headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | A New Algorithm to Diagnose Atrial Ectopic Origin from Multi Lead ECG Systems - Insights from 3D Virtual Human Atria and Torso | journal.pcbi.1004026 | null | [
[
"Rapid atrial arrhythmias such as atrial tachycardia ( AT ) and atrial fibrillation ( AF ) can reduce cardiac output and predispose to ventricular arrhythmias and further complications , such as stroke and even sudden cardiac death [1–3] .",
"Both AT and AF are associated with ectopic activity—rapid and i... | [
"Rapid atrial arrhythmias such as atrial fibrillation ( AF ) predispose to ventricular arrhythmias , sudden cardiac death and stroke .",
"Identifying the origin of atrial ectopic activity from the electrocardiogram ( ECG ) can help to diagnose the early onset of AF in a cost-effective manner .",
"The complex an... | [
"Ectopic activity is associated with multiple cardiac disorders and has been implicated in the initiation of self-sustaining re-entrant excitation .",
"Identifying the presence and origin of ectopic activity may be vital in improving diagnosis and treatment of disorders such as atrial fibrillation , and has been ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"chromosome structure and function",
"cell cycle and cell division",
"immunology",
"cell processes",
"precursor cells",
"cloning",
"cell differentiation",
"telomeres",
"developmental biology",
"cytotoxic t cells",
"molecular bi... | Human TSCM cell dynamics in vivo are compatible with long-lived immunological memory and stemness | journal.pbio.2005523 | null | [
[
"The maintenance of long-lived T cell memory is one of the hallmarks of adaptive immunity [1 , 2] .",
"Multiple studies have shown that the recall response to a previously encountered antigen has a half-life of the order of decades [3 , 4] .",
"It has been hypothesised that this T cell memory is dynam... | [
"Adaptive immunity relies on the generation and maintenance of memory T cells to provide protection against repeated antigen exposure .",
"It has been hypothesised that a self-renewing population of T cells , named stem cell–like memory T ( TSCM ) cells , are responsible for maintaining memory .",
"However , it... | [
"The human immune system remembers previously encountered pathogens so that , on meeting the same pathogen a second time , the response is quicker and more effective .",
"This immune memory is the basis of all vaccinations .",
"Immune memory persists for decades , but how memory is maintained is unclear .",
"... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Genome-Wide Association Studies in Dogs and Humans Identify ADAMTS20 as a Risk Variant for Cleft Lip and Palate | journal.pgen.1005059 | null | [
[
"Nonsyndromic orofacial clefts , notably cleft lip ( CL ) with or without cleft palate ( CL/P ) and isolated cleft palate ( CP ) , are the most common craniofacial birth defects in humans and represent a substantial personal and societal burden .",
"Clefts affect approximately 1 in 700 individuals[1] , wi... | [
"Cleft lip with or without cleft palate ( CL/P ) is the most commonly occurring craniofacial birth defect .",
"We provide insight into the genetic etiology of this birth defect by performing genome-wide association studies in two species: dogs and humans .",
"In the dog , a genome-wide association study of 7 CL... | [
"Cleft lip with or without cleft palate ( CL/P ) is a commonly occurring birth defect that can lead to a lifetime of complications in affected children .",
"To better understand the genetic cause of these disorders , we investigated CL/P in both dogs and humans .",
"Genome-wide association studies in both speci... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"cost-effectiveness analysis",
"clinical research design",
"engineering and technology",
"transportation",
"economic analysis",
"geographical locations",
"tropical diseases",
"social sciences",
"parasitic diseases",
"pediatrics",
"research design",
"pharmaceut... | Cost-effectiveness of meglumine antimoniate versus miltefosine caregiver DOT for the treatment of pediatric cutaneous leishmaniasis | journal.pntd.0005459 | null | [
[
"Cutaneous leishmaniasis ( CL ) is a neglected tropical disease primarily affecting poor , marginalized populations .",
"Worldwide incidence of CL has been estimated at 1–5 million cases per year [1 , 2] .",
"In Latin America , over 57 , 000 annual cases were reported on average between 2001 and 2013 ... | [
"Oral miltefosine has been shown to be non-inferior to first-line , injectable meglumine antimoniate ( MA ) for the treatment of cutaneous leishmaniasis ( CL ) in children .",
"Miltefosine may be administered via in-home caregiver Directly Observed Therapy ( cDOT ) , while patients must travel to clinics to recei... | [
"Cutaneous leishmaniasis ( CL ) is a tropical parasitic disease transmitted by sand flies that causes chronic skin and mucosal ulcers .",
"Current standard of care therapy requires patients to travel to a clinic for twenty consecutive days for injections of meglumine antimoniate ( MA ) .",
"This may represent a... | 2017 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"mathematics",
"gene expression",
"genetics",
"statistics",
"molecular genetics",
"biology",
"human genetics",
"genetics and genomics"
] | Statistical Analysis of Readthrough Levels for Nonsense Mutations in Mammalian Cells Reveals a Major Determinant of Response to Gentamicin | journal.pgen.1002608 | null | [
[
"Translation is terminated by a stop codon entering the A site of the ribosome , inducing the release of the polypeptide chain from the peptidyl-t-RNA [1] .",
"Two polypeptide chain release factors have been identified in eukaryotes: eRF1 ( eukaryotic Release Factor one ) , which recognizes all three nons... | [
"The efficiency of translation termination depends on the nature of the stop codon and the surrounding nucleotides .",
"Some molecules , such as aminoglycoside antibiotics ( gentamicin ) , decrease termination efficiency and are currently being evaluated for diseases caused by premature termination codons .",
"... | [
"Nonsense mutations are single-nucleotide variations within the coding sequence of a gene that result in a premature termination codon .",
"The presence of such mutations leads to the synthesis of a truncated protein unable to fulfill its normal function .",
"Over the last ten years , treatment strategies have ... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"chromosome biology",
"gene expression",
"genetics",
"epigenetics",
"biology",
"genomics",
"chromatin",
"genetics and genomics",
"histone modification"
] | A Key Role for Chd1 in Histone H3 Dynamics at the 3′ Ends of Long Genes in Yeast | journal.pgen.1002811 | null | [
[
"Eukaryotic genomes are packaged as chromatin , whose fundamental repeating subunit , the nucleosome , is composed of 147 bp of DNA wrapped 1 . 7 times around an octameric histone core .",
"Nucleosomes may interact with each other to form higher-order levels of chromatin packaging necessary to compact an ... | [
"Chd proteins are ATP–dependent chromatin remodeling enzymes implicated in biological functions from transcriptional elongation to control of pluripotency .",
"Previous studies of the Chd1 subclass of these proteins have implicated them in diverse roles in gene expression including functions during initiation , e... | [
"Nucleosomes prevent transcription by interfering with transcription factor binding at the beginning of genes and blocking elongating RNA polymerase II across the bodies of genes .",
"To overcome this repression , regulatory proteins move , remove , or structurally alter nucleosomes , allowing the transcription m... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"animal models of infection",
"viral persistence and latency",
"virology",
"biology and life sciences",
"microbiology",
"viral replication"
] | The Murine Gammaherpesvirus Immediate-Early Rta Synergizes with IRF4, Targeting Expression of the Viral M1 Superantigen to Plasma Cells | journal.ppat.1004302 | null | [
[
"MHV68 is a naturally occurring murid gammaherpesvirus that has significant genetic and functional homology to the human gammaherpesviruses Epstein-Barr virus ( EBV ) and Kaposi's sarcoma-associated herpesvirus ( KSHV ) .",
"Among herpesviruses , there are a large number of genes involved in virus replica... | [
"MHV68 is a murine gammaherpesvirus that infects laboratory mice and thus provides a tractable small animal model for characterizing critical aspects of gammaherpesvirus pathogenesis .",
"Having evolved with their natural host , herpesviruses encode numerous gene products that are involved in modulating host immu... | [
"Through coevolution with their hosts , gammaherpesviruses have acquired unique genes that aid in infection of a particular host .",
"Here we study the regulation of the MHV68 M1 gene , which encodes a protein that modulates the host immune response .",
"Using a strategy that allowed us to identify MHV68 infect... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Mitochondrial Activity and Cyr1 Are Key Regulators of Ras1 Activation of C. albicans Virulence Pathways | journal.ppat.1005133 | null | [
[
"Candida albicans , one of the most common human fungal pathogens , is an important cause of morbidity and mortality in immunocompromised individuals , particularly in patients with AIDS or those undergoing cancer chemotherapy or transplantation procedures [1] .",
"The prolonged use of antifungal agents i... | [
"Candida albicans is both a major fungal pathogen and a member of the commensal human microflora .",
"The morphological switch from yeast to hyphal growth is associated with disease and many environmental factors are known to influence the yeast-to-hyphae switch .",
"The Ras1-Cyr1-PKA pathway is a major regulat... | [
"Candida albicans is a successful fungal commensal and pathogen of humans .",
"It is a polymorphic organism and the ability to switch from yeast to hyphal growth is associated with the commensal-to-pathogen switch .",
"Previous research identified the Ras1-cAMP-protein kinase A pathway as a key regulator of hyp... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [] | Overexpression of Cytoplasmic TcSIR2RP1 and Mitochondrial TcSIR2RP3 Impacts on Trypanosoma cruzi Growth and Cell Invasion | journal.pntd.0003725 | null | [
[
"Acetylation is a ubiquitous protein modification present in prokaryotic and eukaryotic cells that participates in the regulation of many cellular processes .",
"A limited set of acetyltransferases and deacetylases , and of the acetyl-lysine “reading” domain ( bromodomain ) are the principal components of... | [
"Trypanosoma cruzi is a protozoan pathogen responsible for Chagas disease .",
"Current therapies are inadequate because of their severe host toxicity and numerous side effects .",
"The identification of new biotargets is essential for the development of more efficient therapeutic alternatives .",
"Inhibition ... | [
"Sirtuins are a family of deacetylases , evolutionary conserved from bacteria to mammals .",
"They participate in the regulation of a wide range of nuclear , cytoplasmic and mitochondrial pathways , and are considered pro-life enzymes .",
"In the last years the search for sirtuin inhibitors was a very active fi... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell motility",
"actin filaments",
"spring",
"seasons",
"integrins",
"cellular structures and organelles",
"cytoskeleton",
"dynamic actin filaments",
"contractile proteins",
"actins",
"physical properties",
"cell adhesion",
"proteins",
"extracellular matrix",
"cell membranes",
"physic... | Multiscale model of integrin adhesion assembly | journal.pcbi.1007077 | null | [
[
"As the linker between cytoskeletal adhesion proteins and extracellular matrix ligands , integrins play a vital role in the formation of adhesions and profoundly influence different phases of cell physiology , such as spreading , differentiation , changes in shape , migration and stiffness sensing [1–5] .",
... | [
"The ability of adherent cells to form adhesions is critical to numerous phases of their physiology .",
"The assembly of adhesions is mediated by several types of integrins .",
"These integrins differ in physical properties , including rate of diffusion on the plasma membrane , rapidity of changing conformation... | [
"Integrin-mediated cell adhesions to the extracellular environment contribute to various cell activities and provide cells with vital environmental cues .",
"Cell adhesions are complex structures that emerge from a number of molecular and macromolecular interactions between integrins and cytoplasmic proteins , be... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genomics",
"cell biology",
"chromosome biology",
"genome evolution",
"genetics",
"biology and life sciences",
"population genetics",
"epigenetics",
"computational biology",
"evolutionary biology",
"chromatin"
] | Nucleosomes Shape DNA Polymorphism and Divergence | journal.pgen.1004457 | null | [
[
"Sequence-dependent differences in the physical properties of DNA influence its associations with the histone core , as well as the kinetics of nucleosome assembly and stability [2]–[9] .",
"One of the most generalizable sequence affinities of the histone octamer is the periodic variation of dinucleotide ... | [
"An estimated 80% of genomic DNA in eukaryotes is packaged as nucleosomes , which , together with the remaining interstitial linker regions , generate higher order chromatin structures [1] .",
"Nucleosome sequences isolated from diverse organisms exhibit ∼10 bp periodic variations in AA , TT and GC dinucleotide f... | [
"In eukaryotic cells , the majority of DNA is packaged in nucleosomes comprised of ∼147 bp of DNA wound tightly around the highly conserved histone octamer .",
"Nucleosomal DNA from diverse organisms shows an anti-correlated ∼10 bp periodicity of AT-rich and GC-rich dinucleotides .",
"These sequence features in... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"parasite groups",
"medicine and health sciences",
"oocysts",
"viral transmission and infection",
"microbiology",
"cryptosporidium",
"parasitic diseases",
"parasitic protozoans",
"parasitology",
"animal models",
"apicomplexa",
"model organisms",
"protozoans",
"pharmaceutics",
"experiment... | A high-throughput phenotypic screen identifies clofazimine as a potential treatment for cryptosporidiosis | journal.pntd.0005373 | null | [
[
"Cryptosporidium species are apicomplexan protozoans that are important causes of diarrhea in humans and some domestic animals .",
"The parasite relies on an oral-fecal route of transmission , and ingestion of water or food contaminated with Cryptosporidium oocysts may lead to infection .",
"Upon inge... | [
"Cryptosporidiosis has emerged as a leading cause of non-viral diarrhea in children under five years of age in the developing world , yet the current standard of care to treat Cryptosporidium infections , nitazoxanide , demonstrates limited and immune-dependent efficacy .",
"Given the lack of treatments with univ... | [
"Diarrheal diseases cause significant morbidity and mortality in the developing world .",
"A recent multi-site study investigating diarrheal disease identified Cryptosporidium as one of the leading causes , responsible for upwards of 25% of cases in some regions .",
"Currently approved therapy for cryptosporidi... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"plasmid construction",
"organisms",
"fungi",
"sporotrichosis",
"dna construction",
"molecular biology techniques",
"fungal diseases",
"sporothrix schenckii",
"fungal pathogens",
"extraction t... | Fast diagnosis of sporotrichosis caused by Sporothrix globosa, Sporothrix schenckii, and Sporothrix brasiliensis based on multiplex real-time PCR | journal.pntd.0007219 | null | [
[
"Sporotrichosis is a subacute or chronic infectious disease caused by dimorphic fungi of Sporothrix spp .",
", which are distributed worldwide , especially in tropical and subtropical regions[1–2] .",
"The infection generally occurs through traumatic inoculation of contaminated plant debris[3–4] or th... | [
