participate in a wide range of biological functions .",
"Cellular Zn ( II ) levels must be high enough to ensure that it can perform its essential roles .",
"Yet , since Zn ( II ) binds to ligan... | [
"Zinc ( Zn ( II ) ) is often considered to be a “first among equals” in metal ion homeostasis .",
"Zn ( II ) is critically important to the proper function of many cellular processes , yet is toxic at high levels .",
"The molecular basis for Zn ( II ) intoxication is poorly understood .",
"Using a forward gen... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"livestock",
"medicine and health sciences",
"parasite groups",
"ixodes",
"pathology and laboratory medicine",
"ruminants",
"pathogens",
"geographical locations",
"microbiology",
"vertebrates",
"buffaloes",
"animals",
"mammals",
"parasitology",
"apicomplexa",
"bovine... | A study of ticks and tick-borne livestock pathogens in Pakistan | journal.pntd.0005681 | null | [
[
"Pakistan , a predominantly farming nation , has an agriculture sector representing 20 . 9% of the country’s total gross domestic product and employs 43 . 4% of the country’s total workforce .",
"According to the 2013/14 Pakistan Livestock Census [1] , the livestock sector within the agricultural economy ... | [
"As obligate blood-feeding arthropods , ticks transmit pathogens to humans and domestic animals more often than other arthropod vectors .",
"Livestock farming plays a vital role in the rural economy of Pakistan , and tick infestation causes serious problems with it .",
"However , research on tick species divers... | [
"Ticks are known for their negative impact on animal and human health through infestation and are capable of transmitting a wide range of pathogens including protozoan , viruses , and bacteria such as the spirochetes and rickettsiae .",
"Ticks are widely distributed in different ecological , and geographical regi... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"pollen",
"developmental biology",
"plant anatomy",
"plant science",
"cell biology",
"fertilization",
"gene expression",
"genetics",
"biology and life sciences",
"molecular cell biology",
"flowering plants",
"plants",
"organisms"
] | An ARID Domain-Containing Protein within Nuclear Bodies Is Required for Sperm Cell Formation in Arabidopsis thaliana | journal.pgen.1004421 | null | [
[
"In contrast to animals , where meiotic products directly become gametes , the germline in plants is established by mitotic divisions after meiosis is completed .",
"The male germline arises by an asymmetric mitotic division of each meiotic product .",
"The resulting vegetative and generative cells of... | [
"In plants , each male meiotic product undergoes mitosis , and then one of the resulting cells divides again , yielding a three-celled pollen grain comprised of a vegetative cell and two sperm cells .",
"Several genes have been found to act in this process , and DUO1 ( DUO POLLEN 1 ) , a transcription factor , pl... | [
"For all eukaryotes , gamete formation is an essential aspect of sexual reproduction .",
"Unlike in animals , where meiotic products directly become gametes , the germline in plants is established by two consecutive mitotic divisions after meiosis is completed .",
"The first mitosis is asymmetric , forming a la... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Material and Methods"
] | [
"phosphorylation",
"rna-binding proteins",
"cellular stress responses",
"rna interference",
"messenger rna",
"cell processes",
"polyribosomes",
"immunoprecipitation",
"epigenetics",
"cellular structures and organelles",
"research and analysis methods",
"heat shock response",
"genetic interfe... | Regulating a Post-Transcriptional Regulator: Protein Phosphorylation, Degradation and Translational Blockage in Control of the Trypanosome Stress-Response RNA-Binding Protein ZC3H11 | journal.ppat.1005514 | null | [
[
"The African trypanosome Trypanosoma brucei is responsible for sleeping sickness in humans and nagana in livestock .",
"Bloodstream-form trypanosomes , which are found in mammalian blood and tissue fluids , are exposed to temperatures ranging from about 36°C to 40°C ( fever ) .",
"Trypanosomes are tra... | [
"The life cycle of the mammalian pathogen Trypanosoma brucei involves commuting between two markedly different environments: the homeothermic mammalian host and the poikilothermic invertebrate vector .",
"The ability to resist temperature and other stresses is essential for trypanosome survival .",
"Trypanosome... | [
"Like other organisms , the mammalian pathogen Trypanosoma brucei is able to sense environmental changes and to change its gene expression accordingly .",
"In contrast with other organisms , however , trypanosomes and related kinetoplastids effect these changes almost exclusively by controlling the translation of... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"respiratory infections",
"pathogens",
"tropical diseases",
"microbiology",
"geographical locations",
"pulmonology",
"fungi",
"lymph nodes",
"signs and symptoms",
"lymphatic system",
"paracoccidioidomycosis",
"paracoccidi... | Clinical and epidemiological features of paracoccidioidomycosis due to Paracoccidioides lutzii | journal.pntd.0007437 | null | [
[
"Paracoccidioidomycosis ( PCM ) is the most prevalent deep mycosis in Latin America , being endemic only in Brazil , Colombia and Venezuela .",
"In Brazil , the state of Mato Grosso ( Middle-West region ) , has a large number of cases , and the recently described new species P . lutzii [1] was recovered f... | [
"The fungus Paracoccidioides lutzii was recently included as a new causative species of paracoccidioidomycosis ( PCM ) and most cases have been reported from Brazil .",
"According to available epidemiological information , P . lutzii is concentrated in the Middle-West region in Brazil , mainly in the state of Mat... | [
"Paracoccidioidomycosis ( PCM ) is an endemic mycosis in Latin America with high incidence in Brazil .",
"The fungi Paracoccidioides brasiliensis ( including genetic groups S1 , PS2 , PS3 and PS4 ) and Paracoccidioides lutzii are the etiological agents , but little is known about the clinical manifestations of PC... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"protein interactions",
"proteins",
"biology"
] | A Receptor-based Switch that Regulates Anthrax Toxin Pore Formation | journal.ppat.1002354 | null | [
[
"Cellular receptors can act as molecular switches that initiate conformational changes in microbial proteins required for cellular entry .",
"Examples of such switches include an anthrax toxin receptor ( described in detail below ) as well as those for a number of viruses including HIV-1 and other retrovi... | [
"Cellular receptors can act as molecular switches , regulating the sensitivity of microbial proteins to conformational changes that promote cellular entry .",
"The activities of these receptor-based switches are only partially understood .",
"In this paper , we sought to understand the mechanism that underlies ... | [
"The bacterium that causes anthrax produces a toxin called anthrax toxin that is largely responsible for causing disease symptoms .",
"The first step in anthrax intoxication involves binding of the toxin to a specific protein , called a receptor , on the cell surface .",
"Receptor-binding acts like a switch to ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"systems biology",
"genetics",
"biology and life sciences",
"microbiology",
"computational biology",
"molecular biology"
] | A Regulatory Hierarchy Controls the Dynamic Transcriptional Response to Extreme Oxidative Stress in Archaea | journal.pgen.1004912 | null | [
[
"All organisms encounter reactive oxygen species ( ROS ) originating from biotic and abiotic sources .",
"ROS are produced at relatively low levels as natural byproducts of aerobic respiration , Fenton reactions , or other biotic sources [1] , [2] .",
"In contrast , abiotic sources include environment... | [
"Networks of interacting transcription factors are central to the regulation of cellular responses to abiotic stress .",
"Although the architecture of many such networks has been mapped , their dynamic function remains unclear .",
"Here we address this challenge in archaea , microorganisms possessing transcript... | [
"Complex circuits of genes rather than a single gene underlie many important processes such as disease , development , and cellular damage repair .",
"Although the wiring of many of these circuits has been mapped , how circuits operate in real time to carry out their functions is poorly understood .",
"Here we ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/nosocomial and healthcare-associated infections",
"cell biology/cell signaling",
"biochemistry/protein chemistry",
"genetics and genomics/disease models",
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis"
] | A Complex Extracellular Sphingomyelinase of Pseudomonas aeruginosa Inhibits Angiogenesis by Selective Cytotoxicity to Endothelial Cells | journal.ppat.1000420 | null | [
[
"The diverse roles that phospholipase C ( PLCs ) and sphingomyelinase ( SMase ) play in biology and medicine are extraordinary .",
"Both types of phosphodiesterases and their substrate products ( e . g . ceramide , diacylglycerol ) have proven to be far more multifaceted than initially perceived , and the... | [
"The hemolytic phospholipase C ( PlcHR ) expressed by Pseudomonas aeruginosa is the original member of a Phosphoesterase Superfamily , which includes phosphorylcholine-specific phospholipases C ( PC-PLC ) produced by frank and opportunistic pathogens .",
"PlcHR , but not all its family members , is also a potent ... | [
"Pseudomonas aeruginosa is a major bacterial opportunistic pathogen responsible for acute ( e . g . , sepsis ) and chronic infections ( e . g . , pulmonary ) .",
"While it expresses assorted extracellular toxins that in one way or another contribute to pathogenesis , the precise cellular and molecular mechanisms ... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"pharmacologic analysis",
"body weight",
"medicine and health sciences",
"body fluids",
"clinical research design",
"diet",
"research design",
"physiological parameters",
"nutrition",
"pharmaceutics",
"drug administration",
"pharmacology",
"research and analysis methods",
"elimination half... | Safety and pharmacokinetic profile of fixed-dose ivermectin with an innovative 18mg tablet in healthy adult volunteers | journal.pntd.0006020 | null | [
[
"The control of Neglected Tropical Diseases ( NTDs ) has in ivermectin ( IVM ) the most significant tool among all the drugs used for morbidity control and interruption of transmision .",
"Due to its impact on onchocerciasis and lymphatic filariasis ( LF ) , this macrocyclic lactone has been used in milli... | [
"ClinicalTrials . gov NCT03173742 ."
