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"
] | [] | Chromosomal Integrity after UV Irradiation Requires FANCD2-Mediated Repair of Double Strand Breaks | journal.pgen.1005792 | null | [
[
"Fanconi anemia ( FA ) is a rare recessive disorder characterized by increased spontaneous rearrangements of chromosomes , tumorigenesis and cell death [1 , 2] .",
"Initial signs of FA include bone or skeleton defects , renal dysfunction , short stature and very frequently abnormal hyper- and hypo-pigment... | [
"Fanconi Anemia ( FA ) is a rare autosomal recessive disorder characterized by hypersensitivity to inter-strand crosslinks ( ICLs ) .",
"FANCD2 , a central factor of the FA pathway , is essential for the repair of double strand breaks ( DSBs ) generated during fork collapse at ICLs .",
"While lesions different ... | [
"Here we show that irradiation with low doses of UV light causes modest accumulation of replication-coupled double strand breaks ( DSBs ) , i . e . collapsed forks .",
"Remarkably , the Fanconi Anemia protein FANCD2 is central to prevent the aberrant processing of UV-triggered DSBs and the generation of micronucl... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"vector biology",
"biology",
"microbiology"
] | Cytoplasmic Incompatibility as a Means of Controlling Culex pipiens quinquefasciatus Mosquito in the Islands of the South-Western Indian Ocean | journal.pntd.0001440 | null | [
[
"The last few years have witnessed an increasing interest in the alpha-proteobacterium Wolbachia ( Rickettsiales ) for the biological control of insect pest populations [for reviews see [1]–[5] .",
"Wolbachia is the most common intracellular bacterium yet described [6] , [7] , present in more than 65% of ... | [
"The use of the bacterium Wolbachia is an attractive alternative method to control vector populations .",
"In mosquitoes , as in members of the Culex pipiens complex , Wolbachia induces a form of embryonic lethality called cytoplasmic incompatibility , a sperm-egg incompatibility occurring when infected males mat... | [
"Mosquitoes of the Culex pipiens complex are important vectors of human pathogens including filarial parasites and many currently expanding arboviruses .",
"The absence of effective vaccines and the evolution of insecticide resistance stress the urgent need for the development of novel control strategies .",
"O... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"tropical diseases",
"microbiology",
"vertebrates",
"geographical locations",
"estonia",
"dogs",
"animals",
"mammals",
"viruses",
"vaccines",
"preventive medicine",
"rabies",
"raccoons",
... | Rabies in the Baltic States: Decoding a Process of Control and Elimination | journal.pntd.0004432 | null | [
[
"Rabies disease is a fatal mammalian encephalomyelitis caused by the rabies virus of the genus Lyssavirus ( family Rhabdoviridae ) [1] .",
"The virus is distributed worldwide , with the exception of the Antarctic , Australia and several islands and although all species of mammals are susceptible to this v... | [
"Rabies is a fatal zoonosis that still causes nearly 70 , 000 human deaths every year .",
"In Europe , the oral rabies vaccination ( ORV ) of red foxes ( Vulpes vulpes ) was developed in the late 1970s and has demonstrated its effectiveness in the eradication of the disease in Western and some Central European co... | [
"This paper reviews ten years of rabies epidemiology in the three Baltic countries .",
"Both surveillance efforts and oral rabies vaccination campaigns have resulted in the near eradication of the disease .",
"Multivariate analysis assessed with generalized linear models ( GLM ) suggested lower oral vaccination... | 2016 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"public health and epidemiology/epidemiology",
"infectious diseases/helminth infections",
"public health and epidemiology/social and behavioral determinants of health",
"mathematics/mathematical computing",
"infectious diseases/tropical and travel-associa... | Bayesian Spatio-Temporal Modeling of Schistosoma japonicum Prevalence Data in the Absence of a Diagnostic ‘Gold’ Standard | journal.pntd.0000250 | null | [
[
"Schistosomiasis japonica is a zoonotic disease caused by the digenetic trematode Schistosoma japonicum .",
"Historically , the disease was endemic in 12 provinces of the People's Republic of China , with more than 10 million individuals infected [1]–[3] .",
"Sustained control efforts implemented over... | [
"Spatial modeling is increasingly utilized to elucidate relationships between demographic , environmental , and socioeconomic factors , and infectious disease prevalence data .",
"However , there is a paucity of studies focusing on spatio-temporal modeling that take into account the uncertainty of diagnostic tech... | [
"Schistosomiasis is a serious public health problem in the People's Republic of China and elsewhere , and mapping of risk areas is important for guiding control interventions .",
"Here , a 10-year surveillance database from Dangtu County in the southeastern part of the People's Republic of China was utilized for ... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials & methods"
] | [
"blood cells",
"medicine and health sciences",
"fish",
"liver",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"vertebrates",
"staphylococcus aureus",
"animals",
"animal models",
"osteichthyes",
"model organisms",
"signs and symptoms",
... | Staphylococcus aureus infection dynamics | journal.ppat.1007112 | null | [
[
"Staphylococcus aureus is a leading opportunistic human pathogen renowned for its ability to evade the immune system and cause a variety of different infections [1] .",
"S . aureus infections can vary from superficial skin lesions , through deep seated abscesses to life threatening sepsis [1] .",
"The... | [
"Staphylococcus aureus is a human commensal that can also cause systemic infections .",
"This transition requires evasion of the immune response and the ability to exploit different niches within the host .",
"However , the disease mechanisms and the dominant immune mediators against infection are poorly unders... | [
"Staphylococcus aureus is a major human pathogen that causes a wide variety of infections .",
"In animal infection models , high doses of S . aureus are generally required to establish infections .",
"We have recently shown in animal models that this is due to very few bacteria within the infecting population g... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"oncology",
"medicine",
"chemotherapy and drug treatment",
"cancer treatment",
"biology",
"microbiology",
"parasitology"
] | A Repurposing Strategy for Hsp90 Inhibitors Demonstrates Their Potency against Filarial Nematodes | journal.pntd.0002699 | null | [
[
"Infections caused by the parasitic filarial nematodes Wuchereria bancrofti , Brugia malayi and Onchocerca volvulus remain a significant cause of pathology in the tropics .",
"The adult stages of these pathogens are extremely difficult to kill with currently available drugs .",
"Treatment relies upon ... | [
"Novel drugs are required for the elimination of infections caused by filarial worms , as most commonly used drugs largely target the microfilariae or first stage larvae of these infections .",
"Previous studies , conducted in vitro , have shown that inhibition of Hsp90 kills adult Brugia pahangi .",
"As numero... | [
"Adult filarial worms are long-lived nematode parasites that have proved very difficult to kill with existing drugs .",
"Current campaigns for the control or elimination of these parasites are largely based on treatment with drugs such as diethylcarbamazine or ivermectin , that preferentially kill the first stage... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell physiology",
"medicine and health sciences",
"action potentials",
"nervous system",
"depolarization",
"membrane potential",
"junctional complexes",
"electrophysiology",
"neuroscience",
"gap junctions",
"ion channels",
"nerve fibers",
"neuronal dendrites",
"sodium channels",
"animal... | Spikelets in Pyramidal Neurons: Action Potentials Initiated in the Axon Initial Segment That Do Not Activate the Soma | journal.pcbi.1005237 | null | [
[
"Brain functions rely on computations in single neurons , but some basic features of neural processing still remain unclear .",
"Here , we focus on spikelets , which are brief , spike-like depolarizations of small amplitude ( < 20 mV ) .",
"Spikelets can be measured in somatic intracellular recordings... | [
"Spikelets are small spike-like depolarizations that can be measured in somatic intracellular recordings .",
"Their origin in pyramidal neurons remains controversial .",
"To explain spikelet generation , we propose a novel single-cell mechanism: somato-dendritic input generates action potentials at the axon ini... | [
"Action potentials ( APs ) are digital , all-or-none signals by which neurons communicate with each other .",
"Therefore , APs are the basis of neural function , yet some of their fundamental features are still not well understood .",
"Here we focus on pyramidal cells , which are the principal neurons in neocor... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Revisiting the Central Metabolism of the Bloodstream Forms of Trypanosoma brucei: Production of Acetate in the Mitochondrion Is Essential for Parasite Viability | journal.pntd.0002587 | null | [
[
"Trypanosoma brucei is a unicellular eukaryote , belonging to the protozoan order Kinetoplastida that causes sleeping sickness in humans and economically important livestock diseases [1] .",
"This parasite undergoes a complex life cycle during transmission from the bloodstream of a mammalian host ( bloods... | [
"The bloodstream forms of Trypanosoma brucei , the causative agent of sleeping sickness , rely solely on glycolysis for ATP production .",
"It is generally accepted that pyruvate is the major end-product excreted from glucose metabolism by the proliferative long-slender bloodstream forms of the parasite , with vi... | [
"Many protists , including parasitic helminthes , trichomonads and trypanosomatids , produce acetate in their mitochondrion or mitochondrion-like organelle , which is excreted as a main metabolic end-product of their energy metabolism .",
"We have recently demonstrated that mitochondrial production of acetate is ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | DNA Exit Ramps Are Revealed in the Binding Landscapes Obtained from Simulations in Helical Coordinates | journal.pcbi.1003980 | null | [
[
"DNA is a charged , semi-flexible polymer , carrying two elementary negative charges per base-pair .",
"Mobile counterions screen the inter-strand electrostatic repulsion , hence , stabilizing the double helix .",
"Moreover , since DNA molecules are highly rigid , mobile ions also influence DNA’s mech... | [
"DNA molecules are highly charged semi-flexible polymers that are involved in a wide variety of dynamical processes such as transcription and replication .",
"Characterizing the binding landscapes around DNA molecules is essential to understanding the energetics and kinetics of various biological processes .",
... | [
"Protein-DNA and ion-DNA interactions are key for many essential biological activities such as DNA condensation , replication , transcription and repair .",
"All these processes require DNA-binding proteins to associate tightly to their specific targets , while also being able to find these sites in an efficient ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/protozoal infections",
"cell biology/extra-cellular matrix",
"cell biology/leukocyte signaling and gene expression"
] | TGF-b2 Induction Regulates Invasiveness of Theileria-Transformed Leukocytes and Disease Susceptibility | journal.ppat.1001197 | null | [
[
"Cellular transformation is a complex , multi-step process and leukocyte transformation by Theileria is no exception , as parasite infection activates several different leukocyte-signalling pathways , the combination of which leads to full host cell transformation [1] .",
"However , Theileria-induced leuk... | [
"Theileria parasites invade and transform bovine leukocytes causing either East Coast fever ( T . parva ) , or tropical theileriosis ( T . annulata ) .",
"Susceptible animals usually die within weeks of infection , but indigenous infected cattle show markedly reduced pathology , suggesting that host genetic facto... | [
"Theileria annulata causes tropical theileriosis that is endemic in cattle in North Africa , the Middle East , India and China .",
"T . parva causes East Coast fever that is prevalent in East and Southern Africa .",
"In endemic countries indigenous cattle are more resistant to pathology , but produce little mea... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"northern analysis",
"deletion mutation",
"molecular probe techniques",
"messenger rna",
"polyribosomes",
"mutation",
"fungi",
"molecular biology techniques",
"cellular structures and organelles",
"gel electrophoresis",
"research and analysis methods",
"electrophoretic techniques",
"proteins... | Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay | journal.pgen.1007818 | null | [
[
"The elongation phase of translation is an imperfect process , during which the ribosome moves with irregular speed along the mRNA template [1] .",
"By and large the elongation speed is determined by sequence and structural features of the coding sequence .",
"For instance , the identity of the A-site... | [
"No-go Decay ( NGD ) is a process that has evolved to deal with stalled ribosomes resulting from structural blocks or aberrant mRNAs .",
"The process is distinguished by an endonucleolytic cleavage prior to degradation of the transcript .",
"While many of the details of the pathway have been described , the ide... | [
"In all organisms , optimum cellular fitness depends on the ability of cells to recognize and degrade aberrant molecules .",
"Messenger RNA is subject to alterations and , as a result , often presents roadblocks for the translating ribosomes .",
"It is not surprising , then , that organisms evolved pathways to ... | 2018 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"cell biology/membranes and sorting",
"virology/viral replication and gene regulation",
"virology/mechanisms of resistance and susceptibility, including host genetics"
] | Identification and Characterization of the Host Protein DNAJC14 as a Broadly Active Flavivirus Replication Modulator | journal.ppat.1001255 | null | [
[
"The Flavivirus , Pestivirus and Hepacivirus genera of the Flaviviridae family each include important human and/or animal pathogens [1] .",
"A major human pathogen hepatitis C virus ( HCV ) is a member of the Hepacivirus genus , while Pestiviruses bovine viral diarrhea ( BVDV ) , border disease and classi... | [
"Viruses in the Flavivirus genus of the Flaviviridae family are arthropod-transmitted and contribute to staggering numbers of human infections and significant deaths annually across the globe .",
"To identify cellular factors with antiviral activity against flaviviruses , we screened a cDNA library using an itera... | [
"Viruses in the Flavivirus genus are transmitted by arthropods and cause significant disease burden across the globe .",
"We undertook a screening approach to select for and identify host factors that provide resistance to death caused by infection with the mosquito-transmitted Flavivirus , yellow fever virus ( Y... | 2011 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"computational biology",
"evolutionary biology",
"genetics and genomics"
] | Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans | journal.pbio.0050310 | Low-coverage genome sequences from multiple Drosophila simulans strains provide the first comprehensive view of polymorphism and divergence in the fruit fly. | [
[
"Given the long history of Drosophila as a central model system in evolutionary genetics beginning with the origins of empirical population genetics in the 1930s , it is unsurprising that Drosophila data have inspired the development of methods to test population genetic theories using DNA variation within an... | [
"The population genetic perspective is that the processes shaping genomic variation can be revealed only through simultaneous investigation of sequence polymorphism and divergence within and between closely related species .",
"Here we present a population genetic analysis of Drosophila simulans based on whole-ge... | [