"The accurate diagnosis of sporotrichosis and identification at the species level are critical for public health and appropriate patient management .",
"Compared with morphological identification methods , molecular diagnostic tests are rapid and have high sensitivity and standardized operating processes .",
"T... | [
"Sporotrichosis is a subacute or chronic infectious disease caused by dimorphic fungi of Sporothrix spp .",
"The genus Sporothrix consists of several species with different geographic distributions , virulence , and antifungal susceptibilities , making species-level identification necessary .",
"S . brasiliensi... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cellular structures",
"subcellular organelles",
"gene function",
"animal models",
"developmental biology",
"caenorhabditis elegans",
"model organisms",
"molecular genetics",
"morphogenesis",
"biology",
"calcium signaling cascade",
"cytoplasm",
"signal transduction",
"genetic screens",
"... | The Secretory Pathway Calcium ATPase PMR-1/SPCA1 Has Essential Roles in Cell Migration during Caenorhabditis elegans Embryonic Development | journal.pgen.1003506 | null | [
[
"Calcium is one of the most versatile and important small molecules in the cell: it is involved in cell processes starting at the beginning of new cell life during fertilization and ending with a role in cell death during apoptosis [1] .",
"One developmental role for calcium is in cell migration .",
"... | [
"Maintaining levels of calcium in the cytosol is important for many cellular events , including cell migration , where localized regions of high calcium are required to regulate cytoskeletal dynamics , contractility , and adhesion .",
"Studies show inositol-trisphosphate receptors ( IP3R ) and ryanodine receptors... | [
"During growth or regeneration after damage , skin cells migrate from basal to superficial layers , forming tight attachments that protect an individual from environmental assaults .",
"Proteins that remove calcium from the cell cytosol into secretory stores , where it is available for future release , play a key... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"molecular biology/histone modification",
"developmental biology/stem cells",
"genetics and genomics/gene expression",
"developmental biology/cell differentiation",
"genetics and genomics/epigenetics",
"molecular biology/chromatin structure"
] | GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells | journal.pgen.1001244 | null | [
[
"Polycomb proteins are epigenetic regulators required for proper gene expression patterning in metazoans .",
"The proteins reside in two main complexes , termed Polycomb repressive complex 1 and 2 ( PRC1 and PRC2 ) .",
"PRC2 catalyzes histone H3 lysine 27 tri-methylation ( K27me3 ) , while PRC1 cataly... | [
"Polycomb proteins are epigenetic regulators that localize to developmental loci in the early embryo where they mediate lineage-specific gene repression .",
"In Drosophila , these repressors are recruited to sequence elements by DNA binding proteins associated with Polycomb repressive complex 2 ( PRC2 ) .",
"Ho... | [
"Key developmental genes are precisely turned on or off during development , thus creating a complex , multi-tissue embryo .",
"The mechanism that keeps genes off , or repressed , is crucial to proper development .",
"In embryonic stem cells , Polycomb repressive complex 2 ( PRC2 ) is recruited to the promoters... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"control theory",
"applied mathematics",
"signaling networks",
"systems science",
"mathematics",
"statistics (mathematics)",
"network analysis",
"complex systems",
"computer and information sciences",
"theoretical biology",
"biophysics",
"systems biology",
"biochemistry",
"biochemical simu... | Model Selection in Systems Biology Depends on Experimental Design | journal.pcbi.1003650 | null | [
[
"Mathematical models provide a rich framework for biological investigation .",
"Depending upon the questions posed , the relevant existing knowledge and alternative hypotheses may be combined and conveniently encoded , ready for analysis via a wealth of computational techniques .",
"The consequences o... | [
"Experimental design attempts to maximise the information available for modelling tasks .",
"An optimal experiment allows the inferred models or parameters to be chosen with the highest expected degree of confidence .",
"If the true system is faithfully reproduced by one of the models , the merit of this approa... | [
"Different models of the same process represent distinct hypotheses about reality .",
"These can be decided between within the framework of model selection , where the evidence for each is given by their ability to reproduce a set of experimental data .",
"Even if one of the models is correct , the chances of i... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"virology/vaccines",
"virology/animal models of infection",
"virology"
] | Vesicular Stomatitis Virus-Based Ebola Vaccine Is Well-Tolerated and Protects Immunocompromised Nonhuman Primates | journal.ppat.1000225 | null | [
[
"Ebola virus ( EBOV ) has been associated with sporadic episodes of hemorrhagic fever ( HF ) that produce severe disease in infected patients .",
"Mortality rates in outbreaks have ranged from 50% for Sudan ebolavirus ( SEBOV ) to up to 90% for Zaire ebolavirus ( ZEBOV ) ( reviewed in [1] ) .",
"A rec... | [
"Ebola virus ( EBOV ) is a significant human pathogen that presents a public health concern as an emerging/re-emerging virus and as a potential biological weapon .",
"Substantial progress has been made over the last decade in developing candidate preventive vaccines that can protect nonhuman primates against EBOV... | [
"Ebola virus is among the most lethal microbes known to man , with case fatality rates often exceeding 80% .",
"Since its discovery in 1976 , outbreaks have been sporadic and geographically restricted , primarily to areas of Central Africa .",
"However , concern about the natural or unnatural introduction of Eb... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"statistics",
"gene regulation",
"regulatory proteins",
"dna-binding proteins",
"dna transcription",
"chi square tests",
"mathematics",
"genome analysis",
"transcription factors",
"sequence motif analysis",
"research and analysis methods",
"sequence analysis",
"bioinformatics",
"proteins",... | Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes | journal.pgen.1007999 | null | [
[
"In eukaryotes , gene transcription by RNA polymerase II ( Pol II ) is initiated by the binding of specific transcription factors to double-stranded DNA .",
"The yeast transcription factors target regulatory regions called UAS or URS ( for Upstream Activating/Repressing Sequences ) , generally directly ad... | [
"GATA transcription factors are highly conserved among eukaryotes and play roles in transcription of genes implicated in cancer progression and hematopoiesis .",
"However , although their consensus binding sites have been well defined in vitro , the in vivo selectivity for recognition by GATA factors remains poor... | [
"GATA transcription factors are highly conserved among eukaryotes and play key roles in cancer progression and hematopoiesis .",
"In budding yeast , four GATA transcription factors are involved in the response to the quality of nitrogen supply .",
"Here , we have determined the whole genome binding profile of t... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials & methods"
] | [
"bacteriology",
"biofilms",
"chinchillas",
"medicine and health sciences",
"pathology and laboratory medicine",
"pneumococcus",
"pathogens",
"microbiology",
"vertebrates",
"animals",
"mammals",
"genome analysis",
"sequence motif analysis",
"bacteria",
"bacterial pathogens",
"research a... | Function of BriC peptide in the pneumococcal competence and virulence portfolio | journal.ppat.1007328 | null | [
[
"Bacteria form sessile communities termed biofilms , where they interact with each other to engage in collaborative and/or competitive behaviors [1] .",
"In Streptococcus pneumoniae ( pneumococcus ) , these cell-cell interactions are commonly mediated by secreted peptides that interact with both producing... | [
"Streptococcus pneumoniae ( pneumococcus ) is an opportunistic pathogen that causes otitis media , sinusitis , pneumonia , meningitis and sepsis .",
"The progression to this pathogenic lifestyle is preceded by asymptomatic colonization of the nasopharynx .",
"This colonization is associated with biofilm formati... | [
"Pneumococcal biofilms occur in chronic otitis media , chronic rhinosinusitis , and nasopharyngeal colonization .",
"These biofilms are an important component of pneumococcal epidemiology , particularly in influencing transmission , maintenance of asymptomatic colonization , and development of disease .",
"The ... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"cell biology",
"molecular biology",
"genetics and genomics"
] | Mapping Meiotic Single-Strand DNA Reveals a New Landscape of DNA Double-Strand Breaks in Saccharomyces cerevisiae | journal.pbio.0050324 | The authors developed a new method to detect DNA damage genome-wide, and they used it to show that meiotic recombination is more uniformly distributed in budding yeast than was previously believed. | [
[
"Meiosis results in the faithful and efficient division of a diploid genome into four haploid gametes .",
"After one round of DNA replication , cells undergo two rounds of chromosome segregation .",
"Recombination between homologous chromosomes ( homologs ) occurs during prophase of the first division... | [
"DNA double-strand breaks ( DSBs ) , which are formed by the Spo11 protein , initiate meiotic recombination .",
"Previous DSB-mapping studies have used rad50S or sae2Δ mutants , which are defective in break processing , to accumulate Spo11-linked DSBs , and report large ( ≥ 50 kb ) “DSB-hot” regions that are sepa... | [
"During meiosis , the two copies of each chromosome present in the full ( diploid ) genome come together and then separate , forming haploid gametes ( sperm and eggs , in animals ) .",
"Recombination , which swaps DNA between chromosomes , is critical for chromosome pairing and separation , and also promotes gene... | 2007 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"neural networks",
"engineering and technology",
"nervous system",
"signal processing",
"signaling networks",
"random variables",
"neuroscience",
"covariance",
"mathematics",
"network analysis",
"computational neuroscience",
"coding mechanisms",
"computer an... | Interpretation of correlated neural variability from models of feed-forward and recurrent circuits | journal.pcbi.1005979 | null | [
[
"In the search for clues about the function of neural circuits , it has become customary to rely upon recordings of the activity of large populations of neurons .",
"These measurements exhibit the concerted responses of neurons in different conditions , such as presentations of different stimuli .",
"... | [
"Neural populations respond to the repeated presentations of a sensory stimulus with correlated variability .",
"These correlations have been studied in detail , with respect to their mechanistic origin , as well as their influence on stimulus discrimination and on the performance of population codes .",
"A num... | [
"The response of neurons to a stimulus is variable across trials .",
"A natural solution for reliable coding in the face of noise is the averaging across a neural population .",
"The nature of this averaging depends on the structure of noise correlations in the neural population .",
"In turn , the correlation... | 2018 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"evolutionary biology/microbial evolution and genomics",
"evolutionary biology/genomics",
"evolutionary biology/bioinformatics",
"evolutionary biology/evolutionary and comparative genetics"
] | The Early Stage of Bacterial Genome-Reductive Evolution in the Host | journal.ppat.1000922 | null | [
[
"The genomes of host-adapted bacteria , including endosymbionts and obligatory intracellular pathogens , go through reductive evolution [1] , [2] , [3] .",
"Such changes are partly due to a reduced pressure to maintain genes that are not essential for survival in the host .",
"Similarly , decreased ef... | [
"The equine-associated obligate pathogen Burkholderia mallei was developed by reductive evolution involving a substantial portion of the genome from Burkholderia pseudomallei , a free-living opportunistic pathogen .",
"With its short history of divergence ( ∼3 . 5 myr ) , B . mallei provides an excellent resource... | [
"It has been known for some time that bacteria undergo genome-reduction when they transition from a free-living state to a constantly host-restricted state .",
"High levels of IS element expansion were also found in these bacteria , and the IS elements were suggested to play a role in genome reductive evolution .... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"chemical compounds",
"behavioral and social aspects of health",
"drugs",
"diet",
"physical activity",
"organic compounds",
"cardiovascular medicine",
"mathematics",
"nutrition",
"statistics (mathematics)",
"pharmacology",
"alcohols",
"research and analysis ... | Reporting bias in the literature on the associations of health-related behaviors and statins with cardiovascular disease and all-cause mortality | journal.pbio.2005761 | null | [
[
"The literature on the association between behavioral risk factors ( e . g . , smoking , alcohol , physical inactivity , and unhealthy diet ) and cardiovascular diseases—the single largest cause of death globally [1]—has grown exponentially in the last decades [2–39] .",
"Observational epidemiological stu... | [
"Reporting bias in the literature occurs when there is selective revealing or suppression of results , influenced by the direction of findings .",
"We assessed the risk of reporting bias in the epidemiological literature on health-related behavior ( tobacco , alcohol , diet , physical activity , and sedentary beh... | [
"In the scientific literature , reporting bias occurs when communication and publication of results are influenced by the direction of findings .",
"Reporting bias can distort scientific evidence and may misguide subsequent clinical and public health efforts .",
"Our study provided an assessment of the degree o... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"luciferase",
"nucleic acid synthesis",
"medicine and health sciences",
"crystal structure",
"pathology and laboratory medicine",
"protein interactions",
"enzymes",
"pathogens",
"condensed matter physics",
"enzymology",
"microbiology",
"negative-sense rna viruses",
"viral structure",
"nucl... | The Ebola Virus VP30-NP Interaction Is a Regulator of Viral RNA Synthesis | journal.ppat.1005937 | null | [
[
"Filoviruses such as Ebola ( EBOV ) and Marburg viruses ( MARV ) are nonsegmented negative-sense RNA viruses that can cause deadly hemorrhagic fevers with up to 90% fatality [1] .",
"The impact of EBOV is highlighted by the recent outbreak in West Africa involving over 28 , 000 cases and claiming more tha... | [
"Filoviruses are capable of causing deadly hemorrhagic fevers .",
"All nonsegmented negative-sense RNA-virus nucleocapsids are composed of a nucleoprotein ( NP ) , a phosphoprotein ( VP35 ) and a polymerase ( L ) .",
"However , the VP30 RNA-synthesis co-factor is unique to the filoviruses .",
"The assembly , ... | [
"Filoviruses use a system of proteins and RNA to regulate viral RNA genome transcription and replication .",
"Here , we have determined crystal structures and the biological functions of the protein complex formed by the filovirus transcriptional activator , VP30 , and the core component of the nucleocapsid machi... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"vesicles",
"pathology and laboratory medicine",
"cell processes",
"egfr signaling",
"vertebrates",
"animals",
"xenopus",
"animal models",
"developmental biology",
"model organisms",