] | [
"Current efforts for the control of poverty-related diseases provide drug treatments through mass drug administration ( MDA ) as a key component .",
"Ivermectin is an antiparasitary drug which has been used to fight some of these diseases , and millions of treatments have been distributed with a favorable toxicit... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"cell death",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"cardiovascular anatomy",
"immunology",
"tropical diseases",
"cell processes",
"parasitic diseases",
"capillaries",
"signs and symptoms",
"red blood cells",
"cytotoxic t cells"... | A quantitative brain map of experimental cerebral malaria pathology | journal.ppat.1006267 | null | [
[
"Cerebral Malaria ( CM ) , one of the most severe complications of Plasmodium falciparum ( Pf ) infection , is defined clinically by an unrousable coma in the presence of Pf parasitemia , with no other known cause of neuropathology [1] .",
"Although the syndrome only occurs in 1% of Pf infections , it has... | [
"The murine model of experimental cerebral malaria ( ECM ) has been utilised extensively in recent years to study the pathogenesis of human cerebral malaria ( HCM ) .",
"However , it has been proposed that the aetiologies of ECM and HCM are distinct , and , consequently , no useful mechanistic insights into the p... | [
"Cerebral malaria ( HCM ) is the most severe complication of malaria infection .",
"Despite this , we have an incomplete understanding of the cause ( pathogenesis ) of the syndrome .",
"To improve our understanding of HCM pathogenesis , animal models of the syndrome have been developed .",
"The most commonly ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant biology"
] | Specific Targeting of a Plasmodesmal Protein Affecting Cell-to-Cell Communication | journal.pbio.0060007 | Little is know about the structure and function of plant cell-to-cell connections, called plasmodesmata. This paper describes a new family of plasmodesmal proteins and the processes controlling their subcellular trafficking. | [
[
"Plasmodesmata are channels that cross the cell wall and establish symplastic continuity throughout most of the plant .",
"Their importance has been highlighted by the range of diverse non–cell-autonomous functions that depend on intercellular macromolecular communication through plasmodesmata .",
"He... | [
"Plasmodesmata provide the cytoplasmic conduits for cell-to-cell communication throughout plant tissues and participate in a diverse set of non–cell-autonomous functions .",
"Despite their central role in growth and development and defence , resolving their modus operandi remains a major challenge in plant biolog... | [
"In plants , cylindrical , microscopic channels called plasmodesmata provide intracellular connections between cells for communication and material transport , and are important for many aspects of plant growth and defence .",
"We identify a novel family of plasmodesmata-located proteins ( called PDLP1 ) with fea... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neuroscience"
] | Iroquois Complex Genes Induce Co-Expression of rhodopsins in Drosophila | journal.pbio.0060097 | Iro-C genes control the co-expression of sensory receptors. | [
[
"The primary role of sensory organs is to probe the environment and to transmit precisely this information to the brain for processing .",
"The visual and olfactory systems are composed of sensory epithelia with thousands of sensory receptor cells , each specifically expressing a single sensory receptor g... | [
"The Drosophila eye is a mosaic that results from the stochastic distribution of two ommatidial subtypes .",
"Pale and yellow ommatidia can be distinguished by the expression of distinct rhodopsins and other pigments in their inner photoreceptors ( R7 and R8 ) , which are implicated in color vision .",
"The pal... | [
"Most sensory systems follow the rule “one receptor molecule per receptor cell . ”",
"For example , photoreceptors in the fly eye and cones in the human eye each express only one light-sensitive rhodopsin .",
"Rhodopsins are G-coupled protein receptors , a class of ancient signaling molecules that mediate not j... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Deletion of the Murine Cytochrome P450 Cyp2j Locus by Fused BAC-Mediated Recombination Identifies a Role for Cyp2j in the Pulmonary Vascular Response to Hypoxia | journal.pgen.1003950 | null | [
[
"Human cytochrome P450 2J2 ( CYP2J2 ) is abundant in cardiovascular tissues and pulmonary endothelium [1] and metabolizes arachidonic acid ( AA ) to epoxyeicosatrienoic acids ( EETs ) and hydroxyeicosatetraenoic acids ( HETEs ) , short-lived mediators that have potent vascular protective properties [2]–[4] ."... | [
"Epoxyeicosatrienoic acids ( EETs ) confer vasoactive and cardioprotective functions .",
"Genetic analysis of the contributions of these short-lived mediators to pathophysiology has been confounded to date by the allelic expansion in rodents of the portion of the genome syntenic to human CYP2J2 , a gene encoding ... | [
"In mice and humans , the CYP2J class of cytochrome P450 epoxygenases metabolizes arachidonic acid ( AA ) to epoxyeicosatrienoic acids ( EETs ) , short-lived mediators with effects on both the pulmonary and systemic vasculature .",
"Genetic dissection of CYP2J function to date has been complicated by allelic expa... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"action potentials",
"medicine and health sciences",
"hek 293 cells",
"membrane potential",
"biological cultures",
"electrophysiology",
"neuroscience",
"animal models",
"mutation",
"model organisms",
"immunoprecipitation",
"experimental organism systems",
"research and analysis methods",
"... | Epilepsy-associated gene Nedd4-2 mediates neuronal activity and seizure susceptibility through AMPA receptors | journal.pgen.1006634 | null | [
[
"A hyperactive brain circuit is a common abnormality observed in patients with various neurological and psychiatric disorders , including epilepsies ( 1 ) .",
"Evidence from human genetic studies implicates genes encoding ion channels or their regulators in the etiology of those pathophysiological conditi... | [
"The neural precursor cell expressed developmentally down-regulated gene 4–2 , Nedd4-2 , is an epilepsy-associated gene with at least three missense mutations identified in epileptic patients .",
"Nedd4-2 encodes a ubiquitin E3 ligase that has high affinity toward binding and ubiquitinating membrane proteins .",
... | [
"Many patients with neurological disorders suffer from an imbalance in neuronal and circuit excitability and present with seizure or epilepsy as the common comorbidity .",
"Human genetic studies have identified many epilepsy-associated genes , but the pathways by which those genes are connected to brain circuit e... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"ecology and environmental sciences",
"population genetics",
"vertebrates",
"animals",
"osteichthyes",
"aquatic environments",
"habitats",
"speciation",
"bodies of water",
"dna recombination",
"dna",
"population biology",
"fishes",
"chromosome biology",
"lakes",
"marine and aquatic sci... | Genomics of Rapid Incipient Speciation in Sympatric Threespine Stickleback | journal.pgen.1005887 | null | [
[
"Several empirical studies have looked for such patterns in divergently adapted ecotypes , incipient species and incompletely isolated species with varying degrees of reproductive isolation [23–30] .",
"Most of them have revealed heterogeneous genomic differentiation across genomes with islands of differe... | [
"Ecological speciation is the process by which reproductively isolated populations emerge as a consequence of divergent natural or ecologically-mediated sexual selection .",
"Most genomic studies of ecological speciation have investigated allopatric populations , making it difficult to infer reproductive isolatio... | [
"Ecological speciation can be defined as the evolution of new , reproductively isolated , species driven by natural selection and ecologically-mediated sexual selection .",
"Its genomic signature has mainly been studied in ecotypes and emerging species that started diverging hundreds to thousands of generations a... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"animal models of infection",
"white blood cells",
"immune cells",
"cell biology",
"animal cells",
"immunity",
"viral persistence and latency",
"virology",
"t cells",
"biology and life sciences",
"cellular types",
"immunology",
"microbiology",
"acquired immune system",
"... | Systemic Hematogenous Maintenance of Memory Inflation by MCMV Infection | journal.ppat.1004233 | null | [
[
"Cytomegaloviruses ( CMVs ) are ubiquitous , β-herpesviruses that establish lifelong infections in their hosts .",
"CMV causes an acute systemic viral infection , followed by latency in many cells throughout the body .",
"Cells of the myeloid lineage and endothelial cells from many organs have been sh... | [
"Several low-grade persistent viral infections induce and sustain very large numbers of virus-specific effector T cells .",
"This was first described as a response to cytomegalovirus ( CMV ) , a herpesvirus that establishes a life-long persistent/latent infection , and sustains the largest known effector T cell p... | [
"Herpesviruses persist for the life of the host and must be continuously controlled by a robust immune surveillance effort .",
"In the case of the cytomegalovirus ( CMV ) , this ongoing immune surveillance promotes the accumulation of CMV-specific T cells in a process known as “memory inflation” .",
"We and oth... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"microtubules",
"microtubule dynamics",
"cell processes",
"organisms",
"mutation",
"chromosome mapping",
"microtubule polymerization",
"molecular biology techniques",
"plants",
"cellular structures and organelles",
"nonvascular plants",
"cytoskeleton",
"research and analysis methods",
"seq... | Conditional genetic screen in Physcomitrella patens reveals a novel microtubule depolymerizing-end-tracking protein | journal.pgen.1007221 | null | [
[
"Early adopters of P . patens as a genetic model plant identified its haploid genetics as a valuable attribute for genetic analysis .",
"Mutants displaying a variety of defects , including metabolic and hormonal deficiencies as well as morphological and physiological alterations , were easily isolated usi... | [
"Our ability to identify genes that participate in cell growth and division is limited because their loss often leads to lethality .",
"A solution to this is to isolate conditional mutants where the phenotype is visible under restrictive conditions .",
"Here , we capitalize on the haploid growth-phase of the mo... | [
"Genes important for cell growth are difficult to identify because their disruption often results in the death of the organism .",
"A solution to this problem is to isolate temperature-sensitive mutants where growth is blocked only at high temperatures .",
"Here , we used the moss Physcomitrella patens , a simp... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"gastroenterology and hepatology/gastrointestinal cancers",
"genetics and genomics/epigenetics",
"gastroenterology and hepatology/esophagus",
"oncology/gastrointestinal cancers"
] | Widespread Hypomethylation Occurs Early and Synergizes with Gene Amplification during Esophageal Carcinogenesis | journal.pgen.1001356 | null | [
[
"The incidence of esophageal adenocarcinoma ( EAC ) is increasing at an alarming pace in the United States ( >600% increase since 1975 ) [1] .",
"Since most patients with EAC present at diagnosis with an advanced disease stage , the 5-year survival rate is a dismal 13% [2] , underscoring the pressing need... | [
"Although a combination of genomic and epigenetic alterations are implicated in the multistep transformation of normal squamous esophageal epithelium to Barrett esophagus , dysplasia , and adenocarcinoma , the combinatorial effect of these changes is unknown .",
"By integrating genome-wide DNA methylation , copy ... | [
"The incidence of esophageal adenocarcinoma ( EA ) is increasing at an alarming pace in the United States .",
"Distinct pathological stages of Barrett's metaplasia and low- and high-grade dysplasia can be seen preceding malignant transformation .",
"These precursor lesions provide a unique in vivo model for dee... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neuroscience/motor systems",
"neuroscience",
"neuroscience/theoretical neuroscience",
"physics/condensed matter"
] | Power-Law Scaling in the Brain Surface Electric Potential | journal.pcbi.1000609 | null | [
[
"Neuronal electrical activity may be measured at many scales , from individual ion channels [1] to the largest scale measurement of electroencephalographic ( EEG ) potentials entirely outside the head [2] .",
"Synaptic current produces a change in the local electric field , and it is believed that large s... | [
"Recent studies have identified broadband phenomena in the electric potentials produced by the brain .",
"We report the finding of power-law scaling in these signals using subdural electrocorticographic recordings from the surface of human cortex .",
"The power spectral density ( PSD ) of the electric potential... | [
"For a very long time , the measurement of the large scale potentials produced by the brain from outside of the head , using electroencephalography and magnetoencephalography , and from inside the head , using electrocorticography , has fixated on changes in specific rhythms and frequency ranges .",
"This fixatio... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell death",
"spermatocytes",
"nuclear staining",
"cell processes",