"Population genomics , the study of genome-wide patterns of sequence variation within and between closely related species , can provide a comprehensive view of the relative importance of mutation , recombination , natural selection , and genetic drift in evolution .",
"It can also provide fundamental insights int... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"model organisms",
"genetics",
"biology",
"molecular cell biology",
"genetics and genomics"
] | UDP-Galactose 4′-Epimerase Activities toward UDP-Gal and UDP-GalNAc Play Different Roles in the Development of Drosophila melanogaster | journal.pgen.1002721 | null | [
[
"Galactose is an essential component of glycoproteins and glycolipids in metazoans , and as a constituent monosaccharide of the milk sugar , lactose , also serves as a key nutrient for mammalian infants .",
"Galactose is also found in notable quantities in some fruits , vegetables , and legumes .",
"G... | [
"In both humans and Drosophila melanogaster , UDP-galactose 4′-epimerase ( GALE ) catalyzes two distinct reactions , interconverting UDP-galactose ( UDP-gal ) and UDP-glucose ( UDP-glc ) in the final step of the Leloir pathway of galactose metabolism , and also interconverting UDP-N-acetylgalactosamine ( UDP-galNAc... | [
"In this manuscript we apply a fruit fly model to explore the relative contributions of each of two different activities attributed to a single enzyme—UDP-galactose 4′-epimerase ( GALE ) ; partial impairment of human GALE results in the potentially severe metabolic disorder epimerase deficiency galactosemia .",
"... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genetics and genomics/gene discovery",
"genetics and genomics/gene expression",
"infectious diseases/neglected tropical diseases",
"microbiology/parasitology",
"infectious diseases/protozoal infections",
"genetics and genomics/bioinformatics"
] | TcTASV: A Novel Protein Family in Trypanosoma cruzi Identified from a Subtractive Trypomastigote cDNA Library | journal.pntd.0000841 | null | [
[
"Trypanosoma cruzi , a kinetoplastid protozoan parasite , is the causative agent of the American trypanosomiasis , also known as Chagas' disease , a zoonotic disease that affects about 8 million individuals in Latin America [1] .",
"The disease is a chronic illness , which symptoms appear 10 or more years... | [
"The identification and characterization of antigens expressed in Trypanosoma cruzi stages that parasitize mammals are essential steps for the development of new vaccines and diagnostics .",
"Genes that are preferentially expressed in trypomastigotes may be involved in key processes that define the biology of try... | [
"Chagas' disease , caused by the kinetoplastid protozoan parasite Trypanosoma cruzi , is endemic in Latin America .",
"At present there are neither vaccines for prevention nor totally effective drugs for the treatment of the disease .",
"T . cruzi has a complex life cycle alternating between a reduviid insect (... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"flow cytometry",
"cell death",
"medicine and health sciences",
"autophagic cell death",
"pathology and laboratory medicine",
"viral transmission and infection",
"cell processes",
"microbiology",
"signs and symptoms",
"bacteria",
"research and analysis methods",
"specimen preparation and treat... | Identification of a Transcription Factor That Regulates Host Cell Exit and Virulence of Mycobacterium tuberculosis | journal.ppat.1005652 | null | [
[
"Apoptosis is a major programmed cell death pathway but now it is well established that necrosis can also be induced via defined signal transduction pathways [1 , 2] .",
"The importance of apoptosis in host defense against pathogens is well described [3 , 4] .",
"In contrast , the function of programm... | [
"The interaction of Mycobacterium tuberculosis ( Mtb ) with host cell death signaling pathways is characterized by an initial anti-apoptotic phase followed by a pro-necrotic phase to allow for host cell exit of the bacteria .",
"The bacterial modulators regulating necrosis induction are poorly understood .",
"H... | [
"Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis , is a highly successful human pathogen .",
"Following entry into host phagocytic cells , Mtb resides within a modified phagosomal compartment and inhibits apoptotic host cell death .",
"Recent studies have demonstrated that Mtb eventuall... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/bacterial infections",
"microbiology/microbial growth and development",
"microbiology/cellular microbiology and pathogenesis",
"microbiology/medical microbiology",
"infectious diseases/antimicrobials and drug resistance"
] | agr-Mediated Dispersal of Staphylococcus aureus Biofilms | journal.ppat.1000052 | null | [
[
"Most bacteria have an inherent ability to form surface-attached communities of cells called biofilms [1] .",
"The opportunistic pathogen Staphylococcus aureus can form biofilms on many host tissues and implanted medical devices often causing chronic infections [2]–[5] .",
"The challenge presented by ... | [
"The agr quorum-sensing system of Staphylococcus aureus modulates the expression of virulence factors in response to autoinducing peptides ( AIPs ) .",
"Recent studies have suggested a role for the agr system in S . aureus biofilm development , as agr mutants exhibit a high propensity to form biofilms , and cells... | [
"A biofilm is a surface-attached community of cells bound together by an extracellular matrix .",
"In a bacterial infection , biofilm-encased cells are protected from antibiotic therapy and host immune response , and these encased cells can develop into a chronic infection .",
"Staphylococcus aureus is a promin... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biology and life sciences",
"veterinary science",
"medicine and health sciences",
"social sciences"
] | Community Knowledge and Attitudes and Health Workers' Practices regarding Non-malaria Febrile Illnesses in Eastern Tanzania | journal.pntd.0002896 | null | [
[
"Febrile illnesses due to different etiological agents are the common causes of morbidity and mortality in developing countries [1] .",
"Malaria has been the leading cause of fever in sub- Saharan Africa for many years [2] .",
"For instance , in Tanzania , malaria was contributing to about 42% of hosp... | [
"Although malaria has been the leading cause of fever for many years , with improved control regimes malaria transmission , morbidity and mortality have decreased .",
"Recent studies have increasingly demonstrated the importance of non-malaria fevers , which have significantly improved our understanding of etiolo... | [
"Understanding the awareness of the community on non-malaria febrile illnesses is crucial , especially during the recent decline of malaria episodes of malaria .",
"This study conducted focus group discussions with communities to assess their awareness of non-malaria febrile illnesses .",
"In addition , in-dept... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"signal transduction",
"medicine and health sciences",
"molecular cell biology",
"pathology and laboratory medicine",
"cell biology",
"host-pathogen interactions",
"genetic screens",
"medical microbiology",
"gene identification and analysis",
"gene expression",
"genetics",
"biology and life sc... | Forward Genetic Screening Identifies a Small Molecule That Blocks Toxoplasma gondii Growth by Inhibiting Both Host- and Parasite-Encoded Kinases | journal.ppat.1004180 | null | [
[
"Toxoplasma gondii infects approximately one-third of the world's population and causes disease primarily in developing fetuses or immunocompromised individuals [1] .",
"Humans and other intermediate hosts are infected with Toxoplasma by digesting either sporozoite-containing oocysts that are shed in feli... | [
"The simultaneous targeting of host and pathogen processes represents an untapped approach for the treatment of intracellular infections .",
"Hypoxia-inducible factor-1 ( HIF-1 ) is a host cell transcription factor that is activated by and required for the growth of the intracellular protozoan parasite Toxoplasma... | [
"Understanding how a compound blocks growth of an intracellular pathogen is important not only for developing these compounds into drugs that can be prescribed to patients , but also because these data will likely provide novel insight into the biology of these pathogens .",
"Forward genetic screens are one estab... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Barcoding T Cell Calcium Response Diversity with Methods for Automated and Accurate Analysis of Cell Signals (MAAACS) | journal.pcbi.1003245 | null | [
[
"Calcium ion acts as a universal second messenger in response to most cellular stimuli [1] .",
"The pattern of the calcium response is biphasic , and primarily results from the production of inositol-3 phosphate ( IP3 ) which triggers the release of calcium from the endoplasmic reticulum ( ER store releas... | [
"We introduce a series of experimental procedures enabling sensitive calcium monitoring in T cell populations by confocal video-microscopy .",
"Tracking and post-acquisition analysis was performed using Methods for Automated and Accurate Analysis of Cell Signals ( MAAACS ) , a fully customized program that associ... | [
"The adaptive immune response to pathogen invasion requires the stimulation of lymphocytes by antigen-presenting cells .",
"We hypothesized that investigating the dynamics of the T lymphocyte activation by monitoring intracellular calcium fluctuations might help explain the high specificity and selectivity of thi... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"cytokines",
"immunology",
"cytomegalovirus infection",
"vaccines",
"preventive medicine",
"developmental biology",
"clinical medicine",
"molecular development",
"cytotoxic t cells",... | The Breadth of Synthetic Long Peptide Vaccine-Induced CD8+ T Cell Responses Determines the Efficacy against Mouse Cytomegalovirus Infection | journal.ppat.1005895 | null | [
[
"Human cytomegalovirus ( HCMV ) contributes substantially to morbidity in immunocompromised individuals .",
"Organ or hematopoietic stem cell transplant recipients , people infected with HIV and patients with lymphocytic leukaemia are particularly vulnerable to HCMV-associated disease [1] .",
"Moreove... | [
"There is an ultimate need for efficacious vaccines against human cytomegalovirus ( HCMV ) , which causes severe morbidity and mortality among neonates and immunocompromised individuals .",
"In this study we explored synthetic long peptide ( SLP ) vaccination as a platform modality to protect against mouse CMV ( ... | [
"The majority of infections with the betaherpesvirus human cytomegalovirus ( HCMV ) are clinically unnoticed , but in immunocompromised hosts HCMV infections can be severe and even fatal .",
"Here we investigated in preclinical mouse models the efficacy and mechanisms of synthetic long peptide ( SLP ) -based vacc... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"ecological metrics",
"mutation",
"population size",
"genetic polymorphism",
"ecology",
"effective population size",
"natural selection",
"genetics",
"biology and life sciences",
"population genetics",
"evolutionary biology",
"evolutionary processes",
"genetic drift"
] | Genetic Diversity in the Interference Selection Limit | journal.pgen.1004222 | null | [
[
"Natural selection maintains existing function and drives adaptation , altering patterns of diversity at the genetic level .",
"Evidence from microbial evolution experiments [1] , [2] and natural populations of nematodes [3] , fruit flies [4] , [5] , and humans [6] , [7] suggests that selection is common ... | [
"Pervasive natural selection can strongly influence observed patterns of genetic variation , but these effects remain poorly understood when multiple selected variants segregate in nearby regions of the genome .",
"Classical population genetics fails to account for interference between linked mutations , which gr... | [
"A central goal of evolutionary genetics is to understand how natural selection influences DNA sequence variability .",
"Yet while empirical studies have uncovered significant evidence for selection in many natural populations , a rigorous characterization of these selection pressures has so far been difficult to... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"microarrays",
"genomics",
"molecular cell biology",
"gene expression",
"biology",
"computational biology",
"microbiology",
"host-pathogen interaction",
"molecular biology",
"genetics and genomics"
] | Transcriptomic Signature of Leishmania Infected Mice Macrophages: A Metabolic Point of View | journal.pntd.0001763 | null | [
[
"Leishmania , the causative agent of vector-borne diseases , known as leishmaniases , lives as an obligate intracellular parasite within mammalian hosts .",
"The outcome of infection depends largely on the activation status of macrophages , the first line of mammalian defense and the major target cells fo... | [
"We analyzed the transcriptional signatures of mouse bone marrow-derived macrophages at different times after infection with promastigotes of the protozoan parasite Leishmania major .",
"Ingenuity Pathway Analysis revealed that the macrophage metabolic pathways including carbohydrate and lipid metabolisms were am... | [
"Leishmania are obligated intracellular pathogens that develop almost exclusively in macrophages .",
"Experimental leishmaniasis in mice is one of the most extensively studied models of intracellular infections both at the level of the parasite and host immune responses .",
"We took advantage of Balb/c mice mod... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"blood cells",
"t helper cells",
"medicine and health sciences",
"immune cells",
"immune physiology",
"immunology",
"cell-mediated immunity",
"cell differentiation",
"vaccines",
"preventive medicine",
"developmental biology",
"vaccination and immunization",
"bacteria",
"public and occupati... | CD4+ T Cells Recognizing PE/PPE Antigens Directly or via Cross Reactivity Are Protective against Pulmonary Mycobacterium tuberculosis Infection | journal.ppat.1005770 | null | [
[
"It is estimated that two billion people are latently infected with Mycobacterium tuberculosis ( Mtb ) , and this huge reservoir is sustaining the pan/epidemic spread of the bacterium .",
"Due to the relative inefficiency of the Mycobacterium bovis BCG ( Bacille Calmette-Guerin ) vaccine in preventing the... | [
"Mycobacterium tuberculosis ( Mtb ) , possesses at least three type VII secretion systems , ESX-1 , -3 and -5 that are actively involved in pathogenesis and host-pathogen interaction .",
"We recently showed that an attenuated Mtb vaccine candidate ( Mtb Δppe25-pe19 ) , which lacks the characteristic ESX-5-associa... | [
"Mycobacterium tuberculosis ( Mtb ) , the causative agent of human tuberculosis , is one of the most widely spread human pathogens , responsible for more than 9 . 6 million of new tuberculosis cases and 1 . 5 million deaths , annually .",
"The resurgence of pulmonary tuberculosis in immuno-compromised patients , ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"biology",
"computational biology",
"evolutionary biology"
] | Spatial Dynamics of Human-Origin H1 Influenza A Virus in North American Swine | journal.ppat.1002077 | null | [
[
"Swine influenza A viruses cause severe respiratory disease in pigs , similar to that which presents in humans , and constitute an important economic concern for the US swine industry and threat to public health .",
"Influenza was first clinically recognized in pigs in the Midwestern US in conjunction wit... | [
"The emergence and rapid global spread of the swine-origin H1N1/09 pandemic influenza A virus in humans underscores the importance of swine populations as reservoirs for genetically diverse influenza viruses with the potential to infect humans .",
"However , despite their significance for animal and human health ... | [
"Since 1998 , genetically and antigenically diverse influenza A viruses have circulated in North American swine due to continuous cross-species transmission and reassortment with avian and human influenza viruses , presenting a pandemic threat to humans .",
"Millions of swine are transported year-round from the s... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"bacteriology",
"cell physiology",
"cell motility",
"medicine and health sciences",
"pathology and laboratory medicine",
"engineering and technology",
"pathogens",
"signal processing",
"microbiology",
"biological locomotion",
"simulation and modeling",
"developmental biology",