"amphibians",
"developmental signaling",
"stem cells",
"experimental orga... | EGF-mediated EGFR/ERK signaling pathway promotes germinative cell proliferation in Echinococcus multilocularis that contributes to larval growth and development | journal.pntd.0005418 | null | [
[
"A population of pluripotent adult somatic stem cells , well known as “neoblasts” , has been extensively characterized and documented for free-living platyhelminthes ( flatworms ) [1–5] .",
"Neoblasts represent the only proliferative cell population , responsible for cell renewal during homeostasis , deve... | [
"Larvae of the tapeworm E . multilocularis cause alveolar echinococcosis ( AE ) , one of the most lethal helminthic infections in humans .",
"A population of stem cell-like cells , the germinative cells , is considered to drive the larval growth and development within the host .",
"The molecular mechanisms cont... | [
"E . multilocularis is considered as one of the most lethal parasitic helminth in humans .",
"It grows like tumors mainly in human liver and infiltrates other tissues , and even metastasizes .",
"It is believed that the parasite possesses a population of stem cell-like cells , the germinative cells .",
"These... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"immune physiology",
"pathology and laboratory medicine",
"yeast infections",
"pathogens",
"immunology",
"microbiology",
"vaccines",
"viruses",
"dna viruses",
"fungal diseases",
"infectious disease control",
"immune system pr... | Recombinant vaccines of a CD4+ T-cell epitope promote efficient control of Paracoccidioides brasiliensis burden by restraining primary organ infection | journal.pntd.0005927 | null | [
[
"Paracoccidioidomycosis ( PCM ) is a neglected dermal , mucosal , and respiratory disease endemic to South America , which is caused by the thermally dimorphic fungi Paracoccidioides spp .",
"[1] .",
"The acquisition of Paracoccidioides spp .",
"occurs mainly by inhalation of air-borne fungal prop... | [
"Paracoccidioidomycosis ( PCM ) is an infectious disease endemic to South America , caused by the thermally dimorphic fungi Paracoccidioides .",
"Currently , there is no effective human vaccine that can be used in prophylactic or therapeutic regimes .",
"We tested the hypothesis that the immunogenicity of the i... | [
"Human paracoccidioidomycosis ( PCM ) represents a serious public health issue due to its disabling sequelae in working-age people and mortality rates ( 8th among chronic infectious parasitic diseases in endemic countries and first among mycoses in Brazil ) .",
"Although antifungal drugs have been widely used and... | 2017 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"phylogenetics",
"animal genetics",
"genetics",
"introgression",
"biology and life sciences",
"animal management",
"animal breeding",
"hybridization",
"evolutionary biology",
"population genetics",
"evolutionary systematics",
"evolutionary processes",
"gene flow",
"population biology",
"... | Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle | journal.pgen.1004254 | null | [
[
"High-throughput genotyping assays have allowed population geneticists to use genome-wide marker sets to analyze the histories of many species , including human [1] , cattle [2]–[4] , sheep [5] , dog [6] , horse [7] , yeast [8] , mouse [9] , [10] , rice [11] , [12] , maize [13]–[16] , grape [17] , and wheat [... | [
"The domestication and development of cattle has considerably impacted human societies , but the histories of cattle breeds and populations have been poorly understood especially for African , Asian , and American breeds .",
"Using genotypes from 43 , 043 autosomal single nucleotide polymorphism markers scored in... | [
"The DNA of domesticated plants and animals contains information about how species were domesticated , exported , and bred by early farmers .",
"Modern breeds were developed by lengthy and complex processes; however , our use of 134 breeds and new analytical models enabled us to reveal some of the processes that ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"microbiology",
"cell differentiation",
"viruses",
"developmental biology",
"dna viruses",
"hpv-31",
"epigenetics",
"molecular biology techniques",
"chromatin",
"research and analysis methods",
"papillomaviru... | SETD2-dependent H3K36me3 plays a critical role in epigenetic regulation of the HPV31 life cycle | journal.ppat.1007367 | null | [
[
"Human papillomaviruses ( HPVs ) are small , circular , double-stranded DNA viruses that have a genome of approximately 8 kilobases .",
"More than 200 types of HPV have been identified and are categorized based on their dominant site of infection; either the cutaneous or mucosal epithelium [1] .",
"Mu... | [
"The life cycle of HPV is tied to the differentiation status of its host cell , with productive replication , late gene expression and virion production restricted to the uppermost layers of the stratified epithelium .",
"HPV DNA is histone-associated , exhibiting a chromatin structure similar to that of the host... | [
"High-risk HPVs are associated with multiple human cancers , most notably cervical cancer .",
"Understanding mechanisms by which HPV co-opts cellular pathways to replicate could identify potential therapeutic targets .",
"The HPV genome is associated with histones in a manner similar to that of cellular DNA , b... | 2018 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"public health and epidemiology",
"soil-transmitted helminths",
"trichuriasis",
"epidemiology",
"neglected tropical diseases",
"hookworm",
"ascariasis"
] | Soil-Transmitted Helminth Infections among Plantation Sector Schoolchildren in Sri Lanka: Prevalence after Ten Years of Preventive Chemotherapy | journal.pntd.0001341 | null | [
[
"Sri Lanka has already achieved several Millennium Development Goals such as universal primary school enrolment , gender parity in school enrolment , and is on track to achieve the desired reduction in under-five and infant mortality .",
"Poverty has markedly reduced in the urban and rural sectors between... | [
"The plantation sector in Sri Lanka lags behind the rest of the country in terms of living conditions and health .",
"In 1992 , a sector-wide survey of children aged 3–12 years and women of reproductive age showed >90% prevalence of soil-transmitted helminth infections .",
"Biannual mass de-worming targeting ch... | [
"Mass de-worming of pre-school and school-age children was introduced in Sri Lanka's plantation sector in 1994 after a survey showed that >90% of children and women of reproductive age were infected with intestinal worms .",
"The present study was carried out to assess the status of infection four years after mas... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"circuit models",
"animal models",
"cellular neuroscience",
"model organisms",
"neural networks",
"computational neuroscience",
"biology and life sciences",
"computational biology",
"neuroscience",
"research and analysis methods"
] | Identifying Crucial Parameter Correlations Maintaining Bursting Activity | journal.pcbi.1003678 | null | [
[
"Vital adaptive rhythmic behaviors such as breathing and heartbeat in invertebrates are produced by central pattern-generating networks ( CPGs ) .",
"Beside their inherent importance in pacing rhythmic movements , CPGs represent fertile test beds for understanding neuronal network dynamics because of the ... | [
"Recent experimental and computational studies suggest that linearly correlated sets of parameters ( intrinsic and synaptic properties of neurons ) allow central pattern-generating networks to produce and maintain their rhythmic activity regardless of changing internal and external conditions .",
"To determine th... | [
"Central pattern-generating networks ( CPGs ) must be remarkably robust , maintaining functional rhythmic activity despite fluctuations in internal and external conditions .",
"Recent experimental evidence suggests that this robustness is achieved by the coordinated regulation of many membrane and synaptic curren... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"enzymes",
"biology",
"biophysics simulations",
"biophysics"
] | A Rigidifying Salt-Bridge Favors the Activity of Thermophilic Enzyme at High Temperatures at the Expense of Low-Temperature Activity | journal.pbio.1001027 | null | [
[
"To cope with the extremely hot habitats , thermophilic enzymes isolated from organisms thriving in these environments have usually evolved towards high thermal stability .",
"Although thermophilic and mesophilic enzymes are comparably active at their respective temperatures where these enzymes function ,... | [
"Thermophilic enzymes are often less active than their mesophilic homologues at low temperatures .",
"One hypothesis to explain this observation is that the extra stabilizing interactions increase the rigidity of thermophilic enzymes and hence reduce their activity .",
"Here we employed a thermophilic acylphosp... | [
"Although enzymes from thermophiles thriving in hot habitats are more stable than their mesophilic homologs , they are often less active at low temperatures .",
"One theory suggests that extra stabilizing interactions found in thermophilic enzymes may increase their rigidity and decrease enzymatic activity at low... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"microbiology/cellular microbiology and pathogenesis"
] | The T3SS Effector EspT Defines a New Category of Invasive Enteropathogenic E. coli (EPEC) Which Form Intracellular Actin Pedestals | journal.ppat.1000683 | null | [
[
"The human pathogens enteropathogenic Escherichia coli ( EPEC ) and enterohemorrhagic E . coli ( EHEC ) [1] and the mouse pathogen Citrobacter rodentium [2] are closely related extra-cellular diarrhoeal agents characterized by their ability to colonize the gut epithelium via attaching and effacing ( A/E ) les... | [
"Enteropathogenic Escherichia coli ( EPEC ) strains are defined as extracellular pathogens which nucleate actin rich pedestal-like membrane extensions on intestinal enterocytes to which they intimately adhere .",
"EPEC infection is mediated by type III secretion system effectors , which modulate host cell signali... | [
"Enteropathogenic E . coli ( EPEC ) is an important diarrheal pathogen responsible for significant infant mortality in the developing world and is increasingly associated with sporadic outbreaks in the developed world .",
"The virulence strategy of EPEC revolves around a conserved Type 3 secretion system ( T3SS )... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"meiosis",
"medicine and health sciences",
"reproductive system",
"microtubules",
"sperm head",
"cell cycle and cell division",
"cell processes",
"reproductive physiology",
"germ cells",
"animal models",
"model organisms",
"experimental organism systems",
"cellular structures and organelles"... | Mutations in ARL2BP, a protein required for ciliary microtubule structure, cause syndromic male infertility in humans and mice | journal.pgen.1008315 | null | [
[
"Cilia are short , protruding organelles often referred to as “signaling hubs” .",
"These microtubule-based structures are involved in diverse functional roles , and impairment of their structure or function often leads to a class of genetic diseases known as “ciliopathies” [1] .",
"Cilia contain a hi... | [
"Cilia are evolutionarily conserved hair-like structures with a wide spectrum of key biological roles , and their dysfunction has been linked to a growing class of genetic disorders , known collectively as ciliopathies .",
"Many strides have been made towards deciphering the molecular causes for these diseases , ... | [
"The flagellated tails of sperm cells require a stringent developmental process that is essential for motility and fertility .",
"The components that comprise the sperm tail assemble in regulated steps with protein processing , transport , and structural assembly dependent on each other for sperm tail maturity ."... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases/sexually transmitted diseases",
"infectious diseases",
"cell biology/cellular death and stress responses",
"microbiology/innate immunity",
"cell biology/membranes and sorting",
"infectious diseases/bacterial infections",
"microbiology/cellular microbiology and pathogenesis",
"micr... | Bacterial Porin Disrupts Mitochondrial Membrane Potential and Sensitizes Host Cells to Apoptosis | journal.ppat.1000629 | null | [
[
"The genus Neisseria is comprised of the human pathogenic species N . gonorrhoeae ( Ngo ) and N . meningitidis , which cause gonorrhea and meningitis , respectively .",
"The attachment of bacteria to epithelial cells results in transfer of the outer membrane porin PorB to the host cell cytoplasmic membran... | [
"The bacterial PorB porin , an ATP-binding β-barrel protein of pathogenic Neisseria gonorrhoeae , triggers host cell apoptosis by an unknown mechanism .",
"PorB is targeted to and imported by host cell mitochondria , causing the breakdown of the mitochondrial membrane potential ( ΔΨm ) .",
"Here , we show that ... | [
"PorB is a bacterial porin that plays an important role in the pathogenicity of Neisseria gonorrhoeae .",
"Upon infection with these bacteria , PorB is transported into mitochondria of infected cells , causing the loss of mitochondrial membrane potential and eventually leading to apoptotic cell death .",
"Here ... | 2009 |
[
"Introduction",
"Results and Discussion",
"Materials and Methods"
] | [
"meiosis",
"chromosome staining",
"spermatocytes",
"immunofluorescence staining",
"chromosome structure and function",
"centromeres",
"cell cycle and cell division",
"cell processes",
"chromatids",
"germ cells",
"telomeres",
"sperm",
"research and analysis methods",
"specimen preparation a... | Distinct Roles of Meiosis-Specific Cohesin Complexes in Mammalian Spermatogenesis | journal.pgen.1006389 | null | [
[
"After completing premeiotic DNA replication mammalian germ cells enter meiosis and undergo two meiotic cell divisions without any further DNA replication .",
"Haploid gametes are produced .",
"Meiosis features highly specific chromosome structures and behaviour to ensure proper chromosome segregation... | [
"Mammalian meiocytes feature four meiosis-specific cohesin proteins in addition to ubiquitous ones , but the roles of the individual cohesin complexes are incompletely understood .",
"To decipher the functions of the two meiosis-specific kleisins , REC8 or RAD21L , together with the only meiosis-specific SMC prot... | [
"Unlike somatic cells , which feature two different cohesin complexes , in spermatocytes at least six distinct cohesin complexes form , whose concerted functions are little understood .",
"This study focuses on three meiosis-specific cohesins .",
"Meiosis features specific chromosome structures and dynamics , a... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"diagnostic radiology",
"ultrasound imaging",
"pathology and laboratory medicine",
"nervous system",
"immunology",
"tropical diseases",
"neuroscience",
"diabetes mellitus",
"bacterial diseases",
"research design",
"endocrine disorders",
"signs and symptoms",
... | Ultrasonography of Leprosy Neuropathy: A Longitudinal Prospective Study | journal.pntd.0005111 | null | [
[
"Leprosy is the leading infectious cause of disability [1 , 2] .",
"Neurological involvement may start before diagnosis or either during or after treatment , leading to functional impairments and deformities [1 , 3–5] .",
"Nerve palpation can detect thickening , but it is examiner-dependent and it dem... | [
"Previous studies have shown that leprosy multi-drug therapy ( MDT ) does not stop the progression of nerve function impairment .",
"There are no prospective studies investigating the evolution of nerve anatomic abnormalities after treatment .",
"We examined leprosy patients aiming to investigate the evolution ... | [
"Leprosy can lead to functional and anatomical changes in the peripheral nerves .",