"germ cells",
"oocytes",
"dna",
"sperm",
"research and analysis methods",
"specimen preparation and treatment",
"staining",
"animal cells",
"proteins",
"recombinant proteins",
"biochemistry",
"dapi staining",
"cell ... | p53 and TAp63 participate in the recombination-dependent pachytene arrest in mouse spermatocytes | journal.pgen.1006845 | null | [
[
"The mammalian p53 family includes p53 [1 , 2] , p63 [3] and p73 [4] , which are transcription factors encoded by three highly conserved genes [5 , 6] .",
"Each member has three major domains: an amino-terminal transactivation ( TA ) domain , a central DNA binding domain , and a carboxy-terminal oligomeri... | [
"To protect germ cells from genomic instability , surveillance mechanisms ensure meiosis occurs properly .",
"In mammals , spermatocytes that display recombination defects experience a so-called recombination-dependent arrest at the pachytene stage , which relies on the MRE11 complex—ATM—CHK2 pathway responding t... | [
"Meiosis is a specialized cell division that generates haploid gametes by halving chromosome content through two consecutive rounds of chromosome segregation .",
"At the onset of the first meiotic division , SPO11 protein introduces double-strand breaks ( DSBs ) throughout the genome .",
"These DSBs are repaire... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell death",
"medicine and health sciences",
"autophagic cell death",
"vacuoles",
"parasite replication",
"pathology and laboratory medicine",
"hela cells",
"cell processes",
"biological cultures",
"parasitic diseases",
"parasitic protozoans",
"parasitology",
"protozoans",
"toxoplasma",
... | K63-Linked Ubiquitination Targets Toxoplasma gondii for Endo-lysosomal Destruction in IFNγ-Stimulated Human Cells | journal.ppat.1006027 | null | [
[
"Host cells invaded by intracellular pathogens have to mount a rapid recognition and cell-autonomous defence program to curb the replication of the intruder [1] .",
"The cytokine gamma interferon ( IFNγ ) can stimulate cell-autonomous defence in immune or non-immune cells and is produced early during infe... | [
"Toxoplasma gondii is the most common protozoan parasitic infection in man .",
"Gamma interferon ( IFNγ ) activates haematopoietic and non-haematopoietic cells to kill the parasite and mediate host resistance .",
"IFNγ-driven host resistance pathways and parasitic virulence factors are well described in mice , ... | [
"Toxoplasma gondii is an intracellular parasite that can invade nucleated cells of any warm-blooded animal into a compartment known as a parasitophorous vacuole ( PV ) .",
"The production of gamma interferon ( IFNγ ) drives the restriction and killing of Toxoplasma .",
"It is not fully known how the parasite in... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"genome engineering",
"medicine and health sciences",
"ecology and environmental sciences",
"pathology and laboratory medicine",
"engineering and technology",
"bacteriophages",
"pathogens",
"synthetic biology",
"synthetic bioengineering",
"crispr",
"viruses",
"mutation",
"evolutionary emerge... | Evolutionary emergence of infectious diseases in heterogeneous host populations | journal.pbio.2006738 | null | [
[
"Understanding the factors that govern the ability of pathogens to invade a new host population is of paramount importance to design better surveillance systems and control policies .",
"Mathematical epidemiology can provide key insights into these dynamics [1–4] .",
"For instance , simple determinist... | [
"The emergence and re-emergence of pathogens remains a major public health concern .",
"Unfortunately , when and where pathogens will ( re- ) emerge is notoriously difficult to predict , as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an... | [
"The probability that an epidemic will break out is highly dependent on the ability of the pathogen to acquire new adaptive mutations and to induce evolutionary emergence .",
"Forecasting pathogen emergence thus requires a good understanding of the interplay between the epidemiology and evolution taking place at ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/complex traits",
"diabetes and endocrinology/obesity",
"gastroenterology and hepatology/hepatology"
] | Genome-Wide Association Analysis Identifies Variants Associated with Nonalcoholic Fatty Liver Disease That Have Distinct Effects on Metabolic Traits | journal.pgen.1001324 | null | [
[
"NAFLD includes a spectrum of disease ranging from fatty infiltration of the liver ( steatosis ) to histologic evidence of inflammation ( nonalcoholic steatohepatitis or NASH ) , to fibrosis or cirrhosis , without a history of excessive alcohol ingestion [1] , [2] .",
"NAFLD can lead to liver failure and ... | [
"Nonalcoholic fatty liver disease ( NAFLD ) clusters in families , but the only known common genetic variants influencing risk are near PNPLA3 .",
"We sought to identify additional genetic variants influencing NAFLD using genome-wide association ( GWA ) analysis of computed tomography ( CT ) measured hepatic stea... | [
"NAFLD is a spectrum of disease that ranges from steatosis to steatohepatitis ( nonalcoholic steatohepatitis or NASH: inflammation around the fat ) to fibrosis/cirrhosis .",
"Hepatic steatosis can be measured non-invasively using computed tomography ( CT ) whereas NASH/fibrosis is assessed histologically .",
"T... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Prolonged Intracellular Na+ Dynamics Govern Electrical Activity in Accessory Olfactory Bulb Mitral Cells | journal.pbio.1002319 | An experimental and computational study reveals a novel mechanism for persistent activity of neurons in response to transient stimulation. Instead of involving feedback mechanisms, it relies on slow changes in intracellular sodium ion concentration, leading to prolonged calcium-dependent inward current. | [
[
"The accessory olfactory system , also known as the vomeronasal system , mediates chemical communication between conspecifics of most mammalian and reptilian species during social interactions [1] .",
"Inputs to this chemosensory system originate from the sensory neurons of the vomeronasal organ ( VNO ) t... | [
"Persistent activity has been reported in many brain areas and is hypothesized to mediate working memory and emotional brain states and to rely upon network or biophysical feedback .",
"Here , we demonstrate a novel mechanism by which persistent neuronal activity can be generated without feedback , relying instea... | [
"The accessory olfactory system is essential for chemical communication in animals during social interactions .",
"During this process , the principle cells of the accessory olfactory bulb ( AOB ) may respond to transient stimulation with prolonged activity , sometimes lasting for minutes—a property known as pers... | 2015 |
[
"Introduction",
"Model and method",
"Results",
"Discussion"
] | [
"cell binding",
"biomacromolecule-ligand interactions",
"cell physiology",
"chemical characterization",
"simulation and modeling",
"membrane proteins",
"membrane receptor signaling",
"receptor-ligand binding assay",
"cellular structures and organelles",
"research and analysis methods",
"binding ... | General principles of binding between cell surface receptors and multi-specific ligands: A computational study | journal.pcbi.1005805 | null | [
[
"Integral membrane proteins are the sensors of extracellular signals , including cell-cell and cell-substrate interactions , as well as environmental queues .",
"Their interactions with extracellular ligands initiate most of the intracellular signaling pathways [1 , 2] , while the dysregulation of these r... | [
"The interactions between membrane receptors and extracellular ligands control cell-cell and cell-substrate adhesion , and environmental responsiveness by representing the initial steps of cell signaling pathways .",
"These interactions can be spatial-temporally regulated when different extracellular ligands are ... | [
"In order to adapt to surrounding environments , multiple signaling pathways have been evolved in cells .",
"The first step of these pathways is to detect external stimuli , which is conducted by the dynamic interactions between cell surface receptors and extracellular ligands .",
"As a result , recognition of ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis",
"microbiology/innate immunity",
"genetics and genomics/functional genomics"
] | Mycobacterium leprae Phenolglycolipid-1 Expressed by Engineered M. bovis BCG Modulates Early Interaction with Human Phagocytes | journal.ppat.1001159 | null | [
[
"Leprosy is a chronic human disease of the skin and peripheral nerves caused by the intracellular pathogen Mycobacterium leprae .",
"Although control programs led by governmental and charitable agencies have reduced the number of patients from ∼10–15 million to less than 1 million over the last 10 years [... | [
"The species-specific phenolic glycolipid 1 ( PGL-1 ) is suspected to play a critical role in the pathogenesis of leprosy , a chronic disease of the skin and peripheral nerves caused by Mycobacterium leprae .",
"Based on studies using the purified compound , PGL-1 was proposed to mediate the tropism of M . leprae... | [
"Mycobacterium leprae , the causative agent of leprosy , is a chronic human disease responsible for irreversible peripheral nerve damage and deformities .",
"Lepromatous leprosy , the most severe form of the disease , is accompanied by T-cell unresponsiveness , suggesting that M . leprae has evolved strategies to... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"none",
"ecology",
"science policy"
] | Landscape as a Model: The Importance of Geometry | journal.pcbi.0030200 | null | [
[
"The focus of this study is spatially explicit predictive models designed to support decisionmaking ( e . g . , population establishment and spread , climate change , and flood risk ) , which should have reliable , probabilistic , and mappable results .",
"In cases in which there are few relevant validati... | [
"In all models , but especially in those used to predict uncertain processes ( e . g . , climate change and nonnative species establishment ) , it is important to identify and remove any sources of bias that may confound results .",
"This is critical in models designed to help support decisionmaking .",
"The ge... | [
"Many different areas of science try to simulate and predict ( model ) how processes act across virtual landscapes .",
"Sometimes these models are abstract , but often they are based on real-world landscapes and are used to make real-world planning or management decisions .",
"We considered two separate issues:... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"autosomal recessive",
"diagnostic medicine",
"pediatric cardiology",
"pediatrics and child health",
"genetics and genomics",
"metabolic disorders",
"pediatrics",
"clinical genetics"
] | Autosomal Recessive Dilated Cardiomyopathy due to DOLK Mutations Results from Abnormal Dystroglycan O-Mannosylation | journal.pgen.1002427 | null | [
[
"Dilated cardiomyopathy ( DCM ) is a life-threatening disease characterized by left ventricular enlargement and systolic dysfunction , which can lead to congestive heart failure and is a common cause of patients requiring heart transplantation .",
"In view of the progressive disease course and the acutene... | [
"Genetic causes for autosomal recessive forms of dilated cardiomyopathy ( DCM ) are only rarely identified , although they are thought to contribute considerably to sudden cardiac death and heart failure , especially in young children .",
"Here , we describe 11 young patients ( 5–13 years ) with a predominant pre... | [
"Idiopathic dilated cardiomyopathy ( DCM ) is estimated to be of genetic origin in 20%–48% of the patients .",
"Almost all currently known genetic defects show dominant inheritance , although especially in younger children recessive causes have been proposed to contribute considerably to DCM .",
"Knowledge of t... | 2011 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"recombination reactions",
"monomers",
"plasmids",
"dna-binding proteins",
"plasmid construction",
"sumoylation",
"dna replication",
"genetic elements",
"forms of dna",
"dna construction",
"dna",
"molecular biology techniques",
"research and analysis methods",
"polymer chemistry",
"prote... | A Flp-SUMO hybrid recombinase reveals multi-layered copy number control of a selfish DNA element through post-translational modification | journal.pgen.1008193 | null | [
[
"The yeast 2-micron plasmid , nearly ubiquitous among Saccharomyces yeast strains , is a highly optimized extrachromosomal selfish DNA element [1–4] .",
"The plasmid resides in the nucleus , offers no apparent fitness advantage to its host , and does not impose any significant disadvantage at its normal c... | [
"Mechanisms for highly efficient chromosome-associated equal segregation , and for maintenance of steady state copy number , are at the heart of the evolutionary success of the 2-micron plasmid as a stable multi-copy extra-chromosomal selfish DNA element present in the yeast nucleus .",
"The Flp site-specific rec... | [
"Plasmids of budding yeasts , exemplified by the 2-micron plasmid of Saccharomyces cerevisiae , and mammalian papilloma and gammaherpes viruses typify eukaryotic extra-chromosomal selfish DNA elements .",
"The plasmid and the viral episomes , despite the long evolutionary divergence of their hosts , share strikin... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"cell biology",
"evolutionary biology",
"homo (human)",
"genetics and genomics",
"mus (mouse)"
] | A Screen for Retrotransposed Imprinted Genes Reveals an Association between X Chromosome Homology and Maternal Germ-Line Methylation | journal.pgen.0030020 | null | [