"methylation",... | The role of intracellular signaling in the stripe formation in engineered Escherichia coli populations | journal.pcbi.1006178 | null | [
[
"Understanding the formation of regularly spaced structures , such as vertebrate segments , hair follicles , fish pigmentation and animal coats , is a fundamental problem in developmental biology [1–7] .",
"These patterns involve the complex interaction of intracellular signaling , cell-cell communication... | [
"Recent experiments showed that engineered Escherichia coli colonies grow and self-organize into periodic stripes with high and low cell densities in semi-solid agar .",
"The stripes develop sequentially behind a radially propagating colony front , similar to the formation of many other periodic patterns in natur... | [
"One of the central problems in biology is to understand the underlying mechanisms responsible for spatial pattern formation in complex systems .",
"This is a difficult task because the essential mechanisms for pattern formation often involve multiple space and time scales and are often buried in overwhelmingly c... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computer science",
"mathematics",
"computational biology",
"homo (human)",
"genetics and genomics"
] | Modeling Cancer Progression via Pathway Dependencies | journal.pcbi.0040028 | null | [
[
"In the past several decades , many genes have been discovered that govern important functions in the development of a variety of different cancers .",
"However , biological insight from the list of genes is still limited and the underlying mechanisms that occur in the cell during tumorigenesis have not b... | [
"Cancer is a heterogeneous disease often requiring a complexity of alterations to drive a normal cell to a malignancy and ultimately to a metastatic state .",
"Certain genetic perturbations have been implicated for initiation and progression .",
"However , to a great extent , underlying mechanisms often remain ... | [
"Cancer is a complex disease with many subtypes that differ substantially with respect to their onset , progression , and response to treatment .",
"Better understanding of the etiology and mechanism of cancer should help improve the diagnosis , prognosis , and treatment of cancer that will kill more than half a ... | 2008 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"neuroscience/cognitive neuroscience",
"neuroscience/theoretical neuroscience",
"computational biology/computational neuroscience"
] | Dual Coding with STDP in a Spiking Recurrent Neural Network Model of the Hippocampus | journal.pcbi.1000839 | null | [
[
"The hippocampus and surrounding medial temporal lobe are implicated in declarative memory function in humans and other mammals [1] .",
"Electrophysiology studies in a range of species have demonstrated that the activity of single pyramidal cells within this region can encode for the presence of both spat... | [
"The firing rate of single neurons in the mammalian hippocampus has been demonstrated to encode for a range of spatial and non-spatial stimuli .",
"It has also been demonstrated that phase of firing , with respect to the theta oscillation that dominates the hippocampal EEG during stereotype learning behaviour , c... | [
"Changes in the strength of synaptic connections between neurons are believed to mediate processes of learning and memory in the brain .",
"A computational theory of this synaptic plasticity was first provided by Donald Hebb within the context of a more general neural coding mechanism , whereby phase sequences of... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"body fluids",
"immune cells",
"pathology and laboratory medicine",
"immune physiology",
"multiple sclerosis",
"nervous system",
"neurodegenerative diseases",
"pathogens",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"demyelinati... | Immunophenotypic characterization of CSF B cells in virus-associated neuroinflammatory diseases | journal.ppat.1007042 | null | [
[
"Various inflammatory neurologic diseases are associated with viral infections .",
"These agents may cause direct cellular damage of infected cells associated with immunological alterations such as chronic activation , immunodeficiency and infiltration of inflammatory cells into the central nervous system... | [
"Intrathecal antibody synthesis is a well-documented phenomenon in infectious neurological diseases as well as in demyelinating diseases , but little is known about the role of B cells in the central nervous systems .",
"We examined B cell and T cell immunophenotypes in CSF of patients with HTLV-1-associated myel... | [
"Regulation of the local immune response is crucial in protecting the central nervous system ( CNS ) from viral infection and immunopathologically mediated tissue damage .",
"Intrathecal antibody synthesis is a well-documented phenomenon in infectious and demyelinating neurological diseases , but little is known ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology/germ cells",
"cell biology/cell growth and division",
"genetics and genomics/chromosome biology",
"evolutionary biology/nuclear structure and function"
] | A High Incidence of Meiotic Silencing of Unsynapsed Chromatin Is Not Associated with Substantial Pachytene Loss in Heterozygous Male Mice Carrying Multiple Simple Robertsonian Translocations | journal.pgen.1000625 | null | [
[
"A series of complex processes takes place during the first meiotic division , including pairing , synapsis , recombination and segregation of homologous chromosomes .",
"Defects in any of these processes can affect the normal progression of meiosis , causing severe fertility reduction or even sterility [... | [
"Meiosis is a complex type of cell division that involves homologous chromosome pairing , synapsis , recombination , and segregation .",
"When any of these processes is altered , cellular checkpoints arrest meiosis progression and induce cell elimination .",
"Meiotic impairment is particularly frequent in organ... | [
"Cells have different mechanisms to assess the proper occurrence of cellular events .",
"These mechanisms are called checkpoints and are involved in the surveillance of processes such as DNA replication and cell division .",
"A checkpoint at the pachytene stage arrests meiosis when defects in the process of hom... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"neuronal differentiation",
"neuroscience",
"animals",
"cell differentiation",
"blastulas",
"animal models",
"developmental biology",
"model organisms",
"embryos",
"echinoderms",
"research and analysis methods",
"ectoderm",
"embryology",
"animal cells",
"signal transdu... | Cooperative Wnt-Nodal Signals Regulate the Patterning of Anterior Neuroectoderm | journal.pgen.1006001 | null | [
[
"Embryonic cells of some animals tend to be differentiated into neuroectoderm cells/neural progenitors unless they receive an extrinsic signal , so-called default model [1 , 2] .",
"This characteristic is also applicable to mammalian embryonic stem cells and induced pluripotent cells ( e . g . , [3 , 4] )... | [
"When early canonical Wnt is experimentally inhibited , sea urchin embryos embody the concept of a Default Model in vivo because most of the ectodermal cell fates are specified as anterior neuroectoderm .",
"Using this model , we describe here how the combination of orthogonally functioning anteroposterior Wnt an... | [
"The sea urchin embryo is similar to vertebrate embryos in that the default cell fate is potentially neurogenic , and normal development restricts the neural fate to the narrow area that locates at the anterior/dorsal region of the embryo .",
"Because maintaining the default neural fate to the anterior/dorsal reg... | 2016 |
[
"Introduction",
"Model",
"Results/Discussion"
] | [
"computer science",
"stochastic processes",
"computer modeling",
"mathematics",
"evolutionary biology",
"population modeling",
"evolutionary modeling",
"biology",
"computational biology",
"evolutionary processes",
"probability theory"
] | Reward from Punishment Does Not Emerge at All Costs | journal.pcbi.1002868 | null | [
[
"Cooperation , understood as an action which incurs a cost c to the individual that performs it , inducing a benefit b>c to the recipient of that action , is ubiquitous at all levels of biological complexity ( i . e . from bacteria to primates ) [1]–[3] .",
"However , cooperation requires the existence of... | [
"The conundrum of cooperation has received increasing attention during the last decade .",
"In this quest , the role of altruistic punishment has been identified as a mechanism promoting cooperation .",
"Here we investigate the role of altruistic punishment on the emergence and maintenance of cooperation in str... | [
"Altruistic punishment — when a cooperative individual pays a cost to punish her defective partner — has been described as one of the mechanisms that help to explain cooperation's ubiquity in nature .",
"Here , we investigate a model population where individuals interact with each other along the links of a netwo... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"helminths",
"tropical diseases",
"fibrosis",
"fascioliasis",
"database searching",
"parasitic diseases",
"animals",
"liver diseases",
"trematodes",
"developmental biology",
"gastroenterology and hepatology",
"neglected tropical diseases",
... | Association of Fasciola hepatica Infection with Liver Fibrosis, Cirrhosis, and Cancer: A Systematic Review | journal.pntd.0004962 | null | [
[
"Food-borne trematodiases are an emerging public health problem in Southeast Asia and Latin America , and are caused by the following flukes: Clonorchis sinensis , Fasciola gigantica , Fasciola hepatica , Opisthorchis felineus , Opisthorchis viverrini , and Paragonimus spp [1] .",
"Globally , it has been ... | [
"Fascioliasis has been sporadically associated with chronic liver disease on previous studies .",
"In order to describe the current evidence , we carried out a systematic review to assess the association between fascioliasis with liver fibrosis , cirrhosis and cancer .",
"A systematic search of electronic datab... | [
"Fascioliasis is a neglected infectious disease caused by the trematode Fasciola .",
"This parasite ( liver fluke ) is endemic in many parts of the world including countries from Asia , Africa , Europe and the Americas .",
"High prevalence rates of fascioliasis has been repeatedly reported in the Andean region ... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"insect metamorphosis",
"geographical locations",
"animals",
"indonesia",
"java",
"age groups",
"developmental biology",
"adults",
"pupae",
"infectious disease control",
"insect vectors",
"zoology",
"infectious diseases",
"epidemiology",... | Dengue in Java, Indonesia: Relevance of Mosquito Indices as Risk Predictors | journal.pntd.0004500 | null | [
[
"Dengue virus ( DENV ) is considered to be the most important arbovirus world wide , with a heavy disease burden in humans [1] .",
"It is transmitted mainly by Aedes aegypti mosquitoes , but Ae .",
"albopictus can also act as a vector [2–5] .",
"Dengue is endemic in many countries around the world... | [
"No vaccine is currently available for dengue virus ( DENV ) , therefore control programmes usually focus on managing mosquito vector populations .",
"Entomological surveys provide the most common means of characterising vector populations and predicting the risk of local dengue virus transmission .",
"Despite ... | [
"Geographically and economically , Indonesia is one of the most prominent countries in SE Asia , yet many of its endemic infectious diseases are poorly managed , controlled and understood .",
"This includes dengue virus ( DENV ) , which can result in serious human disease and is transmitted by mosquitoes .",
"D... | 2016 |
[
"Introduction",
"Results and discussion",
"Material and methods"
] | [
"medicine and health sciences",
"fusarium",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"hormones",
"plant science",
"rice",
"plant hormones",
"experimental organism systems",
"seedlings",
"molecular biology techniques",
"plants",
"fungal pathogens",
"research and a... | Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles | journal.ppat.1006670 | null | [
[
"The heterothallic ascomycete Fusarium fujikuroi Nirenberg is a member of the Fusarium fujikuroi species complex ( FFC ) , a monophyletic lineage which includes at least eleven mating populations ( MPs A-K ) that are sexually infertile with one another , and numerous distinct anamorphic species [1] .",
"F... | [
"Fusarium fujikuroi causes bakanae ( “foolish seedling” ) disease of rice which is characterized by hyper-elongation of seedlings resulting from production of gibberellic acids ( GAs ) by the fungus .",
"This plant pathogen is also known for production of harmful mycotoxins , such as fusarins , fusaric acid , api... | [
"Fusarium fujikuroi causes bakanae disease of rice .",
"Infected seedlings appear to be taller and more slender when compared to healthy seedlings due to its ability to produce gibberellic acids ( GAs ) .",
"The disease is responsible for high yield losses , and its incidence varies with regions , rice cultivar... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Differential Association of the Conserved SUMO Ligase Zip3 with Meiotic Double-Strand Break Sites Reveals Regional Variations in the Outcome of Meiotic Recombination | journal.pgen.1003416 | null | [
[
"During meiosis , the programmed formation of DNA double-strand breaks ( DSBs ) and their repair by homologous recombination ensures that crossovers ( CO ) occur between homologous chromosomes .",
"COs promote the accurate segregation of homologs at the first meiotic division , thus avoiding aneuploidy , ... | [
"During the first meiotic prophase , programmed DNA double-strand breaks ( DSBs ) are distributed non randomly at hotspots along chromosomes , to initiate recombination .",
"In all organisms , more DSBs are formed than crossovers ( CO ) , the repair product that creates a physical link between homologs and allows... | [
"For sexual reproduction , meiosis is an essential step ensuring the formation of haploid gametes from diploid precursors of the germline .",
"This reduction in the genome's content is achieved through a specialized type of division , where a single round of DNA replication is followed by two successive rounds of... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"innate immune system",
"medicine and health sciences",
"immune cells",
"immune physiology",
"cytokines",
"granulomas",
"immunology",
"tropical diseases",
"parasitic diseases",
"liver diseases",
"animal models",
"immune receptor signaling",
"developmental biology",
"model ... | Toll-like receptor-2 regulates macrophage polarization induced by excretory-secretory antigens from Schistosoma japonicum eggs and promotes liver pathology in murine schistosomiasis | journal.pntd.0007000 | null | [
[
"Schistosomiasis is one of the most important health problems in developing countries[1] , and can be used as a chronic disease model for investigating the interplay between the immune response and parasite pathogenicity in the host[2] .",
"Following a schistosome infection , the host immune response grad... | [
"Schistosomiasis is endemic to many regions of the world and affects approximately 200 million people .",
"Conventional adaptive T cell responses are considered to be the primary contributors to the pathogenesis of Schistosoma japonicum infection , leading to liver granuloma and fibrosis .",
"However , the func... | [
"Schistosomiasis is a global health concern that affects primarily tropical and subtropical areas .",
"During a schistosome infection , the eggs are trapped in the host liver and products derived from eggs induce a polarized Th2 response , resulting in granuloma formation and eventually fibrosis .",
"Thus , it ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"evolutionary ecology",
"ecology and environmental sciences",
"medicine and health sciences",
"infectious disease epidemiology",
"population dynamics",
"microbiology",
"parasitic diseases",
"plant science",
"plant pathology",
"theoretical ecology",
"evolutionary adaptation",
"population biolog... | Evolution of Plastic Transmission Strategies in Avian Malaria | journal.ppat.1004308 | null | [
[
"All organisms experience some level of temporal variation in the quality of their environment .",
"In response to these variations , many species have evolved specific strategies that allow them to limit or shut down growth and development until the conditions improve [1] .",