"Previous studies have shown that the anti-bacterial treatment cannot stop the progression of nerve function abnormalities; to our knowledge , there are no previous prospective studies investigating the evolution of nerve anatomic... | 2016 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"biotechnology",
"medicine",
"biochemistry",
"infectious diseases",
"model organisms",
"biology",
"microbiology"
] | Functional Expression of Parasite Drug Targets and Their Human Orthologs in Yeast | journal.pntd.0001320 | null | [
[
"Parasitic diseases such as malaria , schistosomiasis , leishmaniasis , sleeping sickness , and Chagas disease affect millions of people every year , leading to severe morbidity and death .",
"For example malaria , caused by parasites of the genus Plasmodium , kills 1–3 million people every year ( http://... | [
"The exacting nutritional requirements and complicated life cycles of parasites mean that they are not always amenable to high-throughput drug screening using automated procedures .",
"Therefore , we have engineered the yeast Saccharomyces cerevisiae to act as a surrogate for expressing anti-parasitic targets fro... | [
"Parasites kill millions of people every year and leave countless others with chronic debilitating disease .",
"These diseases , which include malaria and sleeping sickness , mainly affect people in developing countries .",
"For this reason , few drugs have been developed to treat them .",
"To make matters wo... | 2011 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"vertebrates",
"physics",
"eukaryotes",
"computational biology",
"evolutionary biology",
"biophysics",
"neuroscience",
"animals"
] | From Morphology to Neural Information: The Electric Sense of the Skate | journal.pcbi.0030113 | null | [
[
"Sensor placement and arrangement are crucial for any sensory system used to locate the distance and bearing of a stimulus source , and this is true for a variety of modalities .",
"In addition to stereo vision in much of the animal kingdom , echolocation ( e . g . , the barn owl ) and mechanosensory loca... | [
"Morphology typically enhances the fidelity of sensory systems .",
"Sharks , skates , and rays have a well-developed electrosense that presents strikingly unique morphologies .",
"Here , we model the dynamics of the peripheral electrosensory system of the skate , a dorsally flattened batoid , moving near an ele... | [
"The electric sense appears in a variety of animals , from the shark to the platypus , and it facilitates short-range prey detection where environments limit sight .",
"Typically , hundreds or thousands of sensors work in concert .",
"In skates , rays , and sharks , each electrosensor includes a small , innerva... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"infectious diseases",
"medicine and health sciences",
"diagnostic medicine",
"pathology and laboratory medicine",
"biology and life sciences",
"proteomics",
"malaria",
"biomarkers",
"parasitic diseases"
] | Affinity Proteomics Reveals Elevated Muscle Proteins in Plasma of Children with Cerebral Malaria | journal.ppat.1004038 | null | [
[
"Human malaria is a life-threatening disease causing an estimated 655 , 000 deaths in 2010 [1] .",
"Although the mortality rates have decreased during the last decade , deaths in Africa due to childhood malaria are still elevated with Plasmodium falciparum attributable to a third of the childhood deaths a... | [
"Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria .",
"However , it is still not understood why some children are more at risks to develop malaria complications than others .",
"To identify human pr... | [
"Why do some malaria-infected children develop severe and lethal forms of the disease , while others only have mild forms ?",
"In order to try to find potential answers or clues to this question , we have here analyzed more than 1 , 000 different human proteins in the blood of more than 500 malaria-infected child... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"body fluids",
"tropical diseases",
"geographical locations",
"vertebrates",
"parasitic diseases",
"dogs",
"parasitic protozoans",
"animals",
"mammals",
"organisms",
"protozoans",
"veterinary diagnostics",
"leishmania",
"neglected tropical diseases",
"mo... | eNose analysis of volatile chemicals from dogs naturally infected with Leishmania infantum in Brazil | journal.pntd.0007599 | null | [
[
"Visceral leishmaniasis ( VL ) is a neglected tropical disease caused by protist parasites belonging to the genus Leishmania .",
"Globally over 350 million people are at risk of infection with an estimated 200–400 thousand cases annually and an estimated 10% fatality rate .",
"Ninety percent of all re... | [
"Visceral leishmaniasis ( VL ) in Brazil is a neglected , vector-borne , tropical parasitic disease that is responsible for several thousand human deaths every year .",
"The transmission route involves sand flies becoming infected after feeding on infected reservoir host , mainly dogs , and then transmitting the ... | [
"Visceral leishmaniasis ( VL ) is an insect transmitted , tropical parasitic disease and in Brazil it causes thousands of human deaths every year .",
"Domestic dogs can also be infected , and they are a risk factor for people .",
"The Brazilian Ministry of Health tries to control the disease in 3 ways; first by... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics",
"microbiology",
"biology",
"bacterial pathogens",
"gene function"
] | A Long-Chain Flavodoxin Protects Pseudomonas aeruginosa from Oxidative Stress and Host Bacterial Clearance | journal.pgen.1004163 | null | [
[
"Microorganisms living in aerobic environments are constantly exposed to the harmful effects of reactive oxygen species ( ROS ) , including H2O2 and the superoxide radical , which are generated as unavoidable by-products of oxygen utilization [1] .",
"In addition , commensal and pathogenic bacteria have t... | [
"Long-chain flavodoxins , ubiquitous electron shuttles containing flavin mononucleotide ( FMN ) as prosthetic group , play an important protective role against reactive oxygen species ( ROS ) in various microorganisms .",
"Pseudomonas aeruginosa is an opportunistic pathogen which frequently has to face ROS toxici... | [
"Coping with toxic reactive oxygen species ( ROS ) generated as by-products of aerobic metabolism is a major challenge for O2-thriving organisms , which deploy multilevel responses to prevent ROS-triggered damage , including membrane modifications , induction of antioxidant and repair systems and/or replacement of ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"mathematics",
"viruses",
"infectious diseases",
"computational biology"
] | HIV-1 Subtype B Protease and Reverse Transcriptase Amino Acid Covariation | journal.pcbi.0030087 | null | [
[
"HIV-1 is a highly mutable pathogen .",
"In the decades since it entered human populations , it has accumulated extensive sequence variation leading to the development of different subtypes and recombinant forms [1] .",
"Although the enzymatic targets of therapy are among the most conserved parts of t... | [
"Despite the high degree of HIV-1 protease and reverse transcriptase ( RT ) mutation in the setting of antiretroviral therapy , the spectrum of possible virus variants appears to be limited by patterns of amino acid covariation .",
"We analyzed patterns of amino acid covariation in protease and RT sequences from ... | [
"The identification of which mutations in a protein covary has played a major role in both structural and evolutionary biology .",
"Covariation analysis has been used to help predict unsolved protein structures and to better understand the functions of proteins with known structures .",
"The large number of pub... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"molecular biology/histone modification",
"virology/persistence and latency",
"cell biology/leukocyte signaling and gene expression",
"cell biology",
"virology",
"infectious diseases/viral infections",
"molecular biology/dna methylation",
"virology/viruses and cancer",
"virology/effects of virus inf... | Epstein-Barr Virus Latency in B Cells Leads to Epigenetic Repression and CpG Methylation of the Tumour Suppressor Gene Bim | journal.ppat.1000492 | null | [
[
"EBV is a B lymphotropic gammaherpes virus that asymptomatically and persistently infects >90% of humans; it occasionally causes infectious mononucleosis in adolescents and in rare instances is associated with the development of several different types of B cell lymphoma and various epithelial tumours [1] .",... | [
"In human B cells infected with Epstein-Barr virus ( EBV ) , latency-associated virus gene products inhibit expression of the pro-apoptotic Bcl-2-family member Bim and enhance cell survival .",
"This involves the activities of the EBV nuclear proteins EBNA3A and EBNA3C and appears to be predominantly directed at ... | [
"Bim is a cellular inducer of programmed cell death ( pcd ) , so the level of Bim is a critical regulator of lymphocyte survival and reduced expression enhances lymphomagenesis in mice and humans .",
"Regulation of Bim is uniquely important in the pathogenesis of Burkitt's lymphoma ( BL ) , since in this human ch... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"community ecology",
"conservation biology",
"conservation science",
"ecology and environmental sciences",
"species extinction",
"ecology",
"species delimitation",
"food web structure",
"predation",
"trophic interactions",
"speciation",
"biology and life sciences",
"theoretical ecology",
"... | How Structured Is the Entangled Bank? The Surprisingly Simple Organization of Multiplex Ecological Networks Leads to Increased Persistence and Resilience | journal.pbio.1002527 | An ecological network synthesizing all known interactions between species exhibits a clear pattern of organization that reflects evolutionary and ecological constraints operating in this entangled bank of species. | [
[
"In his description of the “entangled bank” of species , Darwin illustrated the principle that species must manage complex interdependencies to successfully coexist in natural communities [1–7] .",
"In this context , evolutionary constraints set a landscape of trade-offs over which species must solve thei... | [
"Species are linked to each other by a myriad of positive and negative interactions .",
"This complex spectrum of interactions constitutes a network of links that mediates ecological communities’ response to perturbations , such as exploitation and climate change .",
"In the last decades , there have been great... | [
"Within an ecosystem , species interact with each other in many different ways , including predation , competition , and facilitation , and this can be modelled as a network of multiple interaction types .",
"The variety of interaction types that link species to each other has long been recognized but has rarely ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
""
] | [
"homo (human)",
"genetics and genomics",
"public health and epidemiology"
] | Large-Scale Evaluation of Candidate Genes Identifies Associations between VEGF Polymorphisms and Bladder Cancer Risk | journal.pgen.0030029 | null | [
[
"Bladder cancer is primarily a sporadic disease , and environmental factors such as tobacco smoking and occupational exposure to aromatic amines have been established as strong determinants of risk [1] .",
"A moderate familial component has been demonstrated for bladder cancer , but so far no high-penetra... | [
"Common genetic variation could alter the risk for developing bladder cancer .",
"We conducted a large-scale evaluation of single nucleotide polymorphisms ( SNPs ) in candidate genes for cancer to identify common variants that influence bladder cancer risk .",
"An Illumina GoldenGate assay was used to genotype ... | [
"This article reports findings from a large-scale evaluation of common variation in candidate genes for cancer to identify variants that influence bladder cancer risk .",
"We first evaluated 1 , 433 common variants within or near 386 genes in a large case-control study in Spain .",
"The most significant finding... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"immunology/cellular microbiology and pathogenesis",
"infectious diseases/neglected tropical diseases",
"virology/immunodeficiency viruses",
"virology/mechanisms of resistance and susceptibility, including host genetics",
"infectious diseases/hiv infection and aids",
"infectious diseases/protozoal infecti... | Leishmania infantum Amastigotes Enhance HIV-1 Production in Cocultures of Human Dendritic Cells and CD4+ T Cells by Inducing Secretion of IL-6 and TNF-α | journal.pntd.0000441 | null | [
[
"Leishmaniasis is today recognized as one of the world's most important parasitic diseases , threatening 350 million people in 88 countries [1] .",
"At least 20 Leishmania species can induce various clinical manifestations better known as leishmaniasis .",
"Infection by these trypanosomatid protozoan ... | [
"Visceral leishmaniasis has emerged as an important opportunistic disease among patients infected with HIV-1 .",
"Both HIV-1 and the protozoan parasite Leishmania can productively infect cells of the macrophage-dendritic cell lineage .",
"Here we demonstrate that Leishmania infantum amastigotes increase HIV-1 p... | [
"Visceral leishmaniasis ( VL ) is a potentially deadly parasitic disease afflicting millions worldwide .",
"Although itself an important infectious illness , VL has also emerged as an opportunistic disease among patients infected with HIV-1 .",
"This is partly due to the increasing overlap between urban regions... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"sequencing techniques",
"taxonomy",
"parasite groups",
"plasmodium",
"parasitology",
"apicomplexa",
"phylogenetics",
"data management",
"genome analysis",
"sequence motif analysis",
"molecular biology techniques",
"research and analysis methods",
"sequence analysis",
"computer and informa... | Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence | journal.pcbi.1005038 | null | [
[
"The evolutionary history of eukaryotic proteins involves rapid sequence divergence , addition and deletion of protein domains , fusion and fission of genes .",
"This implies that protein repertoires of distantly related species differ greatly ( new architectures , that is combinations of domains , are ma... | [
"Traditional protein annotation methods describe known domains with probabilistic models representing consensus among homologous domain sequences .",
"However , when relevant signals become too weak to be identified by a global consensus , attempts for annotation fail .",
"Here we address the fundamental questi... | [
"Current sequence databases contain hundreds of billions of nucleotides coding for genes and a classification of these sequences is a primary problem in genomics .",
"A reasonable way to organize these sequences is through their predicted domains , but the identification of domains in very divergent sequences , s... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"control theory",
"medicine and health sciences",
"engineering and technology",
"nervous system",
"social sciences",
"limbs (anatomy)",
"neuroscience",
"learning and memory",
"control engineering",
"probability distribution",
"mathematics",
"cognitive psychology",
"systems scie... | Dissociating error-based and reinforcement-based loss functions during sensorimotor learning | journal.pcbi.1005623 | null | [
[
"Error feedback and reinforcement feedback can each guide motor adaptation in a visuomotor rotation task [1] .",
"It has been proposed that error feedback and reinforcement feedback engage different neural mechanisms [2] .",
"Indeed , depending on the form of feedback used during adaptation , newly ac... | [
"It has been proposed that the sensorimotor system uses a loss ( cost ) function to evaluate potential movements in the presence of random noise .",
"Here we test this idea in the context of both error-based and reinforcement-based learning .",
"In a reaching task , we laterally shifted a cursor relative to tru... | [
"Whether serving a tennis ball on a gusty day or walking over an unpredictable surface , the human nervous system has a remarkable ability to account for uncertainty when performing goal-directed actions .",