[
"Mammals inherit one haploid genome complement from each parent , and in most cases both alleles are expressed and functionally equivalent .",
"Imprinted alleles are an exception to this rule , as their expression in offspring is dependent on the gender of the transmitting parent .",
"These parent-of-... | [
"Imprinted genes undergo epigenetic modifications during gametogenesis , which lead to transcriptional silencing of either the maternally or the paternally derived allele in the subsequent generation .",
"Previous work has suggested an association between imprinting and the products of retrotransposition , but th... | [
"The conventional view is that DNA carries all of our heritable information and our genes control development into adulthood .",
"The discovery of epigenetics , a term coined to describe effects that are not coded for by DNA sequence , but can nonetheless affect our development and well-being , has added another ... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"functional genomics",
"plant biology",
"population genetics",
"metabolic networks",
"plant science",
"genome complexity",
"genetic polymorphism",
"plant genetics",
"biology",
"systems biology",
"plant biochemistry",
"genetics",
"genomics",
"evolutionar... | Combining Genome-Wide Association Mapping and Transcriptional Networks to Identify Novel Genes Controlling Glucosinolates in Arabidopsis thaliana | journal.pbio.1001125 | Genome-wide association mapping is highly sensitive to environmental changes, but network analysis allows rapid causal gene identification. | [
[
"Biologists across fields possess a common need to identify the genetic variation causing natural phenotypic variation .",
"Genome-wide association ( GWA ) studies are a promising route to associate phenotypes with genotypes , at a genome-wide level , using “unrelated” individuals [1] .",
"In contrast... | [
"Genome-wide association ( GWA ) is gaining popularity as a means to study the architecture of complex quantitative traits , partially due to the improvement of high-throughput low-cost genotyping and phenotyping technologies .",
"Glucosinolate ( GSL ) secondary metabolites within Arabidopsis spp .",
"can serve... | [
"Understanding how genetic variation can control phenotypic variation is a fundamental goal of modern biology .",
"A major push has been made using genome-wide association mapping in all organisms to attempt and rapidly identify the genes contributing to phenotypes such as disease and nutritional disorders .",
... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public health and epidemiology",
"neurocysticercosis",
"infectious disease epidemiology",
"parasitic diseases",
"global health",
"neglected tropical diseases",
"infectious disease control",
"veterinary science",
"infectious diseases",
"veterinary diseases",
"veterinary epidemiolog... | Geographic Correlation between Tapeworm Carriers and Heavily Infected Cysticercotic Pigs | journal.pntd.0001953 | null | [
[
"Taenia solium , otherwise known as the pork tapeworm , is a common helminthic infection of the human central nervous system ( CNS ) and a leading cause of acquired epilepsy in low and middle income countries .",
"Neurocysticercosis ( NCC ) is a disease which occurs when T . solium larval cysts infect the... | [
"Neurocysticercosis is a leading cause of preventable epilepsy in the developing world .",
"Sustainable community-based interventions are urgently needed to control transmission of the causative parasite , Taenia solium .",
"We examined the geospatial relationship between live pigs with visible cysticercotic cy... | [
"Taenia solium , aka the pork tapeworm , is an important cause of epilepsy in developing nations .",
"People with intestinal tapeworms , a condition known as taeniasis , pass infectious eggs in their feces which contaminate the environment .",
"These eggs can cause serious disease in both humans and pigs if the... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | KSHV MicroRNAs Mediate Cellular Transformation and Tumorigenesis by Redundantly Targeting Cell Growth and Survival Pathways | journal.ppat.1003857 | null | [
[
"Infection by Kaposi's sarcoma-associated herpesvirus ( KSHV ) is associated with Kaposi's sarcoma ( KS ) , the most common cancer in HIV-infected patients [1] .",
"KSHV is also linked to the development of several other lymphoproliferative malignancies including primary effusion lymphoma ( PEL ) and a su... | [
"Kaposi's sarcoma-associated herpesvirus ( KSHV ) is causally linked to several human cancers , including Kaposi's sarcoma , primary effusion lymphoma and multicentric Castleman's disease , malignancies commonly found in HIV-infected patients .",
"While KSHV encodes diverse functional products , its mechanism of ... | [
"Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the causal agent of several human cancers .",
"KSHV encodes over two dozen genes that regulate diverse cellular pathways .",
"However , the molecular mechanism of KSHV-induced oncogenesis remains unknown .",
"In this study , we determined the roles of KSHV ... | 2013 |
[
"Introduction",
"Material and Methods",
"Results",
"Discussion"
] | [] | Quaternary Structure of Pathological Prion Protein as a Determining Factor of Strain-Specific Prion Replication Dynamics | journal.ppat.1003702 | null | [
[
"Prion disease pathogenesis stems from the post-translational conversion of the monomeric , alpha helix-rich host-encoded prion protein ( PrPC ) into misfolded , β sheet-enriched PrPSc aggregates [1] .",
"The process is believed to be initiated by PrPSc seeds [2] , [3] acquired through infection or arisin... | [
"Prions are proteinaceous infectious agents responsible for fatal neurodegenerative diseases in animals and humans .",
"They are essentially composed of PrPSc , an aggregated , misfolded conformer of the ubiquitously expressed host-encoded prion protein ( PrPC ) .",
"Stable variations in PrPSc conformation are ... | [
"Prions are infectious agents causing irremediably fatal neurodegenerative diseases in human and in farmed or wild animals .",
"They are thought to be formed from abnormally folded assemblies ( PrPSc ) of the host-encoded prion protein ( PrPC ) .",
"Different PrPSc conformational variants associated with distin... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/post-translational regulation of gene expression",
"genetics and genomics/gene expression",
"computational biology/alternative splicing",
"molecular biology/mrna stability",
"molecular biology/rna splicing",
"genetics and genomics/bioinformatics"
] | Genome-Wide Identification of Alternative Splice Forms Down-Regulated by Nonsense-Mediated mRNA Decay in Drosophila | journal.pgen.1000525 | null | [
[
"Nonsense-mediated mRNA decay ( NMD ) is an RNA surveillance system that down-regulates mRNAs containing early stop codons in all eukaryotes examined [1] .",
"NMD functions to clear the cell of transcripts containing potentially harmful nonsense mutations [2] .",
"In addition to this role in surveilla... | [
"Alternative mRNA splicing adds a layer of regulation to the expression of thousands of genes in Drosophila melanogaster .",
"Not all alternative splicing results in functional protein; it can also yield mRNA isoforms with premature stop codons that are degraded by the nonsense-mediated mRNA decay ( NMD ) pathway... | [
"A gene can be processed into multiple mRNAs through alternative splicing .",
"Alternative splicing increases the number of proteins encoded by the genome , but not all alternative mRNAs produce protein .",
"Instead , some are degraded by nonsense-mediated mRNA decay ( NMD ) , a surveillance system that was ori... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | The gendered impact of Buruli ulcer on the household production of health and social support networks: Why decentralization favors women | journal.pntd.0007317 | null | [
[
"Much has been written about the health care seeking process in low and middle income countries ( LMICs ) and the predisposing , enabling , and service-related factors that contribute to health care decision making for different types of health conditions and diseases[1 , 2] .",
"Studies have also address... | [
"Buruli ulcer [BU] is a chronic and debilitating neglected tropical skin disease caused by Mycobacterium ulcerans .",
"The treatment of moderate to severe BU affects the well-being of entire households and places a strain on both gender relations within households and social relations with kin asked for various t... | [
"In this gender-focused study of the neglected tropical disease Buruli ulcer ( BU ) in Benin , West Africa , we document how seeking care for BU is influenced by broad-based concerns about the household production of health and the availability of resources women can mobilize from their social support networks .",
... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/evolutionary modeling",
"computational biology/computational neuroscience"
] | Falling towards Forgetfulness: Synaptic Decay Prevents Spontaneous Recovery of Memory | journal.pcbi.1000143 | null | [
[
"Each association consists of an input vector x and a corresponding target value d .",
"For a network with weight vector w , the response to an input vector x is y = w·x .",
"We define the performance error for input vectors x1 , … , xk and desired outputs d1 , … , dk to be ( 1 ) where yi = w·xi is th... | [
"Long after a new language has been learned and forgotten , relearning a few words seems to trigger the recall of other words .",
"This “free-lunch learning” ( FLL ) effect has been demonstrated both in humans and in neural network models .",
"Specifically , previous work proved that linear networks that learn ... | [
"If you learn a skill , then partially forget it , does relearning part of that skill induce recovery of other parts of the skill ?",
"More generally , if you learn a set of associations , then partially forget them , does relearning a subset induce recovery of the remaining associations ?",
"In previous work ,... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biochemistry",
"cell biology",
"biology and life sciences",
"proteomics",
"microbiology",
"molecular cell biology"
] | Transcriptional and Proteomic Responses to Carbon Starvation in Paracoccidioides | journal.pntd.0002855 | null | [
[
"Metabolic adaptability and flexibility are important attributes for pathogens to successfully colonize , infect , and cause disease in a wide range of hosts .",
"Therefore , they must be able to assimilate various carbon sources .",
"Carbohydrates are the primary and preferred source of metabolic car... | [
"The genus Paracoccidioides comprises human thermal dimorphic fungi , which cause paracoccidioidomycosis ( PCM ) , an important mycosis in Latin America .",
"Adaptation to environmental conditions is key to fungal survival during human host infection .",
"The adaptability of carbon metabolism is a vital fitness... | [
"The species of the Paracoccidioides genus , a neglected human pathogen , represent the causative agents of paracoccidioidomycosis ( PCM ) , one of the most frequent systemic mycoses in Latin America .",
"Despite being phagocytosed , the fungus conidia differentiate into the parasitic yeast form that subverts the... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome-wide association studies",
"urology",
"medicine and health sciences",
"body fluids",
"sociology",
"cancers and neoplasms",
"dna-binding proteins",
"genitourinary tract tumors",
"social sciences",
"oncology",
"bladder cancer",
"mathematics",
"forecasting",
"statistics (mathematics)"... | Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data | journal.pgen.1006493 | null | [
[
"Large genome-wide association studies ( GWAS ) have accelerated the discovery of dozens or even hundreds of common single nucleotide polymorphisms ( SNPs ) associated with individual complex traits and diseases , such as height [1 , 2] , body mass index [3] and common cancers ( e . g . , breast [4] and prost... | [
"Recent heritability analyses have indicated that genome-wide association studies ( GWAS ) have the potential to improve genetic risk prediction for complex diseases based on polygenic risk score ( PRS ) , a simple modelling technique that can be implemented using summary-level data from the discovery samples .",
... | [
"Large GWAS have identified tens or even hundreds of common SNPs significantly associated with individual complex diseases; however , these SNPs typically explain a small proportion of phenotypic variance .",
"Recently , heritability analyses based on GWAS data suggest that common SNPs have the potential to expla... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Trypanosoma cruzi Infection through the Oral Route Promotes a Severe Infection in Mice: New Disease Form from an Old Infection? | journal.pntd.0003849 | null | [
[
"Chagas disease ( American trypanosomiasis ) , caused by the protozoan Trypanosoma cruzi , affects 6–7 million people worldwide , with an annual incidence of 28 thousand cases in the Americas [WHO , 2015] .",
"Chagas disease is endemic in 21 countries in Latin America and was previously confined to this r... | [
"Oral transmission of Chagas disease has been documented in Latin American countries .",
"Nevertheless , significant studies on the pathophysiology of this form of infection are largely lacking .",
"The few studies investigating oral route infection disregard that inoculation in the oral cavity ( Oral infection... | [
"Chagas disease caused by the protozoan Trypanosoma cruzi is endemic in Latin America and a neglected tropical disease , which affects 6–7 million people worldwide .",