"The best reported examp... | [
"Malaria parasites have been shown to adjust their life history traits to changing environmental conditions .",
"Parasite relapses and recrudescences—marked increases in blood parasite numbers following a period when the parasite was either absent or present at very low levels in the blood , respectively—are expe... | [
"Seasonal fluctuations in the environment affect dramatically the abundance of insect species .",
"These fluctuations have important consequences for the transmission of vector-borne diseases .",
"Here we contend that malaria parasites may have evolved plastic transmission strategies as an adaptation to the flu... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"lipolysis",
"medicine and health sciences",
"plant products",
"diet",
"developmental biology",
"nutrition",
"mitochondria",
"bioenergetics",
"peroxisomes",
"cellular structures and organelles",
"lipids",
"crop science",
"life cycles",
"chemistry",
"agriculture",
"biochemistry",
"veg... | Dietary rescue of lipotoxicity-induced mitochondrial damage in Peroxin19 mutants | journal.pbio.2004893 | null | [
[
"Peroxisomes are vesicular organelles originally discovered and described by C . De Duve as catalase-containing organelles important for the degradation of hydrogen peroxide [1] .",
"Recently , it has become more and more apparent that they harbor much more complex metabolic functions , which are still in... | [
"Mutations in peroxin ( PEX ) genes lead to loss of peroxisomes , resulting in the formation of peroxisomal biogenesis disorders ( PBDs ) and early lethality .",
"Studying PBDs and their animal models has greatly contributed to our current knowledge about peroxisomal functions .",
"Very-long-chain fatty acid ( ... | [
"Peroxisomes are organelles that contain several enzymes and fatty acids required for many metabolic tasks in the cell , and upon peroxisome loss , their educts accumulate .",
"One example is the accumulation of very-long-chain fatty acids ( VLCFAs ) with a chain length of more than 20 carbons .",
"These fatty ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/immune response",
"immunology/innate immunity",
"immunology/immunity to infections"
] | Hepatitis C Virus (HCV) Evades NKG2D-Dependent NK Cell Responses through NS5A-Mediated Imbalance of Inflammatory Cytokines | journal.ppat.1001184 | null | [
[
"Natural Killer ( NK ) cells are effectors of the rapidly acting antiviral innate immune system .",
"They kill virally infected cells and are an important source of antiviral cytokines such as IFNγ .",
"In addition , they establish an early and efficient dialogue with professional antigen presenting c... | [
"Understanding how hepatitis C virus ( HCV ) induces and circumvents the host's natural killer ( NK ) cell-mediated immunity is of critical importance in efforts to design effective therapeutics .",
"We report here the decreased expression of the NKG2D activating receptor as a novel strategy adopted by HCV to eva... | [
"Natural killer ( NK ) cells are part of the innate immune response against virus infection .",
"Their activation is the net result of signals emanating from a panel of inhibitory and activating receptors , among which the NKG2D activating receptor plays a major role .",
"NKG2D ligands , the MHC class I related... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Spike-Triggered Covariance Analysis Reveals Phenomenological Diversity of Contrast Adaptation in the Retina | journal.pcbi.1004425 | null | [
[
"Sensory systems have to encode stimuli over wide input ranges , and neurons therefore adapt their processing characteristics to the encountered stimulus statistics .",
"In the vertebrate retina , ganglion cells adjust their sensitivity and temporal filtering characteristics when visual contrast changes [... | [
"When visual contrast changes , retinal ganglion cells adapt by adjusting their sensitivity as well as their temporal filtering characteristics .",
"The latter has classically been described by contrast-induced gain changes that depend on temporal frequency .",
"Here , we explored a new perspective on contrast-... | [
"Our sensory systems have to process stimuli under a wide range of environmental conditions .",
"To cope with this challenge , the involved neurons adapt by adjusting their signal processing to the recently encountered intensity range .",
"In the visual system , one finds , for example , that higher visual cont... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Comparison of Leishmania killicki (syn. L. tropica) and Leishmania tropica Population Structure in Maghreb by Microsatellite Typing | journal.pntd.0004204 | null | [
[
"Leishmaniases are vector-borne diseases caused by several Leishmania species that cycle between their phlebotomine sandfly vectors and mammalian reservoir hosts [1] .",
"Leishmania parasites , like many other microorganisms , have a high adaptation capacity that allows them to invade and survive in vario... | [
"Leishmania ( L . ) killicki ( syn . L . tropica ) , which causes cutaneous leishmaniasis in Maghreb , was recently described in this region and identified as a subpopulation of L . tropica .",
"The present genetic analysis was conducted to explore the spatio-temporal distribution of L . killicki ( syn . L . trop... | [
"Leishmania killicki ( syn . L . tropica ) was discovered in 1986 .",
"Few studies have been conducted on this parasite exclusively described in Maghreb .",
"Consequently , many elements on its epidemiology , transmission , population structure and dynamics remain unknown .",
"To better understand the evoluti... | 2015 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"spring",
"statistics",
"china",
"atmospheric science",
"geographical locations",
"seasons",
"hemorrhagic fever with renal syndrome",
"mathematics",
"research and analysis methods",
"climate change",
"infectious diseases",
"geography",
"mathematical and stat... | Distribution of geographical scale, data aggregation unit and period in the correlation analysis between temperature and incidence of HFRS in mainland China: A systematic review of 27 ecological studies | journal.pntd.0007688 | null | [
[
"Hemorrhagic fever with renal syndrome ( HFRS ) is a rodent-associated zoonosis and also a legally mandated notifiable disease in China [1 , 2] .",
"China has the largest number of HFRS cases in the world [3 , 4] .",
"After the epidemic of HFRS in mainland China in the 1980s , the HFRS incidence fluct... | [
"Changes in climate and environmental conditions could be the driving factors for the transmission of hantavirus .",
"Thus , a thorough collection and analysis of data related to the epidemic status of hemorrhagic fever with renal syndrome ( HFRS ) and the association between HFRS incidence and meteorological fac... | [
"China has the largest number of hemorrhagic fever with renal syndrome ( HFRS ) cases in the world .",
"With the acceleration of China’s urbanization process , especially in the process of rapid transition of China’s agriculture-related landscapes to urban landscapes , the dual role of climate change and environm... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunity",
"innate immunity",
"immunology",
"biology"
] | Encephalomyocarditis Virus Viroporin 2B Activates NLRP3 Inflammasome | journal.ppat.1002857 | null | [
[
"The innate immune system , the first line of defense against pathogens , utilizes pattern-recognition receptors ( PRRs ) to detect pathogen-associated molecular patterns ( PAMPs ) .",
"RNA viruses are detected by host PRRs including Toll-like receptors ( TLRs ) , retinoic acid-inducible gene-I ( RIG-I ) ... | [
"Nod-like receptors ( NLRs ) comprise a large family of intracellular pattern- recognition receptors .",
"Members of the NLR family assemble into large multiprotein complexes , termed the inflammasomes .",
"The NLR family , pyrin domain-containing 3 ( NLRP3 ) is triggered by a diverse set of molecules and signa... | [
"The innate immune system , the first line of defense against invading pathogens , plays a key role not only in limiting microbe replications at early stages of infection , but also in initiating and orchestrating antigen-specific adaptive immune responses .",
"The innate immune responses against viruses usually ... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"evolutionary biology",
"genetics and genomics",
"vertebrates",
"computational biology"
] | SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework | journal.pcbi.0030149 | null | [
[
"Many RNA genes function by assuming a distinct three-dimensional structure in which the molecule folds back onto itself .",
"Contacts are formed by hydrogen bonds between non-consecutive nucleotides that are complementary to each other .",
"These hydrogen bonds are weak compared with covalent bonds .... | [
"Computational methods for predicting evolutionarily conserved rather than thermodynamic RNA structures have recently attracted increased interest .",
"These methods are indispensable not only for elucidating the regulatory roles of known RNA transcripts , but also for predicting RNA genes .",
"It has been noto... | [
"Not only is the prediction of evolutionarily conserved RNA structures important for elucidating the potential functions of RNA sequences and the mechanisms by which these functions are exerted , but it also lies at the core of RNA gene prediction .",
"To get an accurate prediction of the conserved RNA structure ... | 2007 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [] | A Spatially Detailed Model of Isometric Contraction Based on Competitive Binding of Troponin I Explains Cooperative Interactions between Tropomyosin and Crossbridges | journal.pcbi.1004376 | null | [
[
"Tension generation in cardiac muscle is a highly cooperative process , with significant increases in tension caused by relatively small increases in the calcium concentration .",
"The Hill coefficient ( nH ) describing the degree of cooperativity of the force-calcium relationship is typically around nH =... | [
"Biophysical models of cardiac tension development provide a succinct representation of our understanding of force generation in the heart .",
"The link between protein kinetics and interactions that gives rise to high cooperativity is not yet fully explained from experiments or previous biophysical models .",
... | [
"Force generation in cardiac muscle cells is driven by changes in calcium concentration .",
"Relatively small changes in the calcium concentration over the course of a heart beat lead to the large changes in force required to fully contract and relax the heart .",
"This is known as ‘cooperative activation’ , an... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"veterinary diseases",
"emerging infectious diseases",
"virology",
"emerging viral diseases",
"veterinary virology",
"biology",
"microbiology",
"veterinary science"
] | Cedar Virus: A Novel Henipavirus Isolated from Australian Bats | journal.ppat.1002836 | null | [
[
"Henipaviruses were first discovered in the 1990s following investigation of serious disease outbreaks in horses , pigs and humans in Australia and Malaysia [1] , [2] and comprise the only known Biosafety Level 4 ( BSL4 ) agents in the family Paramyxoviridae [3] .",
"Depending upon the geographic location... | [
"The genus Henipavirus in the family Paramyxoviridae contains two viruses , Hendra virus ( HeV ) and Nipah virus ( NiV ) for which pteropid bats act as the main natural reservoir .",
"Each virus also causes serious and commonly lethal infection of people as well as various species of domestic animals , however li... | [
"Hendra and Nipah viruses are 2 highly pathogenic paramyxoviruses that have emerged from bats within the last two decades .",
"Both are capable of causing fatal disease in both humans and many mammal species .",
"Serological and molecular evidence for henipa-like viruses have been reported from numerous locatio... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Methods"
] | [
"morpholino",
"rna interference",
"gene regulation",
"messenger rna",
"vertebrates",
"nucleotides",
"animals",
"xenopus",
"blastulas",
"animal models",
"dna transcription",
"developmental biology",
"model organisms",
"amphibians",
"experimental organism systems",
"epigenetics",
"embr... | Brg1 chromatin remodeling ATPase balances germ layer patterning by amplifying the transcriptional burst at midblastula transition | journal.pgen.1006757 | null | [
[
"Vertebrate BAF protein complexes remodel chromatin with the mutually exclusive help of Brahma ( brm ) or Brahma-related gene 1 ( brg1 ) ATPase subunits .",
"SWI/SNF complexes are known to participate broadly in nucleosome-based aspects of DNA metabolism in normal and malignant cells [1–4] , but their spe... | [
"Zygotic gene expression programs control cell differentiation in vertebrate development .",
"In Xenopus , these programs are initiated by local induction of regulatory genes through maternal signaling activities in the wake of zygotic genome activation ( ZGA ) at the midblastula transition ( MBT ) .",
"These p... | [
"Brahma-related-gene-1 ( Brg1 ) is a catalytic subunit of mammalian SWI/SNF chromatin remodeling complexes .",
"Loss of maternal Brg1 protein arrests development in mice at the 2-cell stage , while null homozygotes die at the blastocyst stage .",
"These early requirements have precluded any analysis of Brg1’s e... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/emerging viral diseases",
"virology/virus evolution and symbiosis",
"evolutionary biology/evolutionary ecology"
] | Diversification of Rice Yellow Mottle Virus and Related Viruses Spans the History of Agriculture from the Neolithic to the Present | journal.ppat.1000125 | null | [
[
"The mechanisms of evolution of plant viruses are being progressively unraveled [1]–[3] , yet the timescale of their evolution remains an enigma .",
"Even the order of magnitude is unknown [4] .",
"Several viruses showed few genetic changes between isolates separated in space and time , sometimes for ... | [
"The mechanisms of evolution of plant viruses are being unraveled , yet the timescale of their evolution remains an enigma .",
"To address this critical issue , the divergence time of plant viruses at the intra- and inter-specific levels was assessed .",
"The time of the most recent common ancestor ( TMRCA ) of... | [
"The timescale of the evolution of plant viruses is an enigma , and even its order of magnitude is unknown .",
"This critical issue is addressed here by calculating the age of plant viruses .",
"An accurate estimate of the age of Rice yellow mottle virus ( RYMV ) was obtained by statistical analysis of a set of... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"genome expression analysis",
"neuroscience",
"animal models",
"model organisms",
"genome analysis",
"bioassays and physiological analysis",
"molecular genetics",
"research and analysis methods",
"gene expression",
"mouse models",
"microarrays",
"gene identification and analysis",
"olfactory... | The Olfactory Transcriptomes of Mice | journal.pgen.1004593 | null | [
[
"Olfaction is used for locating and discriminating between food sources , but also plays a fundamental role in social communication between individuals .",
"Mice heavily rely on their sense of smell to distinguish between animals from their own and different species , and to determine their identity [1] .... | [
"The olfactory ( OR ) and vomeronasal receptor ( VR ) repertoires are collectively encoded by 1700 genes and pseudogenes in the mouse genome .",
"Most OR and VR genes were identified by comparative genomic techniques and therefore , in many of those cases , only their protein coding sequences are defined .",
"S... | [
"The sense of smell in mice involves the detection of odors and pheromones by many hundreds of olfactory and vomeronasal receptors .",
"The genes that encode these receptors account for around 5% of the whole gene catalog , but they are poorly understood because they are very similar to each other , and are thoug... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"poxviruses",
"pathology and laboratory medicine",
"hela cells",
"pathogens",
"biological cultures",
"microbiology",
"viruses",
"immunoprecipitation",
"dna viruses",
"cell cultures",
"research and analysis methods",
"proteins",
"medical microbiology",
"mic... | A paralogous pair of mammalian host restriction factors form a critical host barrier against poxvirus infection | journal.ppat.1006884 | null | [
[