"Here we address how different types of feedback , error and reinforcement , are used to guide such behavi... | 2017 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"immunology",
"tropical diseases",
"microbiology",
"parasitic diseases",
"protozoan life cycles",
"animal models",
"developmental biology",
"model organisms",
"experimental organism systems",
"neglected tropical diseases",
"mol... | Discovery of novel, orally bioavailable, antileishmanial compounds using phenotypic screening | journal.pntd.0006157 | null | [
[
"Leishmaniasis constitutes a spectrum of diseases that range in severity from self-healing to fatal .",
"The disease can present as self-healing but potentially disfiguring cutaneous leishmaniasis [1]; metastatic and highly disfiguring mucocutaneous leishmaniasis [2]; or fatal visceral leishmaniasis [3] ,... | [
"Leishmaniasis is a parasitic infection that afflicts approximately 12 million people worldwide .",
"There are several limitations to the approved drug therapies for leishmaniasis , including moderate to severe toxicity , growing drug resistance , and the need for extended dosing .",
"Moreover , miltefosine is ... | [
"Leishmaniasis , caused by the protozoa of the Leishmania species , represents a spectrum of diseases that afflicts roughly 12 million individuals worldwide .",
"Current drug therapies for this parasitic disease are suboptimal because they are toxic , expensive , difficult to administer , and subject to drug resi... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"computational biology/comparative sequence analysis",
"genetics and genomics/bioinformatics",
"genetics and genomics/microbial evolution and genomics",
"genetics and genomics/gene expression"
] | 1+1 = 3: A Fusion of 2 Enzymes in the Methionine Salvage Pathway of Tetrahymena thermophila Creates a Trifunctional Enzyme That Catalyzes 3 Steps in the Pathway | journal.pgen.1000701 | null | [
[
"The amino acid methionine and its derivative S-adenosylmethionine ( SAM ) are essential substrates in a variety of cellular reactions , including protein and nucleic acid methylation and polypeptide , polyamine and ethylene syntheses [1]–[5] .",
"Ethylene , the hormone that regulates plant growth and dev... | [
"The methionine salvage pathway is responsible for regenerating methionine from its derivative , methylthioadenosine .",
"The complete set of enzymes of the methionine pathway has been previously described in bacteria .",
"Despite its importance , the pathway has only been fully described in one eukaryotic orga... | [
"Fusion genes , composed of the complete sequence of two or more other genes , are excellent markers of evolution .",
"In addition , fused genes are usually composed of genes with related functions , which makes them useful in inferring function when the function of one of their components is known .",
"We dete... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/molecular dynamics",
"biophysics/theory and simulation",
"biophysics/protein folding"
] | The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein | journal.pcbi.1000835 | null | [
[
"The wide range of kinetics that characterizes protein folding has attracted interest from both experimentalists and theoreticians for decades [1] .",
"Proteins fold on time scales that vary from microseconds to minutes [2] , even though the corresponding energy landscape directs folding towards its nativ... | [
"The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration .",
"A kinetic transition network is constructed using the discrete path sampling approach , and the resulting potential energy surface is visualized by ... | [
"Proteins are chains , which must fold into a compact structure for the molecule to perform its biological function .",
"There are a large number of ways the molecule can move into this final shape .",
"Proteins have evolved sequences that perform this difficult task by having strong biases toward the final sha... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Mycobacterium ulcerans in the Elderly: More Severe Disease and Suboptimal Outcomes | journal.pntd.0004253 | null | [
[
"Mycobacterium ulcerans ( M . ulcerans ) is an infection that causes necrotizing lesions of skin and subcutaneous tissue .",
"The majority of cases are reported from west and central Africa , but unlike Africa where the disease occurs mainly in children[1 , 2] , in south-eastern Victoria , Australia it oc... | [
"The clinical presentation of M . ulcerans disease and the safety and effectiveness of treatment may differ in elderly compared with younger populations related to relative immune defficiencies , co-morbidities and drug interactions .",
"However , elderly populations with M . ulcerans disease have not been compre... | [
"Mycobacterium ulcerans is an infection that can affect all age-groups .",
"It causes necrosis of skin and soft-tissue often resulting in severe outcomes and long-term disability .",
"However , due to the majority of infections worldwide occurring in children and young adults , there is a paucity of information... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine and health sciences",
"classical mechanics",
"biological locomotion",
"biomechanics",
"optimization",
"mathematics",
"pelvis",
"bioassays and physiological analysis",
"muscle electrophysiology",
"research and analysis methods",
"musculoskeletal mechanics",
"muscle physiology",
"mus... | Human Leg Model Predicts Muscle Forces, States, and Energetics during Walking | journal.pcbi.1004912 | null | [
[
"Human walking relies on a complex interplay of several physiological systems , with each exhibiting some degree of redundancy .",
"The nervous system directs muscle contraction while receiving input from many different neural pathways .",
"Muscles work together to produce motion , but different combi... | [
"Humans employ a high degree of redundancy in joint actuation , with different combinations of muscle and tendon action providing the same net joint torque .",
"Both the resolution of these redundancies and the energetics of such systems depend on the dynamic properties of muscles and tendons , particularly their... | [
"Neuromuscular systems often employ redundancy in joint actuation , with different combinations of muscle and tendon action producing the same net joint torque .",
"Both the resolution of these redundancies and the energetics of such systems depend strongly on the force-length relations of muscles and tendons .",... | 2016 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"influenza",
"immunology",
"geographical locations",
"social sciences",
"human mobility",
"preventive medicine",
"rural areas",
"norway",
"vaccination and immunization",
"human geography",
"public and occupational health",
"infectious diseases",
"geography",... | A theoretical single-parameter model for urbanisation to study infectious disease spread and interventions | journal.pcbi.1006879 | null | [
[
"We are living in a world which is continuously urbanising .",
"From a United Nations report [1] , we know that in 2014 , 54% of the population was living in urban areas .",
"By 2050 , they estimate that 66% of the population will be living in urban areas .",
"The number of “megacities” is also in... | [
"The world is continuously urbanising , resulting in clusters of densely populated urban areas and more sparsely populated rural areas .",
"We propose a method for generating spatial fields with controllable levels of clustering of the population .",
"We build a synthetic country , and use this method to genera... | [
"We study the interplay between urbanisation and infectious disease spread .",
"As part of the worldwide urbanisation process , people are continuously moving to urban areas , and the cities are growing in size .",
"This causes clusters of areas with high population density and clusters of areas with low popula... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetic polymorphism",
"genetics",
"population genetics",
"biology",
"genetics and genomics"
] | A Quantitative Comparison of the Similarity between Genes and Geography in Worldwide Human Populations | journal.pgen.1002886 | null | [
[
"The geographic structure of human genetic variation has long been of interest for its implications for studying human evolutionary history [1] , [2] , [3] , [4] , [5] .",
"In recent years , the expansion of population-genetic datasets has contributed to an increase in geographic investigations of human g... | [
"Multivariate statistical techniques such as principal components analysis ( PCA ) and multidimensional scaling ( MDS ) have been widely used to summarize the structure of human genetic variation , often in easily visualized two-dimensional maps .",
"Many recent studies have reported similarity between geographic... | [
"The spatial pattern of human genetic variation provides a basis for investigating the history of human migrations .",
"Statistical techniques such as principal components analysis ( PCA ) and multidimensional scaling ( MDS ) have been used to summarize spatial patterns of genetic variation , typically by placing... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome analysis tools",
"genomics",
"biology",
"computational biology",
"microbiology",
"genetics and genomics"
] | Genomic Analysis of the Hydrocarbon-Producing, Cellulolytic, Endophytic Fungus Ascocoryne sarcoides | journal.pgen.1002558 | null | [
[
"Global climate change and decreasing fuel reserves are driving a push towards biologically derived fuels from plant wastes .",
"The optimal biofuel for immediate implementation is one that functions within the context of current infrastructure , in particular with existing engines and distribution system... | [
"The microbial conversion of solid cellulosic biomass to liquid biofuels may provide a renewable energy source for transportation fuels .",
"Endophytes represent a promising group of organisms , as they are a mostly untapped reservoir of metabolic diversity .",
"They are often able to degrade cellulose , and th... | [
"A renewable source of energy is a pressing global need .",
"The biological conversion of lignocellulose to biofuels by microorganisms presents a promising avenue , but few organisms have been studied thoroughly enough to develop the genetic tools necessary for rigorous experimentation .",
"The filamentous-fung... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neuroscience"
] | Proteomic Studies of a Single CNS Synapse Type: The Parallel Fiber/Purkinje Cell Synapse | journal.pbio.1000083 | In a first step toward characterizing a putative molecular "synaptic code," a strategy--using genetically modified mice and cell fractionation to purify one class of synapses followed by mass spectrometric protein identification--reveals new proteins at the parallel fiber/Purkinje cell synapse. | [
[
"Each of the thousands of cell types present in the nervous system receives multiple classes of inputs that are spatially segregated and functionally distinct .",
"The chemoaffinity hypothesis stated that “the establishment and maintenance of synaptic associations were conceived to be regulated by highly ... | [
"Precise neuronal networks underlie normal brain function and require distinct classes of synaptic connections .",
"Although it has been shown that certain individual proteins can localize to different classes of synapses , the biochemical composition of specific synapse types is not known .",
"Here , we have u... | [
"The brain is composed of many different types of neurons that form very specific connections: synapses are formed with specific cellular partners and on precise subcellular domains .",
"It has been proposed that different combinations of molecules encode the specificity of neuronal connections , implying the exi... | 2009 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"learning",
"medicine and health sciences",
"brain",
"social sciences",
"neuroscience",
"learning and memory",
"fear",
"synaptic plasticity",
"cognitive psychology",
"cognition",
"memory",
"developmental neuroscience",
"emotions",
"animal cells",
"behavior",
"memory consolidation",
"... | Uncertainty-Dependent Extinction of Fear Memory in an Amygdala-mPFC Neural Circuit Model | journal.pcbi.1005099 | null | [
[
"The associative memories acquired through both appetitive and aversive conditioning with uncertainty have been shown to exhibit substantial resistance to extinction , known as the “partial reinforcement extinction effect ( PREE ) ” [1–3] .",
"For example , the fear memory acquired through a fear conditio... | [
"Uncertainty of fear conditioning is crucial for the acquisition and extinction of fear memory .",
"Fear memory acquired through partial pairings of a conditioned stimulus ( CS ) and an unconditioned stimulus ( US ) is more resistant to extinction than that acquired through full pairings; this effect is known as ... | [
"Animals live in environments that contain uncertainty .",
"To adapt to uncertain situations , they flexibly learn to associate environmental cues with rewards and punishments .",
"Understanding how the brain processes uncertainty has remained an important issue in neuroscience .",
"To address this question ,... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"trophozoites",
"medicine and health sciences",
"parasite groups",
"pathology and laboratory medicine",
"enzymes",
"enzymology",
"cloning",
"parasitic protozoans",
"parasitology",
"apicomplexa",
"protozoans",
"signs and symptoms",
"molecular biology techniques",
"research and analysis meth... | Overexpression of Differentially Expressed Genes Identified in Non-pathogenic and Pathogenic Entamoeba histolytica Clones Allow Identification of New Pathogenicity Factors Involved in Amoebic Liver Abscess Formation | journal.ppat.1005853 | null | [
[
"The protozoan parasite Entamoeba histolytica is responsible for approximately 50 million cases of invasive amoebiasis per year , resulting in an annual death toll of 40 , 000–100 , 000 [1] .",
"The parasite life cycle is relatively simple , comprising infectious cysts that can survive outside the host an... | [
"We here compared pathogenic ( p ) and non-pathogenic ( np ) isolates of Entamoeba histolytica to identify molecules involved in the ability of this parasite to induce amoebic liver abscess ( ALA ) -like lesions in two rodent models for the disease .",
"We performed a comprehensive analysis of 12 clones ( A1–A12 ... | [
"The pathogen Entamoeba histolytica can live asymptomatically in the human gut , or it can disrupt the intestinal barrier and induce life-threatening abscesses in different organs , most often in the liver .",
"The molecular framework that enables this invasive , highly pathogenic phenotype is still not well unde... | 2016 |
[
"Introduction",
"Model",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"ocular anatomy",
"social sciences",
"light",
"neuroscience",
"animals",
"electromagnetic radiation",
"animal models",
"drosophila melanogaster",
"model organisms",
"phase diagrams",
"network analysis",
"experimental organism systems",
"ey... | Patterning the insect eye: From stochastic to deterministic mechanisms | journal.pcbi.1006363 | null | [
[
"The development of multicellular animals is highly reproducible , with deterministic and orderly processes generating reliable outcomes .",
"Segment boundaries form in the proper place and cell types are set aside in specific proportions in differentiating tissues .",
"Underlying these seemingly prec... | [
"While most processes in biology are highly deterministic , stochastic mechanisms are sometimes used to increase cellular diversity .",
"In human and Drosophila eyes , photoreceptors sensitive to different wavelengths of light are distributed in stochastic patterns , and one such patterning system has been analyz... | [
"A simple model is able to account for a diversity of photoreceptor patterns in different fly species , ranging from highly deterministic to fully random ."