"Currently , oral transmission is the most frequent pathway of infection in Brazil but also occurs in other endemic countries .",
"This importan... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/rna-protein interactions",
"virology/viral replication and gene regulation",
"infectious diseases/respiratory infections"
] | Genetic trans-Complementation Establishes a New Model for Influenza Virus RNA Transcription and Replication | journal.ppat.1000462 | null | [
[
"The influenza A viruses are the causative agents of yearly epidemics of respiratory disease and occasionally more severe pandemics [1] .",
"The latter are the consequence of transfers from the avian virus reservoir to humans by either genetic reassortment or direct adaptation [2] .",
"Thus , current ... | [
"The influenza A viruses genome comprises eight single-stranded RNA segments of negative polarity .",
"Each one is included in a ribonucleoprotein particle ( vRNP ) containing the polymerase complex and a number of nucleoprotein ( NP ) monomers .",
"Viral RNA replication proceeds by formation of a complementary... | [
"The influenza A viruses produce annual epidemics and occasional pandemics of respiratory disease .",
"There is great concern about a potential new pandemic being caused by presently circulating avian influenza viruses , and hence increasing interest in understanding how the virus replicates its genome .",
"Thi... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"developmental biology",
"cell biology",
"ophthalmology"
] | L-DOPA Is an Endogenous Ligand for OA1 | journal.pbio.0060236 | Albinism produces retinal defects, and OA1 is an orphan G-protein-coupled receptor that leads to albinism without acting directly on melanin synthesis. Here the ligand is identified and a mechanism is proposed by which the various forms of albinism signal through OA1, resulting in the same retinal phenotype. | [
[
"Albinism is a group of inherited genetic diseases in which there is a variable loss of pigmentation in the eye , hair , or skin .",
"When the eye is affected , there are significant alterations in neurosensory retina development that lead to low vision [1–8] .",
"There are two broad classes of albini... | [
"Albinism is a genetic defect characterized by a loss of pigmentation .",
"The neurosensory retina , which is not pigmented , exhibits pathologic changes secondary to the loss of pigmentation in the retina pigment epithelium ( RPE ) .",
"How the loss of pigmentation in the RPE causes developmental defects in th... | [
"Albinism is the loss of pigmentation caused by mutations in one of several different genes that alter pigment synthesis by different mechanisms .",
"In the eye , albinism impairs sensory retina development and causes significant vision problems .",
"Regardless of the genetic mutation that causes albinism , the... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"cryptococcus neoformans",
"medicine and health sciences",
"urea",
"cryptococcus",
"immune cells",
"pathology and laboratory medicine",
"chemical compounds",
"ureases",
"yeast infections",
"enzymes",
"pathogens",
"immunology",
"cell processes",
"enzymology",
"microbiolog... | Cryptococcus neoformans urease affects the outcome of intracellular pathogenesis by modulating phagolysosomal pH | journal.ppat.1007144 | null | [
[
"C . neoformans , a major life-threatening fungal pathogen predominantly infects severely immunocompromised patients and causes over 180 , 000 deaths per year worldwide [1] .",
"C . neoformans is ubiquitous , although is most frequently found in soils contaminated with bird excreta or from trees [2–11] ."... | [
"Cryptococcus neoformans is a facultative intracellular pathogen and its interaction with macrophages is a key event determining the outcome of infection .",
"Urease is a major virulence factor in C . neoformans but its role during macrophage interaction has not been characterized .",
"Consequently , we analyze... | [
"Cryptococcus neoformans is a relatively frequent cause of life-threatening infection in severely immunocompromised patients , especially those with AIDS .",
"Persistence of infection involves residence within macrophages , where C . neoformans can survive and replicate while residing in the phagolysosome .",
"... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | The Spatiotemporal Expansion of Human Rabies and Its Probable Explanation in Mainland China, 2004-2013 | journal.pntd.0003502 | null | [
[
"Rabies is a viral zoonotic infection of the central nervous system caused by a lyssavirus , and its mortality rate is nearly 100% without proper post-exposure prophylaxis ( PEP ) .",
"As one of the most feared diseases throughout human history , rabies is widely distributed throughout the world with high... | [
"Human rabies is a significant public health concern in mainland China .",
"However , the neglect of rabies expansion and scarce analyses of the dynamics have made the spatiotemporal spread pattern of human rabies and its determinants being poorly understood .",
"We collected geographic locations and timeline o... | [
"Although the number of human rabies cases has slightly decreased since 2008 in mainland China , the rabies seemed to be gradually expanding to the low-incidence or non-epidemic areas .",
"The neglect of rabies expansion and scarce analyses of the dynamics have made the spatiotemporal spread pattern of human rabi... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"physics",
"biochemistry",
"enzyme structure",
"computational chemistry",
"molecular dynamics",
"biophysic al simulations",
"enzyme regulation",
"enzymes",
"macromolecular assemblies",
"chemistry",
"theoretical chemistry",
"biology",
"computational biology",
"biophysics simulations",
"bi... | Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations | journal.pcbi.1003156 | null | [
[
"Many membrane proteins remain unexplored at the molecular-level despite their clear pharmaceutical relevance [1] , [2] .",
"It is therefore crucial to develop computational methods for the structure prediction of membrane proteins .",
"Homology modeling is a common technique to build an initial model... | [
"Group VI Ca2+-independent phospholipase A2 ( iPLA2 ) is a water-soluble enzyme that is active when associated with phospholipid membranes .",
"Despite its clear pharmaceutical relevance , no X-ray or NMR structural information is currently available for the iPLA2 or its membrane complex .",
"In this paper , we... | [
"The Ca2+-independent phospholipase A2 ( iPLA2 ) enzyme is a potential target for the development of medicinal agents against heart and neurological diseases , multiple sclerosis , arthritis , and cancer .",
"However , no structural information is currently available for the iPLA2 .",
"The binding of the enzyme... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | SERPINB11 Frameshift Variant Associated with Novel Hoof Specific Phenotype in Connemara Ponies | journal.pgen.1005122 | null | [
[
"Many of the signaling molecules involved in patterning ectodermal derivatives , such as teeth and hair , are also involved in organizing mammalian distal limb appendages , including nails , claws and hooves [1] .",
"Perissodactyla ( odd-toed ungulates ) are a diverse group of mammals that include the hor... | [
"Horses belong to the order Perissodactyla and bear the majority of their weight on their third toe; therefore , tremendous force is applied to each hoof .",
"An inherited disease characterized by a phenotype restricted to the dorsal hoof wall was identified in the Connemara pony .",
"Hoof wall separation disea... | [
"Inherited diseases affecting only the nails in humans are rare; however , humans do not support themselves entirely on one appendage .",
"Horses bear their entire weight on their third toe , resulting in a large amount of force on each hoof .",
"An inherited disease characterized by a phenotype restricted to s... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion",
"Conclusions"
] | [] | Diverse Genotypes of Yersinia pestis Caused Plague in Madagascar in 2007 | journal.pntd.0003844 | null | [
[
"Yersinia pestis , the causative agent of plague , is one of the most deadly zoonotic pathogens on record , with hundreds of millions of human deaths attributed to it over the course of three historical pandemics [1] .",
"Human cases typically present in one of three forms , including bubonic , septicemic... | [
"Yersinia pestis is the causative agent of human plague and is endemic in various African , Asian and American countries .",
"In Madagascar , the disease represents a significant public health problem with hundreds of human cases a year .",
"Unfortunately , poor infrastructure makes outbreak investigations chal... | [
"Yersinia pestis is a highly pathogenic bacterium and the causative agent of human plague .",
"It has caused three recognized pandemics and is a current human health problem in many countries of Africa , Asia and the Americas , including Madagascar .",
"The pathogen cannot be eradicated from natural plague foci... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | tRNA Methyltransferase Homolog Gene TRMT10A Mutation in Young Onset Diabetes and Primary Microcephaly in Humans | journal.pgen.1003888 | null | [
[
"Type 2 diabetes ( T2D ) is a heterogeneous polygenic disease with dramatically increasing worldwide incidence as a consequence of the obesity epidemic [1] .",
"Environmental factors ( energy dense diets rich in saturated fat and sedentary lifestyle [2] , [3] ) and genetic predisposition contribute to its... | [
"We describe a new syndrome of young onset diabetes , short stature and microcephaly with intellectual disability in a large consanguineous family with three affected children .",
"Linkage analysis and whole exome sequencing were used to identify the causal nonsense mutation , which changed an arginine codon into... | [
"The inherited predisposition to type 2 diabetes is attributed to common variants in over 60 loci .",
"Among these risk variants is CDKAL1 , which has recently been shown to be a tRNA modifying enzyme ( methylthiotransferase ) .",
"Genetic variants of different severity can generate a spectrum of monogenic and ... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immunology/immunomodulation",
"immunology/leukocyte signaling and gene expression",
"immunology/allergy and hypersensitivity",
"infectious diseases/helminth infections"
] | Lower Expression of TLR2 and SOCS-3 Is Associated with Schistosoma haematobium Infection and with Lower Risk for Allergic Reactivity in Children Living in a Rural Area in Ghana | journal.pntd.0000227 | null | [
[
"In the last few decades , allergic diseases have become a major health burden in the western world .",
"Although these disorders clearly have a genetic component , their rapid change in prevalence points to environmental conditions that have changed during this time frame .",
"In the same time frame ... | [
"Helminth infections are prevalent in rural areas of developing countries and have in some studies been negatively associated with allergic disorders and atopy .",
"In this context little is known of the molecular mechanisms of modulation involved .",
"We have characterized the innate immune responses , at the ... | [
"Inflammatory diseases such as atopic disorders are a major health problem in the Western world , but their prevalence is also increasing in developing countries , especially in urban centres .",
"There is increasing evidence that exposure to a rural environment with high burden of compounds derived from parasite... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Discovering Genetic Interactions in Large-Scale Association Studies by Stage-wise Likelihood Ratio Tests | journal.pgen.1005502 | null | [
[
"Cardiovascular disease , cancers , diabetes and chronic obstructive pulmonary disease , accounting for almost 60% of the causes of death 2013 , globally [1] , are all examples of complex diseases .",
"A complex disease is characterized by an intricate system of interactions between genetic , epigenetic ,... | [
"Despite the success of genome-wide association studies in medical genetics , the underlying genetics of many complex diseases remains enigmatic .",
"One plausible reason for this could be the failure to account for the presence of genetic interactions in current analyses .",
"Exhaustive investigations of inter... | [
"Many of our common diseases are driven by complex interactions between multiple genetic factors .",
"Disease-specific , genome-wide association studies have been the prominent tool for cataloging such factors , by studying the genetic variation of a gene in a population and its association with the disease .",
... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"complex systems",
"systems biology",
"game theory",
"mathematics",
"theoretical biology",
"applied mathematics",
"biology",
"computational biology"
] | Structural Control of Metabolic Flux | journal.pcbi.1003368 | null | [
[
"Organisms perpetually face changes in environmental conditions .",
"Bacteria may be confronted with variations in oxygen [1] or carbon sources [1] , [2] , while plants may be exposed to changes in light quality [3] and intensity [4] as well as in availability of carbon [5] and nitrogen [6] .",
"Anima... | [
"Organisms have to continuously adapt to changing environmental conditions or undergo developmental transitions .",
"To meet the accompanying change in metabolic demands , the molecular mechanisms of adaptation involve concerted interactions which ultimately induce a modification of the metabolic state , which is... | [