"Emerging and reemerging infectious diseases have continued to pose a major threat to public health .",
"In particular , zoonotic viral infections have caused such lethal human diseases as SARS , avian influenza , human monkeypox , and Ebola [1] .",
"For many viruses , including coronaviruses and infl... | [
"Host restriction factors constitute a formidable barrier for viral replication to which many viruses have evolved counter-measures .",
"Human SAMD9 , a tumor suppressor and a restriction factor for poxviruses in cell lines , is antagonized by two classes of poxvirus proteins , represented by vaccinia virus ( VAC... | [
"Zoonotic viral infections represent a major threat to public health .",
"For many viruses , host species-specific difference in viral entry receptors presents a major hurdle for cross-species transmission .",
"Poxviruses , however , can enter nearly any animal cell .",
"Why many poxviruses show strict host s... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"invertebrates",
"medicine and health sciences",
"pathology and laboratory medicine",
"microbiology",
"invertebrate genomics",
"animals",
"wolbachia",
"animal models",
"bacterial diseases",
"developmental biology",
"drosophila melanogaster",
"model organisms",
"microbial growth and developme... | Intensity of Mutualism Breakdown Is Determined by Temperature Not Amplification of Wolbachia Genes | journal.ppat.1005888 | null | [
[
"Symbiosis has played a pivotal role in arthropod diversification , speciation , and the ability of these animals to occupy a variety of niches in the natural world .",
"Symbionts fall into two broad categories: infectious symbionts that often impose severe fitness costs to their host in order to complete... | [
"Wolbachia are maternally transmitted intracellular bacterial symbionts that infect approximately 40% of all insect species .",
"Though several strains of Wolbachia naturally infect Drosophila melanogaster and provide resistance against viral pathogens , or provision metabolites during periods of nutritional stre... | [
"Wolbachia are obligate intracellular , symbiotic bacteria that infect approximately 40% of insect species , as well as filarial nematodes , arachnids and terrestrial isopods .",
"While the vast majority of Wolbachia strains impose few fitness costs to their host , one strain wMelPop is unique as it lacks the abi... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"biophysics",
"biochemistry"
] | Modular Organization and Combinatorial Energetics of Proline–Tyrosine Nuclear Localization Signals | journal.pbio.0060137 | PY-nuclear localization signals contain three binding regions that are not closely related in sequence and are energetically quasi-independent. These modular epitopes can contribute differently to the total binding energy in different signals, to tune their affinity for binding to the carrier protein Karyopherinβ2/Kap1... | [
[
"Karyopherinβ proteins ( Kapβs; Importins/Exportins ) mediate the majority of nucleocytoplasmic protein transport .",
"There are 19 known Kapβs in human and 14 in yeast [1 , 2] .",
"Kapβs bind substrates through nuclear localization or export signals ( NLSs or NESs ) and transport them through the nuc... | [
"Proline–tyrosine nuclear localization signals ( PY-NLSs ) are recognized and transported into the nucleus by human Karyopherin ( Kap ) β2/Transportin and yeast Kap104p .",
"Multipartite PY-NLSs are highly diverse in sequence and structure , share a common C-terminal R/H/KX2–5PY motif , and can be subdivided into... | [
"To travel between the cytoplasm and nucleus , proteins rely on a family of transport proteins known as the karyopherinβ family .",
"Karyopherinβ2 , the human version of a family member , recognizes cargo proteins containing a class of nuclear localization signal known as the PY-NLS .",
"The yeast homolog of Ka... | 2008 |
[
"Introduction",
"Results and discussion",
"Methods"
] | [
"learning",
"organismal evolution",
"acoustics",
"social sciences",
"neuroscience",
"learning and memory",
"developmental biology",
"cognitive psychology",
"sound pressure",
"evolutionary adaptation",
"evolutionary genetics",
"physics",
"psychology",
"phenotypes",
"natural selection",
... | How evolution learns to generalise: Using the principles of learning theory to understand the evolution of developmental organisation | journal.pcbi.1005358 | null | [
[
"Explaining how organisms adapt in novel selective environments is central to evolutionary biology [1–5] .",
"Living organisms are both robust and capable of change .",
"The former property allows for stability and reliable functionality against genetic and environmental perturbations , while the latt... | [
"One of the most intriguing questions in evolution is how organisms exhibit suitable phenotypic variation to rapidly adapt in novel selective environments .",
"Such variability is crucial for evolvability , but poorly understood .",
"In particular , how can natural selection favour developmental organisations t... | [
"A striking feature of evolving organisms is their ability to acquire novel characteristics that help them adapt in new environments .",
"The origin and the conditions of such ability remain elusive and is a long-standing question in evolutionary biology .",
"Recent theory suggests that organisms can evolve des... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Antagonism of miR-328 Increases the Antimicrobial Function of Macrophages and Neutrophils and Rapid Clearance of Non-typeable Haemophilus Influenzae (NTHi) from Infected Lung | journal.ppat.1004549 | null | [
[
"Pathogenic bacterial infections of the respiratory tract are major causes of morbidity , are difficult to treat and can be life-threatening [1] .",
"They also play a critical role in the pathogenesis of many inflammatory conditions of the lung ( e . g . chronic obstructive pulmonary disease ( COPD ) and ... | [
"Pathogenic bacterial infections of the lung are life threatening and underpin chronic lung diseases .",
"Current treatments are often ineffective potentially due to increasing antibiotic resistance and impairment of innate immunity by disease processes and steroid therapy .",
"Manipulation miRNA directly regul... | [
"MicroRNAs regulate pathogen recognition pathways by modulating translation .",
"In the immune system , miRNAs have been identified as important regulators of gene expression programs , which regulate differentiation , growth and function of innate and adaptive immune cells .",
"Using miRNA microarray , we demo... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"animal models",
"drosophila melanogaster",
"model organisms",
"genetics",
"comparative genomics",
"biology",
"genomics",
"evolutionary biology",
"genomic evolution"
] | Evolutionary Rate Covariation Identifies New Members of a Protein Network Required for Drosophila melanogaster Female Post-Mating Responses | journal.pgen.1004108 | null | [
[
"Sexual reproduction is a fundamental biological process by which many eukaryotic organisms transmit their genetic material to the next generation .",
"While the end result of a successful mating is the fusion of the gametes , other molecular interactions must occur to allow this fusion .",
"In intern... | [
"Seminal fluid proteins transferred from males to females during copulation are required for full fertility and can exert dramatic effects on female physiology and behavior .",
"In Drosophila melanogaster , the seminal protein sex peptide ( SP ) affects mated females by increasing egg production and decreasing re... | [
"Reproduction requires more than a sperm and an egg .",
"In animals with internal fertilization , other proteins in the seminal fluid and the female are essential for full fertility .",
"Although hundreds of such reproductive proteins are known , our ability to understand how they interact remains limited .",
... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | The Burden of Parasitic Zoonoses in Nepal: A Systematic Review | journal.pntd.0002634 | null | [
[
"Various parasites infecting humans depend on vertebrate animals to complete their life cycle .",
"Humans most commonly become infected with these zoonotic parasites through consumption of infected hosts or through fecal-oral contamination .",
"The results of these infections may vary from asymptomati... | [
"Parasitic zoonoses ( PZs ) pose a significant but often neglected threat to public health , especially in developing countries .",
"In order to obtain a better understanding of their health impact , summary measures of population health may be calculated , such as the Disability-Adjusted Life Year ( DALY ) .",
... | [
"Various parasites that infect humans require animals in some stage of their life cycle .",
"Infection with these so-called zoonotic parasites may vary from asymptomatic carriership to long-term morbidity and even death .",
"Although data are still scarce , it is clear that parasitic zoonoses ( PZs ) present a ... | 2014 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"enzymes",
"immunology",
"enzymology",
"microbiology",
"parasitic diseases",
"protozoan life cycles",
"parasitic protozoans",
"phosphatases",
"developmental biology",
"protozoans",
"leishmania",
"rna helicases",
"sequence m... | Identification of novel leishmanicidal molecules by virtual and biochemical screenings targeting Leishmania eukaryotic translation initiation factor 4A | journal.pntd.0006160 | null | [
[
"Leishmaniases are neglected diseases caused by multiple protozoan parasite species of the genus Leishmania .",
"These vector-borne diseases affect more than 98 countries that are mainly developing countries with limited public health resources .",
"Additionally , more than 300 million people are at r... | [
"Leishmaniases are neglected parasitic diseases in spite of the major burden they inflict on public health .",
"The identification of novel drugs and targets constitutes a research priority .",
"For that purpose we used Leishmania infantum initiation factor 4A ( LieIF ) , an essential translation initiation fac... | [
"Leishmaniases constitute a group of neglected parasitic diseases that inflict major burden on public health .",
"Novel drugs and targets need to be identified since current therapies have adverse side effects .",
"Herein , we focused on Leishmania infantum translation initiation factor 4A ( LieIF ) , as a pote... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"biofilms",
"cell walls",
"medicine and health sciences",
"fluorescence",
"pathology and laboratory medicine",
"enzymes",
"pathogens",
"microbiology",
"enzymology",
"staphylococcus aureus",
"electromagnetic radiation",
"cellular structures and organelles",
"bacteria",
"ba... | Staphylococcal Bap Proteins Build Amyloid Scaffold Biofilm Matrices in Response to Environmental Signals | journal.ppat.1005711 | null | [
[
"Biofilm formation is universal for all bacteria .",
"The molecular mechanisms governing this process vary among bacteria , but they all culminate in the synthesis of an extracellular matrix .",
"The composition of the extracellular matrix is complex and variable , even within the same bacterial speci... | [
"Biofilms are communities of bacteria that grow encased in an extracellular matrix that often contains proteins .",
"The spatial organization and the molecular interactions between matrix scaffold proteins remain in most cases largely unknown .",
"Here , we report that Bap protein of Staphylococcus aureus self-... | [
"Major components of the biofilm matrix scaffold are proteins that assemble to create a unified structure that maintain bacteria attached to each other and to surfaces .",
"We provide evidence that a surface protein present in several staphylococcal species forms functional amyloid aggregates to build the biofilm... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | The Midline Protein Regulates Axon Guidance by Blocking the Reiteration of Neuroblast Rows within the Drosophila Ventral Nerve Cord | journal.pgen.1004050 | null | [
[
"In the Drosophila nerve cord , about 20 longitudinal axon tracts on either side of the midline , each consisting of axons from several neurons , connect different segments with one another .",
"Several direct players in axon guidance have been identified .",
"For example , previous studies have shown... | [
"Guiding axon growth cones towards their targets is a fundamental process that occurs in a developing nervous system .",
"Several major signaling systems are involved in axon-guidance , and disruption of these systems causes axon-guidance defects .",
"However , the specific role of the environment in which axon... | [
"During nervous system development , once formed from neuroblasts , neurons grow axons in the direction of their synaptic partners .",
"Genetic forces guide these axon growth cones towards the target .",
"This is known as axon guidance or pathfinding .",
"There are a number of proteins that regulate axon-path... | 2013 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"fish",
"vertebrates",
"pigments",
"animals",
"cell differentiation",
"epithelial cells",
"simulation and modeling",
"animal models",
"osteichthyes",
"developmental biology",
"model organisms",
"stem cells",
"materials science",
"experimental organism syst... | A systems biology approach uncovers the core gene regulatory network governing iridophore fate choice from the neural crest | journal.pgen.1007402 | null | [
[
"Despite decades of work , we still have only a superficial idea of how stem cells generate their distinct derivatives .",
"This question becomes more acute if we consider that these fate choices are often made in a physically constrained environment ( e . g . a stem cell niche ) , suggesting that fate-sp... | [
"Multipotent neural crest ( NC ) progenitors generate an astonishing array of derivatives , including neuronal , skeletal components and pigment cells ( chromatophores ) , but the molecular mechanisms allowing balanced selection of each fate remain unknown .",
"In zebrafish , melanocytes , iridophores and xanthop... | [
"Multipotent neural crest ( NC ) progenitors generate an astonishing array of derivatives , including neuronal , skeletal components and pigment cells , but the molecular mechanisms allowing balanced selection of each fate remain unknown .",
"In zebrafish , melanocytes , iridophores and xanthophores , the three c... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"biotechnology",
"genome engineering",
"fish",
"engineering and technology",
"nucleases",
"enzymes",
"synthetic biology",
"dna-binding proteins",
"vertebrates",
"cloning",
"enzymology",
"microhomology-mediated end joining",
"animals",
"synthetic bioengineering",
"animal models",
"ostei... | Robust activation of microhomology-mediated end joining for precision gene editing applications | journal.pgen.1007652 | null | [
[
"Programmable nucleases such as TALEN ( Transcription Activator-like Effector Nuclease ) and CRISPR ( Clustered Regularly Interspaced Short Palindromic Repeats ) systems have enabled a new era of scientific research [1 , 2] .",
"Instead of relying on knock-down models or expensively outsourced knock out l... | [
"One key problem in precision genome editing is the unpredictable plurality of sequence outcomes at the site of targeted DNA double stranded breaks ( DSBs ) .",
"This is due to the typical activation of the versatile Non-homologous End Joining ( NHEJ ) pathway .",
"Such unpredictability limits the utility of so... | [
"New gene editing tools precisely break DNA at pre-defined genomic locations , but cells repair these lesions using diverse pathways that often lead to unpredictable outcomes in the resulting DNA sequences .",
"This sequence diversity in gene editing outcomes represents an important obstacle to the application of... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"transfection",
"medicine and health sciences",
"luciferase",
"diagnostic radiology",
"natural antisense transcripts",
"gene regulation",
"enzymes",
"cancers and neoplasms",
"enzymology",
"basic cancer research",
"in vivo imaging",
"oncology",
"neurological tumors",
"micrornas",
"molecul... | Molecular predictors of brain metastasis-related microRNAs in lung adenocarcinoma | journal.pgen.1007888 | null | [
[
"MicroRNAs ( miRNAs ) are small , ( 18–23 nt ) , single-stranded noncoding RNAs [1] .",
"miRNAs play critical roles in almost all important cellular processes , including tumorigenesis [2] .",
"Compared to long non-coding RNAs ( lncRNAs; >200 nt ) , miRNAs are more stable in vivo [1–2] .",
"As miR... | [