] | 2018 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"developmental biology",
"cell migration",
"genetics",
"biology",
"morphogenesis",
"gene function"
] | Hepatocyte Growth Factor Signaling in Intrapancreatic Ductal Cells Drives Pancreatic Morphogenesis | journal.pgen.1003650 | null | [
[
"The vertebrate pancreas is an endodermal organ that is part endocrine , releasing hormones that regulate glucose metabolism , and part exocrine , releasing pancreatic juices that aid in digestion .",
"Pancreatic endocrine and exocrine developmental dysmorphogenesis and dysregulation , including diabetes ... | [
"In a forward genetic screen for regulators of pancreas development in zebrafish , we identified donuts908 , a mutant which exhibits failed outgrowth of the exocrine pancreas .",
"The s908 mutation leads to a leucine to arginine substitution in the ectodomain of the hepatocyte growth factor ( HGF ) tyrosine kinas... | [
"The pancreas functions as an endocrine and exocrine gland that secretes hormones regulating blood glucose homeostasis , and pancreatic juice that aids the digestion and absorption of nutrients , respectively .",
"Contrary to endocrine tissue development , that of the exocrine pancreas has received less attention... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"clinical research design",
"virology",
"epidemiology",
"global health",
"neglected tropical diseases",
"biology",
"microbiology",
"viral diseases"
] | Unusual Dengue Virus 3 Epidemic in Nicaragua, 2009 | journal.pntd.0001394 | null | [
[
"Dengue is an increasing public health problem in tropical and sub-tropical regions , with tens of millions of cases estimated to occur annually [1] .",
"The four serotypes of dengue virus ( DENV-1–4 ) , a mosquito-borne Flavivirus , cause a range of clinical manifestations , from undifferentiated illness... | [
"The four dengue virus serotypes ( DENV1–4 ) cause the most prevalent mosquito-borne viral disease affecting humans worldwide .",
"In 2009 , Nicaragua experienced the largest dengue epidemic in over a decade , marked by unusual clinical presentation , as observed in two prospective studies of pediatric dengue in ... | [
"Dengue is the most prevalent mosquito-borne viral disease affecting humans worldwide .",
"The four dengue virus serotypes ( DENV1–4 ) cause Dengue Fever and more severe life-threatening syndromes .",
"In 2009 , Nicaragua experienced the largest dengue epidemic in over a decade .",
"In a hospital-based study ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | TSPO, a Mitochondrial Outer Membrane Protein, Controls Ethanol-Related Behaviors in Drosophila | journal.pgen.1005366 | null | [
[
"Alcohol is one of the most widely used drugs worldwide , but long term consumption leads to its abuse and dependence .",
"An estimated 17 . 6 million adults in the United States have AUDs with associated health concerns of alcohol dependence , liver cirrhosis , cancer , and injuries .",
"From 2006 th... | [
"The heavy consumption of ethanol can lead to alcohol use disorders ( AUDs ) which impact patients , their families , and societies .",
"Yet the genetic and physiological factors that predispose humans to AUDs remain unclear .",
"One hypothesis is that alterations in mitochondrial function modulate neuronal sen... | [
"Alcohol use disorders ( AUDs ) affect millions of patients worldwide and result in high social and economic burdens .",
"Although environmental factors are involved , there are clear genetic components to AUDs .",
"Both the acute sedating effect of alcohol exposure and alcohol tolerance contribute to long term... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota | journal.pcbi.1003388 | null | [
[
"The intestinal microbiota has been receiving much attention lately .",
"Recent studies , propelled by metagenomics and next-generation DNA sequencing technologies , establish novel connections between the intestinal microbial species composition and diseases [1]–[3] .",
"An imbalance in bacterial com... | [
"The intestinal microbiota is a microbial ecosystem of crucial importance to human health .",
"Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections .",
"We present a novel method to in... | [
"Recent advances in DNA sequencing and metagenomics are opening a window into the human microbiome revealing novel associations between certain microbial consortia and disease .",
"However , most of these studies are cross-sectional and lack a mechanistic understanding of this ecosystem's structure and its respon... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"decision making",
"engineering and technology",
"electronics",
"social sciences",
"random variables",
"vertebrates",
"neuroscience",
"covariance",
"animals",
"mammals",
"primates",
"cognitive psychology",
"mathematics",
"cognition",
"vision",
"neuronal tuning",
"monkeys",
"animal ... | Inferring decoding strategies for multiple correlated neural populations | journal.pcbi.1006371 | null | [
[
"Although much is known about how single neurons encode information about stimuli , how neurons contribute to reported percepts is less well understood[1] .",
"The latter , called the “decoding problem” , seeks to identify how the brain uses the information contained in neuronal activity .",
"Although... | [
"Studies of neuron-behaviour correlation and causal manipulation have long been used separately to understand the neural basis of perception .",
"Yet these approaches sometimes lead to drastically conflicting conclusions about the functional role of brain areas .",
"Theories that focus only on choice-related ne... | [
"The neocortex is structurally organized into distinct brain areas .",
"The role of specific brain areas in sensory perception is typically studied using two kinds of laboratory experiments: those that measure correlations between neural activity and reported percepts , and those that inactivate a brain region an... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Spatiotemporal Spike Coding of Behavioral Adaptation in the Dorsal Anterior Cingulate Cortex | journal.pbio.1002222 | The decoding of spike trains from the dorsal Anterior Cingulate Cortex reveals that spike timing is relevant for cognitive information transmission and behavioral prediction, and it suggests that downstream areas are unlikely to act as mere neural integrators. | [
[
"Behavioral adaptation is the process by which animals extract the rules of their environment and learn to respond to cues to increase their chances of survival .",
"The frontal areas of the brain , including the dorsal anterior cingulate cortex ( dACC ) , are involved in driving this process , although t... | [
"The frontal cortex controls behavioral adaptation in environments governed by complex rules .",
"Many studies have established the relevance of firing rate modulation after informative events signaling whether and how to update the behavioral policy .",
"However , whether the spatiotemporal features of these n... | [
"In classical views of how information is processed in the brain , cognitive areas are often thought to encode incoming signals by a simple summation of spikes—action potentials fired by neurons and transmitted along the nerves—elicited by different cues .",
"It is through this summation of spikes that cognitive ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genomics",
"genome expression analysis",
"biology",
"computational biology"
] | Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs | journal.pgen.1003569 | null | [
[
"A large fraction of the human genome consists of intergenic sequence .",
"Once referred to as “junk DNA” , it is now clear that functional elements exist in intergenic regions .",
"In fact , genome wide association studies have revealed that approximately half of all disease and trait-associated geno... | [
"Known protein coding gene exons compose less than 3% of the human genome .",
"The remaining 97% is largely uncharted territory , with only a small fraction characterized .",
"The recent observation of transcription in this intergenic territory has stimulated debate about the extent of intergenic transcription ... | [
"Much of the human genome is composed of intergenic sequence , the regions between genes .",
"Intergenic sequence was once thought to be transcriptionally silent “junk DNA , ” but it has recently become apparent that intergenic regions can be transcribed .",
"However , the scope , nature , and identity of this ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"phosphorylation",
"medicine and health sciences",
"membrane staining",
"epithelial cells",
"cytoplasmic staining",
"molecular motors",
"actin motors",
"sexually transmitted diseases",
"motor proteins",
"research and analysis methods",
"specimen preparation and treatment",
"staining",
"infec... | Neisseria gonorrhoeae infects the human endocervix by activating non-muscle myosin II-mediated epithelial exfoliation | journal.ppat.1006269 | null | [
[
"Microbial pathogens establish infection at the mucosal surface by colonization , disruption , and penetration of the epithelium [1] .",
"The epithelium is the first line of the host defense against microbial pathogens , providing a physical barrier and a sensor of invading pathogens [2 , 3] .",
"In t... | [
"Colonization and disruption of the epithelium is a major infection mechanism of mucosal pathogens .",
"The epithelium counteracts infection by exfoliating damaged cells while maintaining the mucosal barrier function .",
"The sexually transmitted bacterium Neisseria gonorrhoeae ( GC ) infects the female reprodu... | [
"Neisseria gonorrhoeae ( GC ) infects human genital epithelium causing gonorrhea , a common sexually transmitted infection .",
"Gonorrhea is a critical public health issue due to increased prevalence of antibiotic-resistant strains .",
"Because humans are the only host for GC , a lack of a human infection model... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"carbohydrate metabolism",
"medicine and health sciences",
"metabolic networks",
"glucose metabolism",
"metabolites",
"network analysis",
"pharmacology",
"molecular biology techniques",
"drug metabolism",
"research and analysis methods",
"cell labeling",
"computer and information sciences",
... | p13CMFA: Parsimonious 13C metabolic flux analysis | journal.pcbi.1007310 | null | [
[
"Fluxomics is the omics field that analyses metabolic fluxes ( i . e . , reaction and transport rates in living cells ) which are a close reflection of the metabolic phenotype .",
"As such , quantitative tracking of metabolic fluxes is vital for deciphering the regulation mechanisms of metabolic networks ... | [
"Deciphering the mechanisms of regulation of metabolic networks subjected to perturbations , including disease states and drug-induced stress , relies on tracing metabolic fluxes .",
"One of the most informative data to predict metabolic fluxes are 13C based metabolomics , which provide information about how carb... | [
"13C Metabolic Flux Analysis ( 13C MFA ) is a well-established technique that has proven to be a valuable tool in quantifying the metabolic flux profile of central carbon metabolism .",
"When a biological system is incubated with a 13C-labeled substrate , 13C propagates to metabolites throughout the metabolic net... | 2019 |
[
"Introduction",
"Results and discussion",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"immune physiology",
"immunology",
"microbiology",
"vertebrates",
"viral structure",
"animals",
"mammals",
"primates",
"molecular biology techniques",
"antibodies",
"antibody response",
"old world monkeys",
"research and an... | B cell clonal lineage alterations upon recombinant HIV-1 envelope immunization of rhesus macaques | journal.ppat.1007120 | null | [
[
"Following HIV-1 infection , serum neutralizing antibody responses against the evolving autologous viral swarm are generated by the vast majority of infected subjects , usually within the first few months of infection [1–6] .",
"In 10–30% of infected subjects , antibodies capable of neutralizing not only ... | [
"Broadly neutralizing HIV-1 antibodies ( bNAbs ) isolated from infected subjects display protective potential in animal models .",
"Their elicitation by immunization is thus highly desirable .",
"The HIV-1 envelope glycoprotein ( Env ) is the sole viral target of bnAbs , but is also targeted by binding , non-ne... | [
"Broadly neutralizing HIV-1 antibodies ( bNAbs ) display protective potentials against experimental animal infection and thus are believed to be a key component of an effective HIV vaccine .",
"bNAbs are derived from B cells that express B cell receptors formed by specific VH/VL alleles .",
"We report that the ... | 2018 |
[
"Introduction",
"Results",
"Materials and Methods",
"Discussion"
] | [] | Do Brain Networks Evolve by Maximizing Their Information Flow Capacity? | journal.pcbi.1004372 | null | [
[
"A plethora of phenomena in nature can be effectively described by networks .",
"Neuroscientists have used tools for the analysis of complex networks that help realize even more deeply the functionality and structure of the brain .",
"It was found that many aspects of brain network structures are typi... | [
"We propose a working hypothesis supported by numerical simulations that brain networks evolve based on the principle of the maximization of their internal information flow capacity .",
"We find that synchronous behavior and capacity of information flow of the evolved networks reproduce well the same behaviors ob... | [
"The study of the function of the brain is of primordial importance in neuroscience .",
"Several brain models have been studied so far that take into account higher level functions of the external stimulus and the behavioral response attributed to ensembles of neurons of cortical areas .",
"If the brain learns ... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"biology and life sciences",
"infectious disease modeling",
"population modeling",
"computational biology"
] | On the Use of Human Mobility Proxies for Modeling Epidemics | journal.pcbi.1003716 | null | [
[
"One of the biggest challenges that modelers have to face when aiming to understand and reproduce the spatial spread of an infectious disease epidemic is to accurately capture population movements between different locations or regions .",
"In developed countries this task is generally facilitated by the ... | [
"Human mobility is a key component of large-scale spatial-transmission models of infectious diseases .",
"Correctly modeling and quantifying human mobility is critical for improving epidemic control , but may be hindered by data incompleteness or unavailability .",
"Here we explore the opportunity of using prox... | [
"The spatial dissemination of a directly transmitted infectious disease in a population is driven by population movements from one region to another allowing mixing and importation .",
"Public health policy and planning may thus be more accurate if reliable descriptions of population movements can be considered i... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"invertebrates",
"organismal evolution",
"medicine and health sciences",
"pathology and laboratory medicine",
"viral transmission and infection",
"parasite evolution",
"population genetics",
"microbiology",
"animals",
"wolbachia",
"parasitology",
"animal models",