"Insight into the functioning of metabolic control to meet changing demands is a first step in rational engineering of biological systems towards a desired behavior .",
"Metabolic control analysis provides the means to examine the impact of change of reaction fluxes on a specific target flux based on kinetic mode... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"medicine and health sciences",
"rift valley fever virus",
"pathology and laboratory medicine",
"togaviruses",
"pathogens",
"tropical diseases",
"microbiology",
"alphaviruses",
"viruses",
"next-generation sequencing",
"chikungunya virus",
"rna viruses",
"genome ana... | Development and preliminary evaluation of a multiplexed amplification and next generation sequencing method for viral hemorrhagic fever diagnostics | journal.pntd.0006075 | null | [
[
"Outbreaks of viral hemorrhagic fever ( VHF ) occur in many parts of the world [1 , 2] .",
"VHFs are caused by various single-stranded RNA viruses , the majority of which are classified in Arenaviridae , Filoviridae , and Flaviviridae families and Bunyavirales order [3] .",
"Human infections show high... | [
"We describe the development and evaluation of a novel method for targeted amplification and Next Generation Sequencing ( NGS ) -based identification of viral hemorrhagic fever ( VHF ) agents and assess the feasibility of this approach in diagnostics .",
"An ultrahigh-multiplex panel was designed with primers to ... | [
"Viral hemorrhagic fever is a severe and potentially lethal disease , characterized by fever , malaise , vomiting , mucosal and gastrointestinal bleeding , and hypotension , in which multiple organ systems are affected .",
"Due to modern transportation and global trade , outbreaks of viral hemorrhagic fevers have... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"pathology and laboratory medicine",
"gene regulation",
"pathogens",
"immunology",
"microbiology",
"viral structure",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"non-coding rna",
"rna viruses",
"cellular structure... | Siglec-1 initiates formation of the virus-containing compartment and enhances macrophage-to-T cell transmission of HIV-1 | journal.ppat.1006181 | null | [
[
"Macrophages are readily infected by HIV and make important contributions to AIDS pathogenesis .",
"Currently there is growing interest in this cell type as a potential reservoir for persistent infection and as an important target in efforts to cure individuals of HIV [1–3] .",
"Macrophages are presen... | [
"HIV-1 particles assemble and bud from the plasma membrane of infected T lymphocytes .",
"Infected macrophages , in contrast , accumulate particles within an apparent intracellular compartment known as the virus-containing compartment or VCC .",
"Many aspects of the formation and function of the VCC remain uncl... | [
"T lymphocytes and macrophages are the two major cell types involved in HIV replication and transmission events .",
"When a T cell is infected , virus particles assemble and bud from the plasma membrane of the cell .",
"In contrast , infected macrophages develop an intracellular collection of viruses termed the... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Meiotic Recombination Initiation in and around Retrotransposable Elements in Saccharomyces cerevisiae | journal.pgen.1003732 | null | [
[
"Meiosis is the specialized cell division that halves the genome complement to produce gametes for sexual reproduction .",
"During meiosis , homologous recombination is induced by programmed DNA double-strand breaks ( DSBs ) made by the topoisomerase-like Spo11 protein in a reaction in which Spo11 attache... | [
"Meiotic recombination is initiated by large numbers of developmentally programmed DNA double-strand breaks ( DSBs ) , ranging from dozens to hundreds per cell depending on the organism .",
"DSBs formed in single-copy sequences provoke recombination between allelic positions on homologous chromosomes , but DSBs c... | [
"Meiosis is the cell division that generates gametes for sexual reproduction .",
"During meiosis , homologous recombination occurs frequently , initiated by DNA double-strand breaks ( DSBs ) made by Spo11 .",
"Meiotic recombination usually occurs between sequences at allelic positions on homologous chromosomes ... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Extensive Decoupling of Metabolic Genes in Cancer | journal.pcbi.1004176 | null | [
[
"All cellular events , from the transduction of signals to the translation of nucleic acids , rely on the interaction of molecular entities .",
"Indeed , one may argue that the fundamental unit of a biological network is not its constituent components ( e . g . proteins or genes ) , but rather the edges r... | [
"Tumorigenesis requires the re-organization of metabolism to support malignant proliferation .",
"We examine how the altered metabolism of cancer cells is reflected in the rewiring of co-expression patterns among metabolic genes .",
"Focusing on breast and clear-cell kidney tumors , we report the existence of k... | [
"The metabolism of malignant tumors is deranged .",
"The transition from healthy to cancerous state involves , among other factors , the transcriptional coordination of genes spread throughout the cell’s metabolic pathways .",
"An examination of this multivariate regulatory effort can offer insights which may r... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"quantitative trait loci",
"diet",
"long non-coding rnas",
"electrocardiography",
"nutrition",
"bioassays and physiological analysis",
"molecular biology techniques",
"research and analysis methods",
"artificial gene amplification and extension",
"rapid amplificat... | Positional cloning of quantitative trait nucleotides for blood pressure and cardiac QT-interval by targeted CRISPR/Cas9 editing of a novel long non-coding RNA | journal.pgen.1006961 | null | [
[
"It is estimated that hypertension affects nearly 75 million Americans ( about 1 in every 3 U . S . adults ) [1] .",
"Essential hypertension is the most common type of hypertension and remains a major risk factor for cardiovascular diseases , such as cardiomyopathy [2] , coronary artery diseases [3] and p... | [
"Multiple GWAS studies have reported strong association of cardiac QT-interval to a region on HSA17 .",
"Interestingly , a rat locus homologous to this region is also linked to QT-intervals .",
"The high resolution positional mapping study located the rat QT-interval locus to a <42 . 5kb region on RNO10 .",
"... | [
"Diseases of the cardiovascular system such as essential hypertension do not have a clear cause , but are known to run in families .",
"The inheritance patterns of essential hypertension and other cardiac diseases suggest that they are not due to a single defective gene but instead are caused by multiple genetic ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"dengue virus",
"medicine and health sciences",
"reproductive system",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"animals",
"wolbachia",
"viruses",
"developmental biology",
"rna viruses",
"insect vectors",
"bacteria",
"digestive system",
"infect... | The Wolbachia strain wAu provides highly efficient virus transmission blocking in Aedes aegypti | journal.ppat.1006815 | null | [
[
"The mosquito Aedes aegypti ( Linneaus ) is the most important vector of human arboviruses .",
"Although native to Africa it now has a broad distribution throughout the tropics and subtropics and is peridomestic , often laying its eggs in man-made water containers , and displaying a strong preference for ... | [
"Introduced transinfections of the inherited bacteria Wolbachia can inhibit transmission of viruses by Aedes mosquitoes , and in Ae .",
"aegypti are now being deployed for dengue control in a number of countries .",
"Only three Wolbachia strains from the large number that exist in nature have to date been intro... | [
"Mosquito-borne viral diseases represent an increasing threat to human and animal health globally .",
"The mosquito species Aedes aegypti , a primary vector of the most significant human arboviral infections including the dengue , Zika and Chikungunya viruses , is highly invasive and is almost ubiquitous in tropi... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biochemistry",
"infectious diseases",
"model organisms",
"neurological disorders",
"neurology",
"genetics",
"biology",
"molecular cell biology",
"neuroscience",
"genetics and genomics"
] | Spreading of a Prion Domain from Cell-to-Cell by Vesicular Transport in Caenorhabditis elegans | journal.pgen.1003351 | null | [
[
"Transmissible spongiform encephalopathies ( TSEs ) or prion diseases are fatal , age-related , and infectious neurodegenerative disorders that affect humans ( e . g . , Creutzfeldt-Jakob disease ) and animals ( e . g . , scrapie in sheep and bovine spongiform encephalopathy in cattle ) [1] .",
"At the mo... | [
"Prion proteins can adopt self-propagating alternative conformations that account for the infectious nature of transmissible spongiform encephalopathies ( TSEs ) and the epigenetic inheritance of certain traits in yeast .",
"Recent evidence suggests a similar propagation of misfolded proteins in the spreading of ... | [
"Alzheimer's , Parkinson's , Huntington's , frontotemporal lobar degeneration ( FTLD ) , amyotrophic lateral sclerosis ( ALS ) , and prion diseases are all age-related , fatal neurodegenerative disorders .",
"Hallmarks of these diseases include the expression of toxic protein species .",
"The ability to spread ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"model organisms",
"genetics",
"biology",
"neuroscience",
"genetics and genomics"
] | VANG-1 and PRKL-1 Cooperate to Negatively Regulate Neurite Formation in Caenorhabditis elegans | journal.pgen.1002257 | null | [
[
"Post-mitotic neurons undergo a transition from a more or less symmetrical morphology to a highly polarized one with axonal and dendritic projections that are precisely oriented along body or tissue axes [1] , [2] .",
"Neurite emergence is the first overt sign of polarization in newly born neurons followe... | [
"Neuritogenesis is a critical early step in the development and maturation of neurons and neuronal circuits .",
"While extracellular directional cues are known to specify the site and orientation of nascent neurite formation in vivo , little is known about the genetic pathways that block inappropriate neurite eme... | [
"Neurons are among the most morphologically complex cells in the body .",
"Early in development , newly born neurons project one or more processes called neurites that will eventually mature into axons and dendrites .",
"While the genetic determinants that promote neurite emergence along specific trajectories a... | 2011 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [] | Allelic Spectra of Risk SNPs Are Different for Environment/Lifestyle Dependent versus Independent Diseases | journal.pgen.1005371 | null | [
[
"Both environmental and genetic factors influence risk of common human diseases , however , the relative significance of genetic and environmental factors in disease etiology differs for different diseases .",
"A number of common human diseases including cardiovascular diseases and type 2 diabetes are bel... | [
"Genome-wide association studies ( GWAS ) have generated sufficient data to assess the role of selection in shaping allelic diversity of disease-associated SNPs .",
"Negative selection against disease risk variants is expected to reduce their frequencies making them overrepresented in the group of minor ( <50% ) ... | [
"We reviewed several thousand genome wide association studies that were conducted to identify genetic variants influencing risk of human diseases .",
"We tested the hypothesis that single nucleotide polymorphisms ( SNPs ) that influence disease risk undergo positive or negative selection more frequently than an a... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"mathematics",
"statistics",
"genetics",
"biology",
"genetics and genomics"
] | A Genome-Wide Association Scan on the Levels of Markers of Inflammation in Sardinians Reveals Associations That Underpin Its Complex Regulation | journal.pgen.1002480 | null | [
[
"Inflammation is a critical response to pathogens and injuries .",
"Its control entails a coordinated cascade of biological events regulated by specific cells and molecular signals , in a complex process that is only partially understood .",
"In this context , genetics can provide important clues , gi... | [
"Identifying the genes that influence levels of pro-inflammatory molecules can help to elucidate the mechanisms underlying this process .",
"We first conducted a two-stage genome-wide association scan ( GWAS ) for the key inflammatory biomarkers Interleukin-6 ( IL-6 ) , the general measure of inflammation erythro... | [
"Inflammation is a protective response of our organism to harmful stimuli—such as germs , damaged cells , or irritants—and to initiate the healing process .",
"It has also been implicated , with both protective and predisposing effects , in a number of different diseases; but many important details of this comple... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/infectious diseases of the nervous system",
"respiratory medicine/respiratory infections",
"genetics and genomics/gene expression",
"genetics and genomics/genetics of disease",
"infectious diseases/bacterial infections",
"immunology/immunity to infections",
"genetics and genomics/po... | Identification of Tuberculosis Susceptibility Genes with Human Macrophage Gene Expression Profiles | journal.ppat.1000229 | null | [
[
"TB , a leading cause of death worldwide , is characterized by different clinical forms including latent TB ( LTB ) , localized pulmonary infection , and various forms of extrapulmonary TB including TBM .",