"Brain metastasis ( BM ) is a major complication of lung adenocarcinoma ( LAD ) .",
"An investigation of the pathogenic mechanisms of BM , as well as the identification of appropriate molecular markers , is necessary .",
"The aim of this study was to determine the expression patterns of microRNAs ( miRNAs ) in ... | [
"Brain metastasis ( BM ) is a major complication of lung carcinoma .",
"Here , we aimed to identify the key miRNAs involved in BM lung cancer .",
"We first profiled miRNA expression in 32 tissues from NSCLC patients with BM and 55 tissues from NSCLC patients without BM .",
"We independently validated our resu... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/sequence motif analysis",
"genetics and genomics/functional genomics",
"genetics and genomics/gene expression",
"computational biology/transcriptional regulation",
"developmental biology/aging"
] | Global Prediction of Tissue-Specific Gene Expression and Context-Dependent Gene Networks in Caenorhabditis elegans | journal.pcbi.1000417 | null | [
[
"Tissue-specific gene expression is a fundamental aspect of multicellular biology , underlying the development , function , and maintenance of diverse cell types within an organism .",
"Accounting for tissue-specific expression is a precursor to any systems-level understanding of metazoan organismal devel... | [
"Tissue-specific gene expression plays a fundamental role in metazoan biology and is an important aspect of many complex diseases .",
"Nevertheless , an organism-wide map of tissue-specific expression remains elusive due to difficulty in obtaining these data experimentally .",
"Here , we leveraged existing whol... | [
"In animals , a crucial facet of any gene's function is the tissue or cell type in which that gene is expressed and the proteins that it interacts with in that cell .",
"However , genome-wide identification of expression across the multitude of tissues of varying size and complexity is difficult to achieve experi... | 2009 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"molecular epidemiology",
"epidemiology",
"dengue fever",
"neglected tropical diseases",
"dengue",
"biology",
"viral diseases",
"evolutionary biology",
"genomic evolution"
] | Molecular Surveillance of Dengue in Semarang, Indonesia Revealed the Circulation of an Old Genotype of Dengue Virus Serotype-1 | journal.pntd.0002354 | null | [
[
"Dengue is one of the most important arthropod-borne viral diseases with large global burden .",
"The disease is caused by dengue virus ( DENV ) , a member of Flaviviridae family , with four distinct serotypes ( DENV-1 , -2 , -3 , and -4 ) circulating in tropical and subtropical regions in the world .",
... | [
"Dengue disease is currently a major health problem in Indonesia and affects all provinces in the country , including Semarang Municipality , Central Java province .",
"While dengue is endemic in this region , only limited data on the disease epidemiology is available .",
"To understand the dynamics of dengue i... | [
"We studied dengue disease in Semarang municipality , Central Java , one of the endemic regions in Indonesia .",
"The disease occurred in wide geographical regions which include urban , rural , coastal , and highland areas .",
"All four dengue virus serotypes were found .",
"The infecting serotypes were not a... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"genome-wide association studies",
"medicine and health sciences",
"cardiovascular anatomy",
"variant genotypes",
"genetic mapping",
"simulation and modeling",
"diabetes mellitus",
"endocrine disorders",
"mathematics",
"statistics (mathematics)",
"materials science",
"test statistics",
"geno... | CERAMIC: Case-Control Association Testing in Samples with Related Individuals, Based on Retrospective Mixed Model Analysis with Adjustment for Covariates | journal.pgen.1006329 | null | [
[
"In genetic association analysis of a binary trait , such as presence or absence of a disease , it can be useful to properly control for relevant covariates .",
"Inclusion of environmental risk factors in the analysis has the potential to increase statistical power by reducing phenotypic noise , and adjus... | [
"We consider the problem of genetic association testing of a binary trait in a sample that contains related individuals , where we adjust for relevant covariates and allow for missing data .",
"We propose CERAMIC , an estimating equation approach that can be viewed as a hybrid of logistic regression and linear mi... | [
"Case-control association testing has proven to be useful for identification of genetic variants that affect susceptibility to disease .",
"One can expect to gain power for detecting such variants by including relevant covariates in the analysis , by accounting for any relatedness of sampled individuals , and by ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"bacteriology",
"bacterial physiology",
"microbial metabolism",
"gene expression",
"gene regulation",
"genetics",
"molecular genetics",
"staphylococci",
"biology",
"microbiology",
"bacterial pathogens",
"gram positive"
] | Methionine Biosynthesis in Staphylococcus aureus Is Tightly Controlled by a Hierarchical Network Involving an Initiator tRNA-Specific T-box Riboswitch | journal.ppat.1003606 | null | [
[
"Staphylococci are important skin and mucosa commensals but also major human pathogens .",
"The most pathogenic species Staphylococcus aureus causes a wide range of diseases and , together with coagulase-negative staphylococci ( CoNS ) , accounts for approximately 30 per cent of all hospital-acquired infe... | [
"In line with the key role of methionine in protein biosynthesis initiation and many cellular processes most microorganisms have evolved mechanisms to synthesize methionine de novo .",
"Here we demonstrate that , in the bacterial pathogen Staphylococcus aureus , a rare combination of stringent response-controlled... | [
"Prokaryote metabolism is key for our understanding of bacterial virulence and pathogenesis and it is also an area with huge opportunity to identify novel targets for antibiotic drugs .",
"Here , we have addressed the so far poorly characterized regulation of methionine biosynthesis in S . aureus .",
"We demons... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular biology/bioinformatics",
"computational biology/protein structure prediction",
"computational biology/macromolecular sequence analysis",
"biochemistry/macromolecular assemblies and machines"
] | Detection of Alpha-Rod Protein Repeats Using a Neural Network and
Application to Huntingtin | journal.pcbi.1000304 | null | [
[
"Tandems of repeated protein sequences forming structural domains occur in at least",
"3% of proteins in eukaryotic organisms [1] .",
"Characterization of",
"these repeats by sequence similarity is sometimes difficult as weak evolutionary",
"constraints cause rapid sequence divergence [2] .",
... | [
"A growing number of solved protein structures display an elongated structural",
"domain , denoted here as alpha-rod , composed of stacked pairs of anti-parallel",
"alpha-helices .",
"Alpha-rods are flexible and expose a large surface , which makes",
"them suitable for protein interaction .",
"Although mo... | [
"Many proteins have an elongated structural domain formed by a stack of alpha",
"helices ( alpha-rod ) , often found to interact with other proteins .",
"The",
"identification of an alpha-rod in a protein can therefore tell something about",
"both the function and the structure of that protein .",
"Though... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | RNA∶DNA Hybrids Initiate Quasi-Palindrome-Associated Mutations in Highly Transcribed Yeast DNA | journal.pgen.1003924 | null | [
[
"RNA∶DNA hybrids exist as normal intermediates during the cellular transactions of transcription and DNA replication .",
"During transcription , a small segment of the nascent RNA is transiently base-paired with the template DNA strand as part of a transcription bubble .",
"More extensive and stable h... | [
"RNase H enzymes promote genetic stability by degrading aberrant RNA∶DNA hybrids and by removing ribonucleotide monophosphates ( rNMPs ) that are present in duplex DNA .",
"Here , we report that loss of RNase H2 in yeast is associated with mutations that extend identity between the arms of imperfect inverted repe... | [
"Mutation rates are correlated with the level of gene expression in budding yeast , demonstrating a link between transcription and stability of the underlying DNA template .",
"In the current work , we describe a novel type of transcription-associated mutation that converts imperfect inverted repeats ( quasi-pali... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious diseases/neglected tropical diseases",
"immunology/innate immunity",
"genetics and genomics/genetics of the immune system"
] | Human TLR1 Deficiency Is Associated with Impaired Mycobacterial Signaling and Protection from Leprosy Reversal Reaction | journal.pntd.0000231 | null | [
[
"Mycobacterium tuberculosis ( MTb ) has established latent infection in one-third of the world's population and , among those with progressive disease , causes about 2 million deaths per year [1] .",
"Mycobacterium leprae ( ML ) , a related organism , is the etiologic agent of leprosy , an ancient scourge... | [
"Toll-like receptors ( TLRs ) are important regulators of the innate immune response to pathogens , including Mycobacterium leprae , which is recognized by TLR1/2 heterodimers .",
"We previously identified a transmembrane domain polymorphism , TLR1_T1805G , that encodes an isoleucine to serine substitution and is... | [
"Mycobacterium leprae ( ML ) causes a disabling and stigmatizing disease that is characterized by distinct immune responses .",
"ML produces a spectrum of illness in humans , and several lines of evidence indicate that host genetic factors influence susceptibility and clinical manifestations .",
"Leprosy can oc... | 2008 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"cell motility",
"medicine and health sciences",
"actin filaments",
"myofibrils",
"classical mechanics",
"muscle tissue",
"cardiovascular anatomy",
"mathematical models",
"muscle contraction",
"mechanical energy",
"molecular motors",
"actin motors",
"thermodynamics",
"motor proteins",
"r... | Including Thermal Fluctuations in Actomyosin Stable States Increases the Predicted Force per Motor and Macroscopic Efficiency in Muscle Modelling | journal.pcbi.1005083 | null | [
[
"Intracellular forces and motions are generated by cyclic interactions between myosin and actin filaments .",
"Myosin–actin interactions govern many important phenomena , such as molecular transport and muscle contraction .",
"In the currently accepted theory , the globular portion of myosin firmly at... | [
"Muscle contractions are generated by cyclical interactions of myosin heads with actin filaments to form the actomyosin complex .",
"To simulate actomyosin complex stable states , mathematical models usually define an energy landscape with a corresponding number of wells .",
"The jumps between these wells are d... | [
"Mathematical models are of fundamental importance in the quantitative verification of biological hypotheses .",
"Muscle contraction models assume the existence of several stable states for the myosin head , whereas the transition rates between states are defined to fit experimental data .",
"The ratio of the f... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Seizures Are Regulated by Ubiquitin-specific Peptidase 9 X-linked (USP9X), a De-Ubiquitinase | journal.pgen.1005022 | null | [
[
"Mutations in the PRICKLE genes can cause seizures in humans , zebrafish , mice , and flies , suggesting the seizure-suppression pathway is evolutionarily conserved .",
"[1–5] .",
"Prickle binding partners have been studied extensively only in either non-neuronal vertebrate cell lines or non-neuronal ... | [
"Epilepsy is a common disabling disease with complex , multifactorial genetic and environmental etiology .",
"The small fraction of epilepsies subject to Mendelian inheritance offers key insight into epilepsy disease mechanisms; and pathologies brought on by mutations in a single gene can point the way to general... | [
"Epilepsy is a common disabling disorder characterized by seizures with complex genetic and environmental components .",
"The absence of a definitive pathophysiology for epilepsy stymies the development of effective treatment strategies .",
"In a small fraction of epilepsy cases however , single gene mutations ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"genome-wide association studies",
"chemical compounds",
"quantitative trait loci",
"population genetics",
"brassica",
"nitrates",
"model organisms",
"experimental organism systems",
"genome analysis",
"population biology",
"plants",
"flowering plants",
"arabidopsis thaliana",
"research an... | Natural variation in Arabidopsis shoot branching plasticity in response to nitrate supply affects fitness | journal.pgen.1008366 | null | [
[
"Most organisms experience environmental heterogeneity .",
"For mobile organisms , adverse environments can be avoided by migration and habitat selection .",
"Immobile organisms , such as higher plants , can avoid adverse environments by early reproduction and survival as seeds , or they may mitigate ... | [
"The capacity of organisms to tune their development in response to environmental cues is pervasive in nature .",
"This phenotypic plasticity is particularly striking in plants , enabled by their modular and continuous development .",
"A good example is the activation of lateral shoot branches in Arabidopsis , ... | [
"Many organisms adjust their development depending on environmental conditions .",
"This is particularly striking in plants , with development constantly tuned throughout their lives .",
"A good example is the modulation of shoot branching in response to external environmental cues .",
"We characterised hundr... | 2019 |
[
"Introduction",
"Methods",
"Results and Discussion"
] | [] | Characterization of the Paracoccidioides Hypoxia Response Reveals New Insights into Pathogenesis Mechanisms of This Important Human Pathogenic Fungus | journal.pntd.0004282 | null | [
[
"The genus Paracoccidioides is a complex of thermodimorphic fungi , and are causative agents of paracoccidioidomycosis ( PCM ) a deep systemic granulomatous mycosis , endemic in Latin America [1 , 2] .",
"Paracoccidioides spp .",
"grows as yeast in host tissue and in vitro at 36°C , and as mycelium un... | [
"Hypoxic microenvironments are generated during fungal infection .",
"It has been described that to survive in the human host , fungi must also tolerate and overcome in vivo microenvironmental stress conditions including low oxygen tension; however nothing is known how Paracoccidioides species respond to hypoxia ... | [
"The genus Paracoccidioides is composed of species that are causative agents of paracoccidioidomycosis ( PCM ) , a neglected human granulomatous mycosis , endemic in Latin America .",
"To survive in the human host , fungi must tolerate and overcome in vivo micro environmental stress conditions , including low oxy... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"complex systems",
"mathematics",
"biophysic al simulations",
"computational neuroscience",
"applied mathematics",
"biology",
"computational biology"
] | A Canonical Model of Multistability and Scale-Invariance in Biological Systems | journal.pcbi.1002634 | null | [
[
"Biological systems are optimized to survive in environments whose properties may vary greatly , such as changes in the biochemical environment of bacteria across several orders of magnitude , or even qualitatively , such as seasonal variations that banish food sources and prohibit foraging behavior in some m... | [
"Multistability and scale-invariant fluctuations occur in a wide variety of biological organisms from bacteria to humans as well as financial , chemical and complex physical systems .",
"Multistability refers to noise driven switches between multiple weakly stable states .",
"Scale-invariant fluctuations arise ... | [
"Biological systems are able to adapt to rapidly and widely changing environments .",
"Many biological organisms employ two distinct mechanisms that improve their survival in these circumstances: Firstly they exhibit rapid , qualitative changes in their internal dynamics; secondly they possess the ability to resp... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology/breast cancer",
"developmental biology/stem cells",
"cell biology",
"molecular biology",