"drosophila melanogaster",
... | Drosophila Adaptation to Viral Infection through Defensive Symbiont Evolution | journal.pgen.1006297 | null | [
[
"Animals and plants live in close association with numerous symbiotic bacteria that often cause strong phenotypic changes in their hosts [1] .",
"For example , defensive symbionts can increase host resistance to pathogens and parasitoids [2–8] .",
"In insects , several defensive symbionts are maternal... | [
"Microbial symbionts can modulate host interactions with biotic and abiotic factors .",
"Such interactions may affect the evolutionary trajectories of both host and symbiont .",
"Wolbachia protects Drosophila melanogaster against several viral infections and the strength of the protection varies between variant... | [
"Animals live in close association with microbial partners that can shape many aspects of their lives .",
"For instance , several insects carry bacteria that defend them against parasites and infectious diseases .",
"The intracellular bacterium Wolbachia protects the fruit fly Drosophila melanogaster against vi... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"metagenomics",
"genetics",
"biology and life sciences",
"genomics",
"computational biology"
] | Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue | journal.pcbi.1003706 | null | [
[
"Metagenomic sequencing of the human microbiome has contributed to our understanding of the microbial communities that live in symbiosis with humans and their genomic capabilities [1] , [2] .",
"The human gut microbiome is associated with a range of metabolic diseases and likely influences our physiology ... | [
"Metagenomic sequencing has contributed important new knowledge about the microbes that live in a symbiotic relationship with humans .",
"With modern sequencing technology it is possible to generate large numbers of sequencing reads from a metagenome but analysis of the data is challenging .",
"Here we present ... | [
"Our bodies are home to a myriad of microbial cells and our intestinal tract is especially densely populated with bacteria .",
"Alterations in the composition of the gut microbiota have been associated with common human diseases .",
"By sequencing the genomes of the microbes , the metagenome , detailed informat... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Material and methods"
] | [
"medicine and health sciences",
"toxins",
"pathology and laboratory medicine",
"endoplasmic reticulum",
"cell processes",
"fungal structure",
"toxic agents",
"toxicology",
"molecular motors",
"actin motors",
"cellular structures and organelles",
"motor proteins",
"cytoskeleton",
"contracti... | The fungal myosin I is essential for Fusarium toxisome formation | journal.ppat.1006827 | null | [
[
"Fusarium head blight ( FHB ) caused predominately by Fusarium graminearum is an economically devastating disease of small grain cereal crops [1] .",
"This disease not only reduces yield and seed quality but also poses a great risk to human and animal health owing to its ability to contaminate grains with... | [
"Myosin-I molecular motors are proposed to function as linkers between membranes and the actin cytoskeleton in several cellular processes , but their role in the biosynthesis of fungal secondary metabolites remain elusive .",
"Here , we found that the myosin I of Fusarium graminearum ( FgMyo1 ) , the causal agent... | [
"The mycotoxin deoxynivalenol ( DON ) is the most frequently detected secondary metabolite produced by Fusarium graminearum and other Fusarium spp .",
"To date , relatively few studies have addressed how mycotoxin biosynthesis occurs in fungal cells .",
"Here we found that myosin I governs translation of DON bi... | 2018 |
[
"Introduction",
"Models and Results",
"Discussion"
] | [] | Tamping Ramping: Algorithmic, Implementational, and Computational Explanations of Phasic Dopamine Signals in the Accumbens | journal.pcbi.1004622 | null | [
[
"In the main class of TD models of the phasic dopamine response [1 , 2 , 16] , the computational goal of learning is to predict from each state s the expected discounted sum V ( s ) of the rewards that will be encountered during a trial",
"V ( s ) = E { γ 0 r t + γ 1 r t + 1 + γ 2 r t + 2 + … | s t = s } ... | [
"Substantial evidence suggests that the phasic activity of dopamine neurons represents reinforcement learning’s temporal difference prediction error .",
"However , recent reports of ramp-like increases in dopamine concentration in the striatum when animals are about to act , or are about to reach rewards , appear... | [
"Dopamine has long been implicated in reward-motivated behaviour .",
"Theory and experiments suggest that activity of dopamine-containing neurons resembles a temporally-sophisticated prediction error used to learn expectations of future reward .",
"This account would appear to be inconsistent with recent observ... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Material and Methods"
] | [
"evolutionary biology/microbial evolution and genomics",
"molecular biology/chromosome structure",
"microbiology/microbial evolution and genomics",
"genetics and genomics/chromosome biology"
] | Segmental Duplications Arise from Pol32-Dependent Repair of Broken Forks through Two Alternative Replication-Based Mechanisms | journal.pgen.1000175 | null | [
[
"In humans , segmental duplications ( SD ) cover up to 5 . 2% of the genome [1] and are responsible for numerous gene-dosage imbalances [2] , gene fusions and disruption events 3 , 4 , 5 .",
"Together with large insertions/deletions , SDs lead to gene copy number variations ( CNVs ) which represent a majo... | [
"The propensity of segmental duplications ( SDs ) to promote genomic instability is of increasing interest since their involvement in numerous human genomic diseases and cancers was revealed .",
"However , the mechanism ( s ) responsible for their appearance remain mostly speculative .",
"Here , we show that in... | [
"Duplications of long segments of chromosomes are frequently observed in multicellular organisms ( ∼5% of our genome , for instance ) .",
"They appear as a fundamental trait of the recent genome evolution in great apes and are often associated with chromosomal instability , capable of increasing genetic polymorph... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/post-translational regulation of gene expression",
"microbiology/cellular microbiology and pathogenesis"
] | Intrinsic Thermal Sensing Controls Proteolysis of Yersinia Virulence Regulator RovA | journal.ppat.1000435 | null | [
[
"Most microbial pathogens occupy different ecological niches inside and outside their mammalian hosts .",
"The temperature shift during entry from the surrounding biosphere or vector reservoirs , where temperature is generally lower than 30°C , into a thermally controlled host environment of 37°C is an im... | [
"Pathogens , which alternate between environmental reservoirs and a mammalian host , frequently use thermal sensing devices to adjust virulence gene expression .",
"Here , we identify the Yersinia virulence regulator RovA as a protein thermometer .",
"Thermal shifts encountered upon host entry lead to a reversi... | [
"Temperature is one of the most crucial environmental signals sensed by pathogens to adjust expression of their virulence factors and host survival programs after entry from a cold external environment into a warm-blooded host .",
"Thermo-induced structural changes in bent or supercoiled DNA or mRNA secondary str... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics",
"biology",
"genomics",
"microbiology",
"genetics and genomics"
] | Transformation of Natural Genetic Variation into Haemophilus Influenzae Genomes | journal.ppat.1002151 | null | [
[
"For many bacteria , natural transformation is the dominant mode of genetic transfer between close relatives .",
"These naturally competent bacterial species can actively take up DNA fragments from their surroundings and incorporate it into their chromosomes by homologous recombination [1]–[3] .",
"Li... | [
"Many bacteria are able to efficiently bind and take up double-stranded DNA fragments , and the resulting natural transformation shapes bacterial genomes , transmits antibiotic resistance , and allows escape from immune surveillance .",
"The genomes of many competent pathogens show evidence of extensive historica... | [
"The ability of bacteria to acquire genetic information from their relatives—called natural competence—poses a major health risk , since recombination between pathogenic bacterial lineages can help bacteria develop resistance to antibiotics and adapt to host defenses .",
"In this study we transformed competent ce... | 2011 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"body fluids",
"chemical compounds",
"monomers",
"carbohydrates",
"animals",
"organic compounds",
"glucose",
"cold hardiness",
"insect vectors",
"polymer chemistry",
"infectious diseases",
"aedes aegypti",
"cryobiology",
"culex quinquefa... | Water-induced strong protection against acute exposure to low subzero temperature of adult Aedes albopictus | journal.pntd.0007139 | null | [
[
"Cold tolerance or cold hardiness , the ability of an insect to survive at low temperature , is important in defining the distribution and survival of insects .",
"There are two different cold hardening in insects at present .",
"One is accomplished by long term ( weeks or months ) cold acclimatizatio... | [
"As an important vector of dengue and Zika , Aedes albopictus has been the fastest spreading invasive mosquitoes in the world over the last 3–4 decades .",
"Cold tolerance is important for survival and expansion of insects .",
"Ae .",
"albopictus adults are generally considered to be cold-intolerant that cann... | [
"Aedes albopictus is one of two most important vectors for dengue and zika .",
"During the last 3–4 decades , this mosquito has spread from native Asian area to all continents except Antarctica , becoming the most invasive mosquitoes which imposed extensive public health threat to human beings throughout the worl... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"medicine and health sciences",
"immune cells",
"vesicles",
"gene regulation",
"immunology",
"phagosomes",
"infectious disease control",
"cellular structures and organelles",
"bacteria",
"small interfering rnas",
"infectious diseases",
"white blood cells",
"animal cells",
... | Alternate splicing of transcripts shape macrophage response to Mycobacterium tuberculosis infection | journal.ppat.1006236 | null | [
[
"Infection of host macrophages with Mycobacterium tuberculosis results in significant alterations in the macrophage physiology .",
"This includes altered regulation of common microbicidal processes like phagosome maturation , autophagy , apoptosis and other innate immune functions [1 , 2] .",
"While t... | [
"Transcriptional reprogramming of macrophages upon Mycobacterium tuberculosis ( Mtb ) infection is widely studied; however , the significance of alternate splicing ( AS ) in shaping cellular responses to mycobacterial infections is not yet appreciated .",
"Alternate splicing can influence transcript stability or ... | [
"Eukaryotic gene expression is a complex process where several intermediary processing steps of transcripts are required before translation can take place .",
"Change in gene expression is a fundamental means through which cells adapt to environmental cues or stimuli like infections .",
"The professional phagoc... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"decision making",
"social sciences",
"neuroscience",
"cognitive neuroscience",
"cognitive psychology",
"human performance",
"cognition",
"behavior",
"consciousness",
"pain",
"psychology",
"pain management",
"motivation",
"psychophysics",
"biology and li... | How the Brain Decides When to Work and When to Rest: Dissociation of Implicit-Reactive from Explicit-Predictive Computational Processes | journal.pcbi.1003584 | null | [
[
"Suppose that you are given a job whose payoff is proportional to the effort made within a limited time , say for instance the number of Christmas cards sold at the end of the day .",
"Maximizing your payoff would require running from house to house , but this effort would induce such fatigue that you dec... | [
"A pervasive case of cost-benefit problem is how to allocate effort over time , i . e . deciding when to work and when to rest .",
"An economic decision perspective would suggest that duration of effort is determined beforehand , depending on expected costs and benefits .",
"However , the literature on exercise... | [
"Imagine that ahead of you is a long time of work: when will you take a break ?",
"This sort of issue – how to allocate effort over time – has been addressed by distinct theoretical fields , with different emphasis on reactive and predictive processes .",
"An intuitive view is that you start working , stop when... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"invertebrates",
"animal types",
"moths and butterflies",
"artificial selection",
"domestic animals",
"animals",
"invertebrate genomics",
"silkworms",
"zoology",
"nutrient and storage proteins",
"proteins",
"insects",
"animal genomics",
"arthropoda",
"biochemistry",
"eukaryota",
"gen... | Artificial selection on storage protein 1 possibly contributes to increase of hatchability during silkworm domestication | journal.pgen.1007616 | null | [
[
"The silkworm , Bombyx mori , is the only fully domesticated insect species , originating from its wild ancestor , B . mandarina , approximately 5000 years ago .",
"During the domestication process , the domestic silkworm evolved rapidly under human-preferred selection .",
"Deciphering the way in whic... | [
"Like other domesticates , the efficient utilization of nitrogen resources is also important for the only fully domesticated insect , the silkworm .",
"Deciphering the way in which artificial selection acts on the silkworm genome to improve the utilization of nitrogen resources and to advance human-favored domest... | [
"Like other domesticates , nitrogen resources are also important for the only fully domesticated insect , the silkworm .",
"Deciphering the way in which artificial selection acts on the silkworm genome to improve the utilization of nitrogen resources , thereby advancing human-favored domestication traits , will p... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Material and Methods"
] | [
"vertebrates",
"mice",
"animals",
"mammals",
"primates",
"analysis of variance",
"amphibians",
"mathematics",
"statistics (mathematics)",
"genome analysis",
"mammalian genomics",
"research and analysis methods",
"mathematical and statistical techniques",
"gene expression",
"statistical m... | Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs | journal.pcbi.1005274 | null | [
[
"The ortholog conjecture is widely used to transfer annotation among genes , for example in newly sequenced genomes .",
"But has been difficult to establish whether and how much orthologs share more similar functions than paralogs [1 , 2] .",
"The most widely accepted model is that orthologs diverge s... | [
"The ortholog conjecture implies that functional similarity between orthologous genes is higher than between paralogs .",
"It has been supported using levels of expression and Gene Ontology term analysis , although the evidence was rather weak and there were also conflicting reports .",