"90% of people infected with Mtb have latent infection with no symptoms and an immune response that... | [
"Although host genetics influences susceptibility to tuberculosis ( TB ) , few genes determining disease outcome have been identified .",
"We hypothesized that macrophages from individuals with different clinical manifestations of Mycobacterium tuberculosis ( Mtb ) infection would have distinct gene expression pr... | [
"Although TB is a leading cause of death worldwide , the vast majority of infected individuals are asymptomatic and contains the bacillus in a latent form .",
"Among those with active disease , 80% have localized pulmonary disease and 20% have disseminated forms .",
"TB meningitis ( TBM ) is the most severe for... | 2008 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"neuroscience/natural and synthetic vision",
"neuroscience/theoretical neuroscience"
] | Towards a Mathematical Theory of Cortical Micro-circuits | journal.pcbi.1000532 | null | [
[
"Understanding the computational and information processing roles of cortical circuitry is one of the outstanding problems in neuroscience .",
"The circuits of the neocortex are bewildering in their complexity and anatomical detail .",
"Although enormous progress has been made in the collection and as... | [
"The theoretical setting of hierarchical Bayesian inference is gaining acceptance as a framework for understanding cortical computation .",
"In this paper , we describe how Bayesian belief propagation in a spatio-temporal hierarchical model , called Hierarchical Temporal Memory ( HTM ) , can lead to a mathematica... | [
"Understanding the computational and information processing roles of cortical circuitry is one of the outstanding problems in neuroscience .",
"In this paper , we work from a theory of neocortex that models it as a spatio-temporal hierarchical system to derive a biological cortical circuit .",
"This is achieved... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology/membranes and sorting",
"infectious diseases/protozoal infections"
] | Identification of Rhoptry Trafficking Determinants and Evidence for a Novel Sorting Mechanism in the Malaria Parasite Plasmodium falciparum | journal.ppat.1000328 | null | [
[
"Malaria is a disease that causes severe morbidity , mortality and socio-economic hardship in tropical and sub-tropical areas of Africa , South America and Asia .",
"Plasmodium falciparum causes the most serious form of the disease and is responsible for more than 2 million deaths annually [1]–[3] .",
... | [
"The rhoptry of the malaria parasite Plasmodium falciparum is an unusual secretory organelle that is thought to be related to secretory lysosomes in higher eukaryotes .",
"Rhoptries contain an extensive collection of proteins that participate in host cell invasion and in the formation of the parasitophorous vacuo... | [
"The malaria parasite Plasmodium falciparum is a eukaryotic organism with multiple membrane bound organelles with discrete functions .",
"The rhoptry is an unusual secretory organelle that participates in host cell invasion and the formation of a specialised vacuole that the parasite occupies during the intracell... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology/infectious diseases"
] | Insecticide Susceptibility of Phlebotomus argentipes in Visceral Leishmaniasis Endemic Districts in India and Nepal | journal.pntd.0000859 | null | [
[
"Approximately 200 million people are at risk of visceral leishmaniasis ( VL ) – also known as kala-azar – in Bangladesh , India and Nepal [1] .",
"In South East Asia , VL is caused by Leishmania donovani Laveran & Mesnil ( Kinetoplastida: Trypanosomatidae ) which is transmitted by Phlebotomus argentipes ... | [
"To investigate the DDT and deltamethrin susceptibility of Phlebotomus argentipes , the vector of Leishmania donovani , responsible for visceral leishmaniasis ( VL ) , in two countries ( India and Nepal ) with different histories of insecticide exposure .",
"Standard WHO testing procedures were applied using 4% D... | [
"Visceral leishmaniasis ( VL ) , also know as kala azar , is one of the major public health concerns India , Nepal and Bangladesh .",
"In the Indian subcontinent , VL is caused by Leishmania donovani which is transmitted by Phlebotomus argentipes .",
"To date , Indoor Residual Spraying ( IRS ) campaigns have be... | 2010 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"ecology/theoretical ecology",
"ecology/population ecology",
"ecology/evolutionary ecology",
"genetics and genomics/population genetics"
] | Polymorphism Data Can Reveal the Origin of Species Abundance Statistics | journal.pcbi.1000359 | null | [
[
"One of the most interesting peculiarities of mother nature is the large variance in abundance of otherwise similar species .",
"In the tropical rainforest , for example , there are differences of 4–5 orders of magnitude in the observed abundance of tropical trees [1]–[5] .",
"Moreover , the abundance... | [
"What is the underlying mechanism behind the fat-tailed statistics observed for species abundance distributions ?",
"The two main hypotheses in the field are the adaptive ( niche ) theories , where species abundance reflects its fitness , and the neutral theory that assumes demographic stochasticity as the main f... | [
"One purchases 100 wineglasses and 100 pairs of pants .",
"After one year , 10 glasses and 10 pants survive .",
"What can be said about the relative quality of the survivors ?",
"Well , clothes “die” as a result of accumulated wear; the surviving items are of better quality .",
"The breaking of a wineglass ... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Cofilin1 Controls Transcolumnar Plasticity in Dendritic Spines in Adult Barrel Cortex | journal.pbio.1002070 | In vivo measurement of the electrophysiology and shape of neurons reveals that cofilin1 is needed for remodeling dendritic spines in circuits that connect mouse whisker barrels, so aiding experience-dependent plasticity in the neocortex. | [
[
"Experience-dependent plasticity ( EDP ) in adult neuronal circuits is considered to form the basis of learning and memory [1–3] .",
"EDP is also related to the recovery of cortical responses after the disruption of peripheral inputs [4–6] .",
"The rodent barrel cortex provides a key model system for ... | [
"During sensory deprivation , the barrel cortex undergoes expansion of a functional column representing spared inputs ( spared column ) , into the neighboring deprived columns ( representing deprived inputs ) which are in turn shrunk .",
"As a result , the neurons in a deprived column simultaneously increase and ... | [
"Plasticity in the adult neocortex is the basis of our learning and memory .",
"However , its molecular mechanisms are still unclear .",
"In the sensory barrel cortex of rodents , a well-characterized model for neocortical plasticity , neurons directly code for whisker displacement—neurons within a given barrel... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"cell physiology",
"medicine and health sciences",
"action potentials",
"muscle tissue",
"nervous system",
"membrane potential",
"condensed matter physics",
"junctional complexes",
"electrophysiology",
"neuroscience",
"simulation and modeling",
"gap junctions",
"waves",
"research and analy... | Estimating the probabilities of rare arrhythmic events in multiscale computational models of cardiac cells and tissue | journal.pcbi.1005783 | null | [
[
"In cardiac myocytes , dyads are sites where the junctional sarcoplasmic reticulum ( JSR ) membrane closely approaches ( ~ 15 nm ) invaginations of the cell membrane known as transverse tubules ( TTs ) .",
"Voltage-sensitive L-type calcium ( Ca2+ ) channels ( LCCs ) are preferentially localized to the TT ... | [
"Ectopic heartbeats can trigger reentrant arrhythmias , leading to ventricular fibrillation and sudden cardiac death .",
"Such events have been attributed to perturbed Ca2+ handling in cardiac myocytes leading to spontaneous Ca2+ release and delayed afterdepolarizations ( DADs ) .",
"However , the ways in which... | [
"Arrhythmias are electrical abnormalities of the heart that can degenerate into fibrillation , thus preventing normal heartbeats and leading to sudden cardiac death .",
"The mechanisms leading to ventricular arrhythmias and the unexpected nature of sudden cardiac death are not fully understood .",
"One hypothes... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"ecology and environmental sciences",
"medicine and health sciences",
"ecological niches",
"ecology",
"neglected tropical diseases",
"biology and life sciences",
"tropical diseases"
] | Topography and Land Cover of Watersheds Predicts the Distribution of the Environmental Pathogen Mycobacterium ulcerans in Aquatic Insects | journal.pntd.0003298 | null | [
[
"Knowledge of the spatial distribution of an environmentally persistent pathogen is often key in creation of environmental hazard maps for disease control .",
"Yet , despite the importance of this spatial information , only 4% of such pathogens have been mapped [1] .",
"The reason for this gap in our ... | [
"An understanding of the factors driving the distribution of pathogens is useful in preventing disease .",
"Often we achieve this understanding at a local microhabitat scale; however the larger scale processes are often neglected .",
"This can result in misleading inferences about the distribution of the pathog... | [
"Many pathogens persist in the environment , and an understanding of where they are can assist in disease control , allowing us to identify areas of risk to local human populations .",
"Herein , we use general linear models to describe the distribution of a particular environmental pathogen , Mycobacterium ulcera... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/animal models of infection",
"virology/antivirals, including modes of action and resistance",
"virology",
"virology/effects of virus infection on host gene expression",
"virology/host invasion and cell entry"
] | Phosphoinositide-3 Kinase-Akt Pathway Controls Cellular Entry of Ebola Virus | journal.ppat.1000141 | null | [
[
"Ebola virus , a member of the family Filoviridae , is an emerging infectious agent that causes severe and often fatal hemorrhagic fever in humans and nonhuman primates .",
"In many outbreaks , especially those caused by Zaire Ebola virus ( ZEBOV ) , mortality rates close to 90% have been reported [1] .",... | [
"The phosphoinositide-3 kinase ( PI3K ) pathway regulates diverse cellular activities related to cell growth , migration , survival , and vesicular trafficking .",
"It is known that Ebola virus requires endocytosis to establish an infection .",
"However , the cellular signals that mediate this uptake were unkno... | [
"Each year , filoviruses such as Ebola virus claim many human lives and decimate gorilla populations in Africa .",
"Infection results in an acute fever often associated with profuse internal and external bleeding and death rates of up to 90% .",
"Due to these symptoms and high pathogenicity , these viruses have... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Platelet Activating Factor Contributes to Vascular Leak in Acute Dengue Infection | journal.pntd.0003459 | null | [
[
"Dengue is thought to infect 390 million individuals per year resulting in approximately 96 million clinically apparent infections[1] .",
"The annual burden of dengue has been estimated to be 750 , 000 disability adjusted life years ( DALYs ) [2] which is higher than the global burden of 17 other disease ... | [
"Although plasma leakage is the hallmark of severe dengue",
"infections , the factors that cause increased vascular permeability have not been identified .",
"As platelet activating factor ( PAF ) is associated with an increase in vascular permeability in other diseases , we set out to investigate its role in a... | [
"Although plasma leakage is the hallmark of severe dengue",
"infections , the factors that cause increased vascular permeability have not been identified .",
"As platelet activating factor ( PAF ) is associated with an increase in vascular permeability in other diseases , we set out to investigate its role in a... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure | journal.pcbi.1004108 | null | [
[
"A half-century ago , Zuckerkandl and Pauling [1] discovered that amino acid substitutions often occur with sufficient regularity as to constitute a “molecular clock” .",
"Theoretical support for this observation was provided by Kimura [2] , who argued that observed rates of amino acid substitution could ... | [
"Over time , a population acquires neutral genetic substitutions as a consequence of random drift .",
"A famous result in population genetics asserts that the rate , K , at which these substitutions accumulate in the population coincides with the mutation rate , u , at which they arise in individuals: K = u .",
... | [
"Evolution is driven by genetic mutations .",
"While some mutations affect an organism’s ability to survive and reproduce , most are neutral and have no effect .",
"Neutral mutations play an important role in the study of evolution because they generally accrue at a consistent rate over time .",
"This result ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"phosphorylation",
"innate immune system",
"medicine and health sciences",
"immune physiology",
"cytokines",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"molecular probe techniques",
"gene regulation",
"pathogens",
"immunology",
"tropical diseases",
"immunoblotting",
... | The Myeloid LSECtin Is a DAP12-Coupled Receptor That Is Crucial for Inflammatory Response Induced by Ebola Virus Glycoprotein | journal.ppat.1005487 | null | [