"genetics and genomics/cancer genetics",
"pathology/molecular pathology"
] | A Targeted Constitutive Mutation in the Apc Tumor Suppressor Gene Underlies Mammary But Not Intestinal Tumorigenesis | journal.pgen.1000547 | null | [
[
"Epithelial malignancies such as colorectal and breast cancer are thought to arise and progress towards malignancy due to alterations in signal transduction pathways that regulate the balance between self-renewal and differentiation in adult stem cell compartments [1] .",
"The canonical Wnt/β-catenin sign... | [
"Germline mutations in the adenomatous polyposis coli ( APC ) gene are responsible for familial adenomatous polyposis ( FAP ) , an autosomal dominant hereditary predisposition to the development of multiple colorectal adenomas and of a broad spectrum of extra-intestinal tumors .",
"Moreover , somatic APC mutation... | [
"Although signal transduction pathways are often described as “on–off” systems , the more quantitative aspects of signalling are likely to represent a very important means of regulation of the downstream biological outcomes .",
"Mutations in members of the canonical Wnt signaling pathway represent among the most ... | 2009 |
[
"The VSG Coat",
"The Roles of VSG N-linked Oligosaccharides",
"Non-VSG Proteins Present in the VSG Coat",
"Interactions with the Adaptive and Innate Immune System",
"Investigation of How the VSG Coat Functions",
"VSG Monoclonal Antibodies",
"VSG Single Domain Monoclonal Antibodies",
"Antibodies Recogn... | [] | How Does the VSG Coat of Bloodstream Form African Trypanosomes Interact with External Proteins? | journal.ppat.1005259 | null | [
[
"VSGs are homodimers of two 50–60 kDa subunits held on the extracellular face of the plasma membrane by a glycosylphosphatidylinositol ( GPI ) anchor .",
"VSGs have a large N-terminal domain of 350–400 residues and one or two small C-terminal domains of 20–40 residues each .",
"The domains are connect... | [
"Variations on the statement “the variant surface glycoprotein ( VSG ) coat that covers the external face of the mammalian bloodstream form of Trypanosoma brucei acts a physical barrier” appear regularly in research articles and reviews .",
"The concept of the impenetrable VSG coat is an attractive one , as it pr... | [
"African trypanosomes have evolved two key strategies to prevent killing by the host immune response and , thus , maintain a long-term infection in a mammal .",
"Both are based on a densely packed coat of a single protein , the variant surface glycoprotein ( VSG ) , which covers the entire extracellular surface o... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"test evaluation",
"schistosomiasis",
"public health and epidemiology",
"diagnostic medicine",
"epidemiology",
"neglected tropical diseases",
"epidemiological methods",
"parasitic diseases"
] | Evaluation of Circulating Cathodic Antigen (CCA) Urine-Tests for Diagnosis of Schistosoma mansoni Infection in Cameroon | journal.pntd.0001758 | null | [
[
"Schistosomiasis remains of significant public health importance worldwide , with an estimated 207 million people infected .",
"Over 90% of all schistosomiasis cases are found in sub-Saharan Africa [1] , [2] .",
"The disease is caused by six species of blood flukes: Schistosoma haematobium , S . manso... | [
"The Kato-Katz is the most common diagnostic method for Schistosoma mansoni infection .",
"However , the day-to-day variability in host egg-excretion and its low detection sensitivity are major limits for its use in low transmission zones and after widespread chemotherapy .",
"We evaluated the accuracy of circu... | [
"Recent momentum for the control of neglected tropical diseases has generated a renewed interest in the control of schistosomiasis , resulting in the increase of large scale mass drug administration of praziquantel in several countries .",
"As a consequence , there is a need to develop more sensitive diagnostic t... | 2012 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"reverse transcriptase-polymerase chain reaction",
"invertebrates",
"medicine and health sciences",
"immune physiology",
"ixodes",
"immunology",
"social sciences",
"vertebrates",
"parasitic diseases",
"animals",
"euthanasia",
"animal behavior",
"molecular biology techniques",
"ticks",
"a... | Susceptibility of spotted doves (Streptopelia chinensis) to experimental infection with the severe fever with thrombocytopenia syndrome phlebovirus | journal.pntd.0006982 | null | [
[
"Severe fever with thrombocytopenia syndrome virus ( SFTSV ) is a phlebovirus in the family Phenuiviridae and causes severe fever with thrombocytopenia syndrome ( SFTS ) , a severe hemorrhagic fever disease in East Asia [1 , 2] .",
"The disease is characterized by high fever and a drastic reduction of pla... | [
"Severe fever with thrombocytopenia syndrome virus ( SFTSV ) , an emerging human pathogen naturally transmitted by ticks , has spread widely since it was first detected in 2010 .",
"Although SFTSV-specific antibodies have been detected in wild birds , these natural reservoir and amplifying hosts for the virus hav... | [
"Severe fever with thrombocytopenia syndrome virus ( SFTSV ) is an emerging human pathogen naturally transmitted by ticks .",
"Our recent study has showed that some species of migratory birds , such as swan geese and spotted doves , can be parasitized by Haemaphysalis longicornis , an SFTSV vector , and antibodie... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | The Role of ATM in the Deficiency in Nonhomologous End-Joining near Telomeres in a Human Cancer Cell Line | journal.pgen.1003386 | null | [
[
"The repair of DNA double-strand breaks ( DSBs ) is vital for preventing gross chromosome rearrangements ( GCRs ) leading to cell death or cancer [1] .",
"There are multiple mechanisms for DSB repair , including classical nonhomologous end joining ( C-NHEJ ) [1] , homologous recombination repair ( HRR ) [... | [
"Telomeres distinguish chromosome ends from double-strand breaks ( DSBs ) and prevent chromosome fusion .",
"However , telomeres can also interfere with DNA repair , as shown by a deficiency in nonhomologous end joining ( NHEJ ) and an increase in large deletions at telomeric DSBs .",
"The sensitivity of telome... | [
"The ends of chromosomes , called telomeres , prevent chromosome ends from appearing as DNA double-strand breaks ( DSBs ) and prevent chromosome fusion by forming a specialized nucleo-protein complex .",
"The critical function of telomeres in end protection has a downside , in that it interferes with the repair o... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"cell biology",
"genetics and genomics"
] | The Inhibition of Polo Kinase by Matrimony Maintains G2 Arrest in the Meiotic Cell Cycle | journal.pbio.0050323 | The restart of the meiotic cycle in Drosophila depends on both the controlled expression of Polo kinase and a protein called Matrimony (Mtrm), which binds to and physically inactivates Polo. | [
[
"The mechanism of the lengthy arrest in G2 that separates the end of pachytene from nuclear envelope breakdown ( NEB ) —which is a characterization of many female meiotic systems—has remained a mystery .",
"One can imagine that both the maintenance and the termination of this arrest might involve either o... | [
"Many meiotic systems in female animals include a lengthy arrest in G2 that separates the end of pachytene from nuclear envelope breakdown ( NEB ) .",
"However , the mechanisms by which a meiotic cell can arrest for long periods of time ( decades in human females ) have remained a mystery .",
"The Drosophila Ma... | [
"Many meiotic systems in females animals include a lengthy arrest period ( spanning days in flies and to decades in humans ) that separates the early and late stages of meiosis .",
"Such an arrest raises the question: how can the quiescent meiotic cell cycle be precisely awakened or re-started ?",
"At least in ... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"functional genomics",
"rna interference",
"gene function",
"developmental biology",
"molecular development",
"proteins",
"gene expression",
"structural proteins",
"biology",
"extracellular matrix proteins",
"morphogens",
"biochemistry",
"genetics",
"genomics",
"genetics and genomics",
... | Formation of Rigid, Non-Flight Forewings (Elytra) of a Beetle Requires Two Major Cuticular Proteins | journal.pgen.1002682 | null | [
[
"How arthropods manufacture exoskeletons with a wide array of mechanical properties , ranging from hard and rigid to soft and flexible , is an important question in developmental biology .",
"The insect exoskeleton , or cuticle , covers the entire body wall and attached appendages as well as the foregut ,... | [
"Insect cuticle is composed primarily of chitin and structural proteins .",
"To study the function of structural cuticular proteins , we focused on the proteins present in elytra ( modified forewings that become highly sclerotized and pigmented covers for the hindwings ) of the red flour beetle , Tribolium castan... | [
"Primitive insects have two pairs of membranous flight wings , but during the evolution of the beetle lineage the forewings lost their flight function and became modified as hard , rigid covers called elytra for protection of soft body parts of the abdomen and also the delicate flexible hindwings , which retained t... | 2012 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"typhus",
"medicine and health sciences",
"leptospira",
"pathology and laboratory medicine",
"pathogens",
"tropical diseases",
"microbiology",
"organisms",
"bacterial diseases",
"neglected tropical diseases",
"molecular biology techniques",
"murine typhus",
"bacteria",
"bacterial pathogens... | Development of multiplex PCR for neglected infectious diseases | journal.pntd.0007440 | null | [
[
"Scrub typhus , murine typhus , and leptospirosis are widely neglected infectious diseases , especially in the tropical and temperate climate regions , caused by Orientia tsutsugamushi , Rickettsia typhi , and pathogenic Leptospira spp .",
", respectively .",
"Orientia and Rickettsia are obligate intr... | [
"Scrub typhus , murine typhus , and leptospirosis are widely neglected infectious diseases caused by Orientia tsutsugamushi , Rickettsia typhi , and pathogenic Leptospira spp .",
", respectively .",
"Patients usually present with non-specific symptoms and therefore are commonly diagnosed with acute undifferenti... | [
"Scrub typhus , murine typhus , and leptospirosis are diagnosed as acute undifferentiated febrile illness .",
"Diagnostic tests for these diseases depend on antibody detection .",
"However , antibody detection is still limited by its tendency to return negative results during the early phase of aforementioned d... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"urinary system procedures",
"medicine and health sciences",
"organ transplantation",
"immune cells",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"cytomegalovirus infection",
"cloning",
"surgical and invasive medical procedures",
"viruses",
... | HCMV triggers frequent and persistent UL40-specific unconventional HLA-E-restricted CD8 T-cell responses with potential autologous and allogeneic peptide recognition | journal.ppat.1007041 | null | [
[
"Human cytomegalovirus ( HCMV; human herpesvirus 5 ) is the prototype member of β-herpesvirus and a widespread opportunistic pathogen .",
"In healthy individuals , primary infection is asymptomatic and is followed by a life-long , persistent , infection that is controlled by host immune system [1] .",
... | [
"Immune response against human cytomegalovirus ( HCMV ) includes a set of persistent cytotoxic NK and CD8 T cells devoted to eliminate infected cells and to prevent reactivation .",
"CD8 T cells against HCMV antigens ( pp65 , IE1 ) presented by HLA class-I molecules are well characterized and they associate with ... | [
"Understanding the mechanisms of immune control of viral infection is crucial to improve diagnosis and to design efficient immunotherapies .",
"CD8 T lymphocytes are key components of the cellular immunity against human cytomegalovirus ( HCMV ) , a widespread pathogen that cause severe illness and poor outcome in... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"organismal evolution",
"medicine and health sciences",
"pathology and laboratory medicine",
"viral transmission and infection",
"pathogens",
"geographical locations",
"microbiology",
"uganda",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"rna viruses",
"microbial evolution",
"vi... | Evolution of HIV-1 within untreated individuals and at the population scale in Uganda | journal.ppat.1007167 | null | [
[
"Infection by HIV-1 is lifelong , and characterized by ongoing viral replication , and consequently the virus can undergo hundreds of rounds of replication between transmission events .",
"This , combined with error-prone viral replication during reverse transcription , means that the viruses an individua... | [
"HIV-1 undergoes multiple rounds of error-prone replication between transmission events , resulting in diverse viral populations within and among individuals .",
"In addition , the virus experiences different selective pressures at multiple levels: during the course of infection , at transmission , and among indi... | [
"The speed at which HIV-1 evolves within individuals and across epidemics is substantially different .",
"Identifying the mechanisms shaping this phenomenon has important implications for understanding disease severity and transmission of HIV-1 , especially when considering the spread of viruses that are resistan... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"condensation",
"face",
"bmp signaling",
"condensed matter physics",
"vertebrates",
"animals",
"notch signaling",
"animal models",
"osteichthyes",
"immune receptor signaling",
"developmental biology",
"model organisms",
"membrane receptor signaling",
"embr... | Competition between Jagged-Notch and Endothelin1 Signaling Selectively Restricts Cartilage Formation in the Zebrafish Upper Face | journal.pgen.1005967 | null | [
[
"Morphogenesis of the facial skeleton in zebrafish is tightly linked with the early differentiation of pharyngeal arch neural crest-derived cells ( NCCs ) into cartilage .",
"Shortly after migration into the pharyngeal arches , NCCs form a series of pre-cartilage condensations that prefigure the distinct ... | [
"The intricate shaping of the facial skeleton is essential for function of the vertebrate jaw and middle ear .",
"While much has been learned about the signaling pathways and transcription factors that control facial patterning , the downstream cellular mechanisms dictating skeletal shapes have remained unclear .... | [
"The exquisite functions of the vertebrate face require the precise formation of its underlying bones .",
"Remarkably , many of the genes required to shape the facial skeleton are the same from fish to man .",
"In this study , we use the powerful zebrafish system to understand how the skeletal components of the... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"circuit models",
"neural networks",
"computational neuroscience",
"psychophysics",
"sensory systems",
"biology",
"computational biology",
"sensory perception",
"neuroscience",
"learning and memory",
"coding mechanisms"
] | Learning Multisensory Integration and Coordinate Transformation via Density Estimation | journal.pcbi.1003035 | null | [
[
"The brain often receives information about the same feature of the same object from multiple sources; e . g . , in a visually guided reach , both vision and proprioception provide information about hand location .",
"Were both signals infinitely precise , one could simply be ignored; but fidelity is limi... | [
"Sensory processing in the brain includes three key operations: multisensory integration—the task of combining cues into a single estimate of a common underlying stimulus; coordinate transformations—the change of reference frame for a stimulus ( e . g . , retinotopic to body-centered ) effected through knowledge ab... | [
"Over the first few years of their lives , humans ( and other animals ) appear to learn how to combine signals from multiple sense modalities: when to “integrate” them into a single percept , as with visual and proprioceptive information about one's body; when not to integrate them ( e . g . , when looking somewher... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | cAMP-Signalling Regulates Gametocyte-Infected Erythrocyte Deformability Required for Malaria Parasite Transmission | journal.ppat.1004815 | null | [