[
"Ebola virus ( EBOV ) , a member of the family Filoviridae , is the causative agent of severe hemorrhagic fever in humans , which is responsible for the outbreak in West African countries in 2014 [1] .",
"Following EBOV infection , dendritic cells ( DCs ) and macrophages are the early and preferred replic... | [
"Fatal Ebola virus infection is characterized by a systemic inflammatory response similar to septic shock .",
"Ebola glycoprotein ( GP ) is involved in this process through activating dendritic cells ( DCs ) and macrophages .",
"However , the mechanism is unclear .",
"Here , we showed that LSECtin ( also know... | [
"Ebola virus ( EBOV ) , a highly virulent pathogen , causes a severe hemorrhagic fever syndrome .",
"The fatal infection is characterized by a systemic inflammatory response similar to septic shock .",
"Ebola glycoprotein ( GP ) is thought to contribute to disease pathogenesis , as high amounts of shed GP from ... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"innate immune system",
"medicine and health sciences",
"immune physiology",
"cytokines",
"pathology and laboratory medicine",
"china",
"antiviral therapy",
"pathogens",
"immunology",
"tropical diseases",
"microbiology",
"geographical locations",
"hepatitis b virus",
"liver diseases",
"v... | Clonorchis sinensis Co-infection Could Affect the Disease State and Treatment Response of HBV Patients | journal.pntd.0004806 | null | [
[
"Clonorchiasis , caused by Clonorchis sinensis ( C . sinensis ) , is one of the parasitic zoonosis .",
"It is estimated that approximately 35 million people are infected in Asia , among which approximately 15 million infected people were in China [1–3] .",
"Previous epidemiological data showed that cl... | [
"Clonorchis sinensis ( C . sinensis ) is considered to be an important parasitic zoonosis because it infects approximately 35 million people , while approximately 15 million were distributed in China .",
"Hepatitis B virus ( HBV ) infection is a major public health issue .",
"Two types of pathogens have the pot... | [
"Clonorchiasis and hepatitis B infection are infectious diseases that affect millions of people worldwide , especially in China .",
"These two diseases are caused by two different pathogens , C . sinensis and hepatitis B virus , respectively .",
"Concurrent infection between HBV and C . sinensis is often observ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"ecology and environmental sciences",
"variant genotypes",
"crop genetics",
"genetic mapping",
"cereal crops",
"plant science",
"crops",
"molecular biology techniques",
"molecular genetics",
"plants",
"research and analysis methods",
"ecological metrics",
"grasses",
"crop science",
"gene... | A large-scale pedigree resource of wheat reveals evidence for adaptation and selection by breeders | journal.pbio.3000071 | null | [
[
"Information of variety pedigree ( i . e . , ancestry or genealogy ) can be used by breeders to prioritise crosses between highly performing parents whilst maintaining genetic diversity in the offspring for selection .",
"However , development of varieties by commercial breeding companies in recent decade... | [
"Information on crop pedigrees can be used to help maximise genetic gain in crop breeding and allow efficient management of genetic resources .",
"We present a pedigree resource of 2 , 657 wheat ( Triticum aestivum L . ) genotypes originating from 38 countries , representing more than a century of breeding and va... | [
"Breeding activities undertaken in the world’s most important crop species have resulted in large increases in yield potential over the last century .",
"Bread wheat is a key crop for both human and animal nutrition worldwide .",
"To help inform future breeding and research activities , we have developed a pedi... | 2019 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"genetics and genomics/genetics of the immune system",
"immunology/genetics of the immune system",
"infectious diseases/viral infections",
"infectious diseases/tropical and travel-associated diseases",
"immunology/immunity to infections"
] | DC-SIGN (CD209) Promoter −336 A/G Polymorphism Is Associated with Dengue Hemorrhagic Fever and Correlated to DC-SIGN Expression and Immune Augmentation | journal.pntd.0000934 | null | [
[
"Dengue viruses ( DEN ) are arthropod-borne flaviviruses that cause dengue fever ( DF ) with significant morbidity and mortality in tropical and subtropical regions of the world .",
"There are four serotypes of dengue viruses ( DEN types 1–4 ) .",
"Classic DF is a self-limited illness characterized by... | [
"The C-type lectin DC-SIGN ( CD209 ) is known to be the major dengue receptor on human dendritic cells , and a single nucleotide polymorphism ( SNP ) in the promoter region of CD209 ( −336 A/G; rs4804803 ) is susceptible to many infectious diseases .",
"We reason that variations in the DC-SIGN gene might have a b... | [
"Dengue fever ( DF ) is an arthropod-borne disease that is prevalent in tropical and subtropical regions of the world .",
"DC-SIGN [dendritic cell-specific intercellular adhesion molecule 3 ( ICAM-3 ) -grabbing non-integrin] is a major receptor for dengue infection .",
"DC-SIGN , also called CD209 , expresses o... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"cell fate determination",
"functional genomics",
"gene expression",
"genetics",
"biology",
"genomics",
"genetics and genomics",
"cell differentiation",
"dna transcription",
"gene function"
] | Insulin and IGF1 Receptors Are Essential for XX and XY Gonadal Differentiation and Adrenal Development in Mice | journal.pgen.1003160 | null | [
[
"Both the gonads and the adrenal cortex originate from a common structure referred to as the adreno-genital primordium ( AGP ) .",
"In mice , the AGP is visible at embryonic day ( E ) 9 [1] , and is composed of a population of precursor cells expressing the nuclear receptor steroidogenic factor 1 ( SF1 , ... | [
"Mouse sex determination provides an attractive model to study how regulatory genetic networks and signaling pathways control cell specification and cell fate decisions .",
"This study characterizes in detail the essential role played by the insulin receptor ( INSR ) and the IGF type I receptor ( IGF1R ) in adren... | [
"Congenital disorders of sexual differentiation are rare diseases in which there is discordance between chromosomal , gonadal , and phenotypic sex .",
"Unfortunately , only a minority of patients clinically diagnosed with disorders of sex development ( DSD ) obtains a molecular diagnosis , indicating that our und... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"statistical mechanics",
"neuroscience",
"biomechanics",
"animal models",
"developmental biology",
"model organisms",
"cell mechanics",
"morphogenesis",
"pattern formation",
"developmental neuroscience",
"theoretical biology",
"biophysics theory",
"biology",
"biophysics",
"physics",
"s... | Coupling Mechanical Deformations and Planar Cell Polarity to Create Regular Patterns in the Zebrafish Retina | journal.pcbi.1002618 | null | [
[
"Epithelia are one of the basic building blocks from which animals sculpt complex tissues and organs during development [1]–[5] .",
"These sheets of cells are held together by specialized structures—notably apical junctional complexes , including adherens junctions—that allow cells to adhere tightly to th... | [
"The orderly packing and precise arrangement of epithelial cells is essential to the functioning of many tissues , and refinement of this packing during development is a central theme in animal morphogenesis .",
"The mechanisms that determine epithelial cell shape and position , however , remain incompletely unde... | [
"Many tissues and organs , including sensory organs like the vertebrate retina and inner ear , are built from sheets of connected cells called epithelia .",
"The precise arrangement of different types of cells within these epithelia can be essential to their function .",
"( For example , photoreceptor cells in ... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"glycolipids",
"medicine and health sciences",
"enzyme-linked immunoassays",
"immune physiology",
"pathology and laboratory medicine",
"chikungunya infection",
"sphingolipids",
"pathogens",
"immunology",
"tropical diseases",
"microbiology",
"viruses",
"clinical medicine",
"rna viruses",
... | Anti-ganglioside antibodies in patients with Zika virus infection-associated Guillain-Barré Syndrome in Brazil | journal.pntd.0007695 | null | [
[
"Zika virus is an arbovirus ( arthropod-borne ) of the Flaviviridae family , which like dengue viruses and alphavirus chikungunya virus is transmitted by Aedes mosquitoes .",
"Although discovered in 1947 in Uganda , the first large Zika virus outbreak was reported in Micronesia in 2007 [1] followed by the... | [
"Zika virus infection is associated with the development of Guillain-Barré syndrome ( GBS ) , a neurological autoimmune disorder caused by immune recognition of gangliosides and other components at nerve membranes .",
"Using a high-throughput ELISA , we have analyzed the anti-glycolipid antibody profile , includi... | [
"Zika virus infection can trigger the development of Guillain Barré syndrome ( GBS ) , a neurological autoimmune disorder mediated by antibodies recognizing gangliosides in nerve membranes .",
"Mechanisms such as molecular mimicry have been identified as a cause for GBS development in certain infections , such as... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"morphogens",
"developmental biology",
"molecular development",
"biology and life sciences",
"cell fate determination",
"evolutionary developmental biology"
] | Modeling of the Dorsal Gradient across Species Reveals Interaction between Embryo Morphology and Toll Signaling Pathway during Evolution | journal.pcbi.1003807 | null | [
[
"The embryonic patterning and development of limbs rely on morphogenetic gradients that set up territories of gene expression in a dosage-dependent fashion [1] , [2] .",
"Rather than a static process , cell fate specification normally occurs under dynamically changing environments that involve cell divisi... | [
"Morphogenetic gradients are essential to allocate cell fates in embryos of varying sizes within and across closely related species .",
"We previously showed that the maternal NF-κB/Dorsal ( Dl ) gradient has acquired different shapes in Drosophila species , which result in unequally scaled germ layers along the ... | [
"Embryo size can vary greatly among closely related species .",
"How tissue specification either scales or is modified in the developing embryo in different species is an ongoing investigation in developmental biology .",
"Here we asked how embryo morphology and specific molecular pathways influence tissue spec... | 2014 |
[
"Introduction",
"Materials and methods",
"Discussion"
] | [
"medicine and health sciences",
"rift valley fever virus",
"enzyme-linked immunoassays",
"immune physiology",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"tropical diseases",
"microbiology",
"viruses",
"rift valley fever",
"nucleoproteins",
"rna viruses",
"neglected tro... | Development and validation of a pen side test for Rift Valley fever | journal.pntd.0007700 | null | [
[
"Rift Valley fever ( RVF ) is an emerging mosquito-borne disease that affects a wide range of animals and human beings in Africa and the Arabian Peninsula .",
"It is caused by the mosquito-borne Rift Valley fever phlebovirus ( RVFV ) that belongs to the genus Phlebovirus in the family Phenuiviridae of the... | [
"Rift Valley fever ( RVF ) is one of the main vector borne zoonotic diseases that affects a wide range of ruminants and human beings in Africa and the Arabian Peninsula .",
"A rapid and specific test for RVF diagnosis at the site of a suspected outbreak is crucial for the implementation of control measures .",
... | [
"Rift Valley fever ( RVF ) is a viral disease that affects a wide range of animals and human beings in Africa and the Arabian Peninsula involving low case fatality rates .",
"A rapid and specific test for RVF diagnosis at the site of a suspected outbreak is crucial for the implementation of control measures .",
... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biotechnology",
"medicine and health sciences",
"pathology and laboratory medicine",
"engineering and technology",
"pathogens",
"sociology",
"microbiology",
"social sciences",
"light microscopy",
"logic circuits",
"fungi",
"model organisms",
"microscopy",
"fungal pathogens",
"genetic en... | Implementation of Complex Biological Logic Circuits Using Spatially Distributed Multicellular Consortia | journal.pcbi.1004685 | null | [
[
"Synthetic biological devices have been built to perform a variety of functions [1–3] .",
"Currently , the creation of complex logic circuits capable of integrating a high number of different inputs and of performing non-trivial decision making processes is one of the major challenges of synthetic biology... | [
"Engineered synthetic biological devices have been designed to perform a variety of functions from sensing molecules and bioremediation to energy production and biomedicine .",
"Notwithstanding , a major limitation of in vivo circuit implementation is the constraint associated to the use of standard methodologies... | [
"Synthetic biological circuits have been built for different purposes .",
"Nevertheless , the way these devices have been designed so far present several limitations: complex genetic engineering is required to implement complex circuits , and once the parts are built , they are not reusable .",
"We proposed to ... | 2016 |
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