[
"Recent renewed emphasis on the eradication of malaria has highlighted the need for novel interventions to target the parasite during transmission from the human host to the mosquito .",
"Drug treatments to clear asexual blood stage parasites ( that cause pathology ) do not kill mature gametocytes and the... | [
"Blocking Plasmodium falciparum transmission to mosquitoes has been designated a strategic objective in the global agenda of malaria elimination .",
"Transmission is ensured by gametocyte-infected erythrocytes ( GIE ) that sequester in the bone marrow and at maturation are released into peripheral blood from wher... | [
"Malaria transmission is ensured by deformable mature gametocyte-infected erythrocytes being taken up when a mosquito bites .",
"Non-deformable immature gametocyte stages are sequestered in the bone marrow , as their lack of deformability would lead to their splenic clearance .",
"In the present study , we appl... | 2015 |
[
"Introduction",
"Methods",
"Results and Discussion"
] | [
"infectious diseases/bacterial infections",
"infectious diseases/neglected tropical diseases",
"infectious diseases/tropical and travel-associated diseases",
"infectious diseases/skin infections"
] | A Tractable Experimental Model for Study of Human and Animal Scabies | journal.pntd.0000756 | null | [
[
"Scabies , or sarcoptic mange , is an infectious skin disease caused by the mite Sarcoptes scabiei .",
"Human scabies is a widespread disease in developing regions of the world , and remains a significant problem amongst indigenous populations in developed countries [1] .",
"Secondary bacterial infect... | [
"Scabies is a parasitic skin infestation caused by the burrowing mite Sarcoptes scabiei .",
"It is common worldwide and spreads rapidly under crowded conditions , such as those found in socially disadvantaged communities of Indigenous populations and in developing countries .",
"Pruritic scabies lesions facilit... | [
"Scabies , a neglected parasitic disease caused by the microscopic mite Sarcoptes scabiei , is a major driving force behind bacterial skin infections in tropical settings .",
"Aboriginal and Torres Strait Islander peoples are nearly twenty times more likely to die from acute rheumatic fever and rheumatic heart di... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Molecular Diversity of Trypanosoma cruzi Detected in the Vector Triatoma protracta from California, USA | journal.pntd.0004291 | null | [
[
"Trypanosoma cruzi is a protozoan parasite that , in both humans and dogs , may cause an insidious onset of fatal cardiac disease[1] .",
"Known as Chagas disease , T . cruzi is the most economically important parasitic infection in Latin America , where an estimated 8–9 million people are living with the ... | [
"Trypanosoma cruzi , causative agent of Chagas disease in humans and dogs , is a vector-borne zoonotic protozoan parasite that can cause fatal cardiac disease .",
"While recognized as the most economically important parasitic infection in Latin America , the incidence of Chagas disease in the United States of Ame... | [
"Trypanosoma cruzi is a protozoan parasite that causes Chagas disease in humans and dogs and may eventually lead to mortalities related to cardiac failure .",
"This parasite is most frequently transmitted by triatomine bug vectors , commonly called “kissing bugs . ”",
"Although Chagas disease is predominately a... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"macromolecular complex analysis",
"systems biology",
"biochemistry",
"physics",
"proteomic databases",
"protein interactions",
"proteins",
"protein structure",
"macromolecular assemblies",
"biology",
"computational biology",
"proteomics",
"biophysics",
"macromolecular structure analysis"
... | Interface-Resolved Network of Protein-Protein Interactions | journal.pcbi.1003065 | null | [
[
"Protein-protein interaction ( PPI ) networks aim to capture the interactions between proteins that mediate many of their molecular functions [1]–[3] .",
"However , with one node per protein and one edge per binary interaction , PPIs provide only a coarse rendering of the nuanced molecular level interacti... | [
"We define an interface-interaction network ( IIN ) to capture the specificity and competition between protein-protein interactions ( PPI ) .",
"This new type of network represents interactions between individual interfaces used in functional protein binding and thereby contains the detail necessary to describe t... | [
"Much of the work inside the cell is carried out by proteins interacting with other proteins .",
"Each edge in a protein-protein interaction network reflects these functional interactions and each node a separate protein , creating a complex structure that nevertheless follows well-established global and local pa... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"genome-wide association studies",
"plant growth and development",
"brassica",
"plant physiology",
"developmental biology",
"plant science",
"model organisms",
"experimental organism systems",
"genome analysis",
"seedlings",
"plants",
"arabidopsis thaliana",
"research and analysis methods",
... | Natural allelic variation of the AZI1 gene controls root growth under zinc-limiting condition | journal.pgen.1007304 | null | [
[
"Zinc ( Zn ) is an essential micronutrient for humans , animals , and plants [1] .",
"It is of particular importance for the function of numerous metalloenzymes that are involved in a plethora of processes such as energy metabolism , nucleic acid and protein synthesis , and protein catabolism [2] .",
... | [
"Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development , and immunity .",
"However , it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function .",
"Here we used natural variation in... | [
"Plants have evolved mechanisms to cope with complex environments in which resources as well as potential threats are fluctuating .",
"Thereby , plants modulate their growth based on multiple cues from the environment .",
"In this study , by exploring natural genetic variation in Arabidopsis to study the role o... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics and genomics/disease models",
"genetics and genomics/genetics of disease",
"microbiology/medical microbiology",
"infectious diseases/bacterial infections"
] | Highly Frequent Mutations in Negative Regulators of Multiple Virulence Genes in Group A Streptococcal Toxic Shock Syndrome Isolates | journal.ppat.1000832 | null | [
[
"Streptococcus pyogenes ( group A Streptococcus; GAS ) is one of the most common human pathogens .",
"It causes a wide variety of infections , ranging from uncomplicated pharyngitis and skin infections to severe and even life-threatening manifestations , such as necrotizing fasciitis ( NF ) and bacteremia... | [
"Streptococcal toxic shock syndrome ( STSS ) is a severe invasive infection characterized by the sudden onset of shock and multiorgan failure; it has a high mortality rate .",
"Although a number of studies have attempted to determine the crucial factors behind the onset of STSS , the responsible genes in group A ... | [
"Group A streptococcus ( GAS ) causes life-threatening severe invasive diseases , including necrotizing fasciitis and streptococcal toxic shock-like syndrome .",
"Although many studies have attempted to determine factors that are crucial for the onset of streptococcal toxic shock syndrome ( STSS ) , bacterial fac... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"breast tumors",
"cancer risk factors",
"cancers and neoplasms",
"protein abundance",
"oncology",
"epigenetics",
"dna",
"medical risk factors",
"dna methylation",
"chromatin",
"research and analysis methods",
"chromosome biology",
"epidemiology",
"gene exp... | The impact of DNA methylation on the cancer proteome | journal.pcbi.1007245 | null | [
[
"Genomic characterization can elucidate underlying biology , disease etiology and reveal biomarkers of cancer development and progression; however , each molecular feature is susceptible to different sources of biological and technical measurement noise and provides only one view on the cell state .",
"Th... | [
"Aberrant DNA methylation disrupts normal gene expression in cancer and broadly contributes to oncogenesis .",
"We previously developed MethylMix , a model-based algorithmic approach to identify epigenetically regulated driver genes .",
"MethylMix identifies genes where methylation likely executes a functional ... | [
"To elucidate the molecular basis of cancer we examine the variation and dynamics characterizing the flow of information from epigenome to the transcriptome and proteome .",
"Conducting the first genome wide analysis of epigenome-proteome associations , we present a MethylMix analysis that leverages protein abund... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology and life sciences"
] | Arabidopsis RRP6L1 and RRP6L2 Function in FLOWERING LOCUS C Silencing via Regulation of Antisense RNA Synthesis | journal.pgen.1004612 | null | [
[
"The regulation of gene silencing occurs at multiple levels and non-coding RNAs ( ncRNAs ) have emerged as important regulators of genome silencing at the transcriptional and posttranscriptional levels [1] .",
"At the chromatin structure level , chromatin remodeling factors and DNA- and histone-modifying ... | [
"The exosome complex functions in RNA metabolism and transcriptional gene silencing .",
"Here , we report that mutations of two Arabidopsis genes encoding nuclear exosome components AtRRP6L1 and AtRRP6L2 , cause de-repression of the main flowering repressor FLOWERING LOCUS C ( FLC ) and thus delay flowering in ea... | [
"Arabidopsis FLOWERING LOCUS C ( FLC ) delays flowering; therefore , repressing expression of FLC provides a critical mechanism to regulate flowering .",
"This mechanism involves multiple levels of regulation , including genetic regulation by transcription factors , and epigenetic regulation by modifications of g... | 2014 |
[
"Introduction",
"Model",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"infectious disease epidemiology",
"applied mathematics",
"immunology",
"sociology",
"social sciences",
"vaccines",
"preventive medicine",
"social epidemiology",
"probability distribution",
"mathematics",
"network analysis",
"social networks",
"infectious di... | Epidemic prevalence information on social networks can mediate emergent collective outcomes in voluntary vaccine schemes | journal.pcbi.1006977 | null | [
[
"Immunization through the vaccination of populations has been estimated to annually prevent 2-3 million deaths from infectious diseases such as measles , diphtheria , pertussis and tetanus [1] .",
"This number may rise substantially with the development of strategies to further increase global vaccine cov... | [
"The effectiveness of a mass vaccination program can engender its own undoing if individuals choose to not get vaccinated believing that they are already protected by herd immunity .",
"This would appear to be the optimal decision for an individual , based on a strategic appraisal of her costs and benefits , even... | [
"A major factor underlying the success of voluntary vaccination schemes is the public perception about the costs and benefits associated with vaccines .",
"Individuals may avoid vaccination if they perceive the risk of infection to be low compared to the potential hazards and inconveniences associated with gettin... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biochemistry",
"infectious diseases",
"biology",
"microbiology",
"molecular cell biology"
] | A Novel Human Cytomegalovirus Locus Modulates Cell Type-Specific Outcomes of Infection | journal.ppat.1002444 | null | [
[
"Human cytomegalovirus ( HCMV ) is a member of the β-herpesvirus subfamily that , like all herpesviruses , persists indefinitely in infected individuals through a latent infection .",
"HCMV persistence is associated with an increased risk of age-related pathologies including atherosclerosis [1] , [2] , im... | [
"Clinical strains of HCMV encode 20 putative ORFs within a region of the genome termed ULb′ that are postulated to encode functions related to persistence or immune evasion .",
"We have previously identified ULb′-encoded pUL138 as necessary , but not sufficient , for HCMV latency in CD34+ hematopoietic progenitor... | [
"Human cytomegalovirus is a ubiquitous herpesvirus that , like all herpesviruses , establishes a life long relationship with its host through a latent infection .",
"The molecular basis of viral latency is poorly understood , in part , because viral determinants of latency and the corresponding virus-host interac... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"test evaluation",
"schistosomiasis",
"research monitoring",
"diagnostic medicine",
"science policy",
"neglected tropical diseases",
"government laboratories",
"parasitic diseases",
"research assessment",
"research laboratories"
] | Tools to Support Policy Decisions Related to Treatment Strategies and Surveillance of Schistosomiasis Japonica towards Elimination | journal.pntd.0001408 | null | [
[
"Following great efforts by the Chinese government and professionals in public health , the People's Republic of China ( P . R . China ) has became one of the most successful countries in the world for schistosomiasis control [1]–[3] .",
"Transmission had been interrupted in five provinces , Guangdong , G... | [
"Appropriate diagnostics to monitor disease trends and assess the effectiveness and impact of interventions are essential for guiding treatment strategies at different thresholds of schistosomiasis transmission and for certifying elimination .",
"Field validation of these assays is urgently needed before they can... | [
"Immunodiagnostic assays are widely applied in the field to control schistosomiasis in P . R . China as the prevalence and infection intensity of schistosome infections decrease .",
"Field evaluations are urgently needed before they can be adopted to support policy decisions of the national programme for the cont... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Turning Escherichia coli into a Frataxin-Dependent Organism | journal.pgen.1005134 | null | [
[
"Fe-S bound proteins are ubiquitous and involved in a wide variety of cellular processes such as respiration , regulation of gene expression and central metabolism [1 , 2] .",
"Maturation of Fe-S proteins is an essential cellular process for both eukaryotic and prokaryotic organisms .",
"The mitochond... | [
"Fe-S bound proteins are ubiquitous and contribute to most basic cellular processes .",
"A defect in the ISC components catalyzing Fe-S cluster biogenesis leads to drastic phenotypes in both eukaryotes and prokaryotes .",
"In this context , the Frataxin protein ( FXN ) stands out as an exception .",
"In eukar... | [
"Iron sulfur ( Fe-S ) clusters are ubiquitous cofactors found in proteins which function in very diverse pathways ranging from respiration to DNA repair .",
"The mitochondrial Fe-S biogenesis machinery ISC was inherited from the bacterial ancestor of mitochondria .",
"In both prokaryotes and eukaryotes , defici... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases",
"immunology"
] | A Signaling Protease Required for Melanization in Drosophila Affects Resistance and Tolerance of Infections | journal.pbio.0060305 | It isn't easy to predict how mutations will affect a host's immune response. Mutations that affect the interaction of a fly with one pathogen can increase or decrease resistance or tolerance to other pathogens. | [
[
"Evolutionary theory suggests that a host can protect itself against an infectious pathological threat by evolving two different mechanisms to increase fitness or health .",
"The first is to reduce the fitness of the pathogen , thereby reducing the number of pathogens attacking the host .",
"The secon... | [
"Organisms evolve two routes to surviving infections—they can resist pathogen growth ( resistance ) and they can endure the pathogenesis of infection ( tolerance ) .",
"The sum of these two properties together defines the defensive capabilities of the host .",
"Typically , studies of animal defenses focus on ei... | [
"To boost its defenses , an organism may increase its resistance to infection by reducing the fitness of the invading pathogen; alternatively , the host may increase its tolerance by reducing the damage caused by a given quantity of pathogen .",
"Melanization is an immune response that has been linked to defense ... | 2008 |
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