"In this study on 12 spe... | [
"From specific examples , it has been assumed by comparative biologists that the same gene in different species has the same function , whereas duplication of a gene inside one species to create several copies allows them to acquire different functions .",
"Yet this model was little tested until recently , and th... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"blood cells",
"fluorescence imaging",
"medicine and health sciences",
"immune cells",
"immunology",
"light microscopy",
"bacterial diseases",
"developmental biology",
"microscopy",
"embryos",
"neutrophils",
"research and analysis methods",
"embryology",
"infectious diseases",
"white blo... | Neutrophils use superoxide to control bacterial infection at a distance | journal.ppat.1007157 | null | [
[
"The innate immune system is the first line of defence of the host .",
"It includes large phagocytes ( such as macrophages and granulocytes ) equipped with a battery of weapons to destroy the invader within minutes or hours .",
"Since the seminal work of Elie Metchnikoff [1] , the defence mechanisms r... | [
"Understanding the roles of neutrophils and macrophages in fighting bacterial infections is a critical issue in human pathologies .",
"Although phagocytic killing has been extensively studied , little is known about how bacteria are eliminated extracellularly in live vertebrates .",
"We have recently developed ... | [
"Deciphering the defence mechanisms of leukocytes remains a challenge for public health .",
"Although phagocytic killing has been extensively studied , little is known about how bacteria are eliminated extracellularly in live vertebrates .",
"Herein we use the notochord infection model in the zebrafish embryo t... | 2018 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"invertebrates",
"livestock",
"medicine and health sciences",
"plagues",
"pathology and laboratory medicine",
"ruminants",
"pathogens",
"microbiology",
"vertebrates",
"genomic library construction",
"animals",
"mammals",
"ethnicities",
"bacterial diseases",
"yersinia",
"fleas",
"dna ... | Human plague associated with Tibetan sheep originates in marmots | journal.pntd.0006635 | null | [
[
"Plague is an acute infectious disease caused by Yersinia pestis that killed millions of people in Europe in the 14th century and tens of thousands in China in the 19th century [1] .",
"Plague is mainly a disease of wild rodents , and their parasitic fleas are considered the transmitting vectors .",
"... | [
"The Qinghai-Tibet plateau is a natural plague focus and is the largest such focus in China .",
"In this area , while Marmota himalayana is the primary host , a total of 18 human plague outbreaks associated with Tibetan sheep ( 78 cases with 47 deaths ) have been reported on the Qinghai-Tibet plateau since 1956 .... | [
"Plague is mainly a disease of wild rodents , and their parasitic fleas are considered the transmitting vectors .",
"However , human plague originating from Ovis aries ( Tibetan sheep ) is found in the Qinghai-Tibet plateau in China , where Marmota .",
"himalayana is the primary plague host .",
"Tibetan sheep... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"ecology"
] | Assessing Evidence for a Pervasive Alteration in Tropical Tree Communities | journal.pbio.0060045 | An analysis of changes in biomass and primary productivity across ten large tropical forest plots revealed that aboveground biomass increased significantly, fast-growing species increased significantly in dominance at a single site, and slow-growing species increased significantly at half of our sites. | [
[
"Tropical rain forests play a major role in the global carbon cycle: they encompass over a third of terrestrial carbon stocks [1] , and they contribute approximately 30% of terrestrial net primary productivity [2] .",
"Not only are many tropical forests under direct threat from land-use changes and loggin... | [
"In Amazonian tropical forests , recent studies have reported increases in aboveground biomass and in primary productivity , as well as shifts in plant species composition favouring fast-growing species over slow-growing ones .",
"This pervasive alteration of mature tropical forests was attributed to global envir... | [
"Recent studies have reported major changes in mature tropical forests , with increases in both forest biomass and net primary productivity , as well as shifts in plant species composition that favour fast-growing species over slow-growing ones .",
"These pervasive alterations were attributed to global environmen... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"hiv",
"medicine",
"infectious diseases",
"viral diseases"
] | Blocking TLR7- and TLR9-mediated IFN-α Production by Plasmacytoid Dendritic Cells Does Not Diminish Immune Activation in Early SIV Infection | journal.ppat.1003530 | null | [
[
"Chronic immune activation is a driving factor in CD4+ T cell loss and disease progression in HIV-infected individuals , yet the mechanisms responsible for this process are not completely understood [1] .",
"Recent comparative studies in nonhuman primate models have shed light on the etiology of chronic i... | [
"Persistent production of type I interferon ( IFN ) by activated plasmacytoid dendritic cells ( pDC ) is a leading model to explain chronic immune activation in human immunodeficiency virus ( HIV ) infection but direct evidence for this is lacking .",
"We used a dual antagonist of Toll-like receptor ( TLR ) 7 and... | [
"A persistent type I interferon ( IFN ) response is thought to be important in driving immune activation and progression to AIDS in human immunodeficiency virus ( HIV ) -infected individuals .",
"Plasmacytoid dendritic cells ( pDC ) produce copious amounts of type I IFN upon virus exposure through engagement of T... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Neonatal Restriction of Tactile Inputs Leads to Long-Lasting Impairments of Cross-Modal Processing | journal.pbio.1002304 | Reducing unisensory experience during neonatal development causes permanent disruption of connectivity between primary sensory cortices, resulting in impaired multisensory abilities. | [
[
"Most environmental events provide inputs to multiple senses that need to be integrated into a unified percept .",
"Multisensory interactions have been observed both in higher-order brain regions and in primary sensory cortices [1–4] .",
"Exposure to cross-modal stimuli has been shown to modulate the ... | [
"Optimal behavior relies on the combination of inputs from multiple senses through complex interactions within neocortical networks .",
"The ontogeny of this multisensory interplay is still unknown .",
"Here , we identify critical factors that control the development of visual-tactile processing by combining in... | [
"Our senses , working together , enable us to interact with the environment .",
"To obtain a unified percept of the world , diverse sensory inputs need to be bound together within distributed but strongly interconnected neuronal networks .",
"Many multisensory abilities emerge or mature late in life , long afte... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public health and epidemiology/global health",
"public health and epidemiology/infectious diseases"
] | National Mass Drug Administration Costs for Lymphatic Filariasis Elimination | journal.pntd.0000067 | null | [
[
"Lymphatic filariasis ( LF ) , commonly known as elephantiasis , is a profoundly disfiguring parasitic disease caused by thread-like nematode worms .",
"The World Health Organization ( WHO ) places the number of people at risk in 83 countries at 1 . 307 billion . [1]",
"Globally , the reduced producti... | [
"Because lymphatic filariasis ( LF ) elimination efforts are hampered by a dearth of economic information about the cost of mass drug administration ( MDA ) programs ( using either albendazole with diethylcarbamazine [DEC] or albendazole with ivermectin ) , a multicenter study was undertaken to determine the costs ... | [
"Lymphatic filariasis ( LF ) , commonly known as elephantiasis , is a profoundly disfiguring parasitic disease caused by thread-like nematode worms .",
"This disease can often be disabling , thus reducing the potential productivity of the affected individuals .",
"The WHO places the number of people at risk in ... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology and life sciences",
"medicine and health sciences"
] | Rgs6 is Required for Adult Maintenance of Dopaminergic Neurons in the Ventral Substantia Nigra | journal.pgen.1004863 | null | [
[
"Parkinson disease ( PD ) is characterised by the progressive loss of midbrain dopaminergic ( mDA ) neurons [1] .",
"Although the clinical manifestations of PD can be variable , the appearance of motor deficits is the hallmark of this neurodegenerative disease .",
"Similarly , the etiology of PD appea... | [
"Parkinson disease ( PD ) is characterized by the preferential , but poorly understood , vulnerability to degeneration of midbrain dopaminergic ( mDA ) neurons in the ventral substantia nigra compacta ( vSNc ) .",
"These sensitive mDA neurons express Pitx3 , a transcription factor that is critical for their survi... | [
"The locomotor deficits associated with Parkinson disease result from the death of a specific subset of dopamine neurons in the ventral part of the midbrain .",
"The reason for the greater sensitivity to degeneration of those , relative to other , neurons is not clear .",
"Prior work showed that the Pitx3 trans... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"dermatology/skin cancers, including melanoma and lymphoma",
"oncology/skin cancers",
"virology/viruses and cancer",
"virology/emerging viral diseases"
] | Distinct Merkel Cell Polyomavirus Molecular Features in Tumour and Non Tumour Specimens from Patients with Merkel Cell Carcinoma | journal.ppat.1001076 | null | [
[
"Polyomaviruses are small , non enveloped double stranded DNA viruses which infect many species with a restricted host range .",
"The initial discovery of Murine polyomavirus ( MPyV ) and Simian vacuolating 40 ( SV40 ) was closely linked to the demonstration of their experimental tumorigenic properties [1... | [
"Merkel Cell Polyomavirus ( MCPyV ) is associated with Merkel Cell carcinoma ( MCC ) , a rare , aggressive skin cancer with neuroendocrine features .",
"The causal role of MCPyV is highly suggested by monoclonal integration of its genome and expression of the viral large T ( LT ) antigen in MCC cells .",
"We in... | [
"Merkel cell polyomavirus ( MCPyV ) is a recently discovered virus highly associated with a rare skin cancer , Merkel cell carcinoma ( MCC ) .",
"The causal role of MCPyV in cancer is suggested by integration of viral sequences into the cell genome and by a specific molecular signature .",
"We looked for and co... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"oncology",
"systems biology",
"medicine",
"public health and epidemiology",
"genomics",
"epidemiology",
"genetics",
"biology",
"computational biology",
"genetics and genomics",
"clinical genetics"
] | Rare Copy Number Variants Observed in Hereditary Breast Cancer Cases Disrupt Genes in Estrogen Signaling and TP53 Tumor Suppression Network | journal.pgen.1002734 | null | [
[
"Breast cancer is the most common malignancy affecting women .",
"It is a complex disease with a well-established genetic component [1]; however , most of the familial and young breast cancer cases still remain unexplained by inherited mutations in the known susceptibility genes [2] .",
"Multiple geno... | [
"Breast cancer is the most common cancer in women in developed countries , and the contribution of genetic susceptibility to breast cancer development has been well-recognized .",
"However , a great proportion of these hereditary predisposing factors still remain unidentified .",
"To examine the contribution of... | [
"Although genetic susceptibility to breast cancer has been well-established , the majority of the predisposing factors still remain unidentified .",
"Here , we have taken advantage of recent technical and methodological advances to examine the role of a new class of genomic variation , rare copy number variants (... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"learning",
"ecology and environmental sciences",
"neural networks",
"community structure",
"signaling networks",
"social sciences",
"teachers",
"neuroscience",
"learning and memory",
"cognitive psychology",
"recurrent neural networks",
"network analysis",
"cellular structures and organelles... | Interactive reservoir computing for chunking information streams | journal.pcbi.1006400 | null | [
[
"When a sequence of stimuli is repeated , they may be segmented into “chunks , ” which are then processed and stored as discrete units .",
"This process , called “chunking” or \"bracketing\" [1] , takes place during various cognitive behaviors that require hierarchical sequence processing [2–5] .",
"F... | [
"Chunking is the process by which frequently repeated segments of temporal inputs are concatenated into single units that are easy to process .",
"Such a process is fundamental to time-series analysis in biological and artificial information processing systems .",
"The brain efficiently acquires chunks from var... | [
"Varieties of information processing require chunking , but chunking arbitrary complex sequences as flexibly as the brain does remains a challenge .",
"In this study , we solved this important but difficult problem of chunking by \"reservoir computing\" inferred from brain computation .",
"In the method , chunk... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"microbial mutation",
"medicine and health sciences",
"immune cells",
"microbiome",
"antigen-presenting cells",
"immunology",
"microbiology",
"cancers and neoplasms",
"wnt signaling cascade",
"oncology",
"mutation",
"mathematics",
"forecasting",
"statistics (mathematics)",
"mutation data... | Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment | journal.pgen.1007376 | null | [
[
"The human gut is host to approximately a thousand different microbial species consisting of both commensal and potentially pathogenic members[1] .",
"In the context of colorectal cancer ( CRC ) , it is clear that bacteria in the microbiome play a role in human cell signaling[2–11]; for example , in the c... | [
"Variation in the gut microbiome has been linked to colorectal cancer ( CRC ) , as well as to host genetic variation .",
"However , we do not know whether , in addition to baseline host genetics , somatic mutational profiles in CRC tumors interact with the surrounding tumor microbiome , and if so , whether these ... | [
"Although the gut microbiome—the collection of microorganisms that inhabit our gastrointestinal tract—has been implicated in colorectal cancer , colorectal tumors are caused by genetic mutations in host DNA .",
"Here , we explored whether various mutations in colorectal tumors are correlated with specific changes... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"infectious diseases",
"avian influenza a viruses",
"zoonoses",
"rna viruses",
"viral immune evasion",
"immunity",
"virology",
"innate immunity",
"viral classification",
"biology",
"microbiology"
] | Species-Specific Inhibition of RIG-I Ubiquitination and IFN Induction by the Influenza A Virus NS1 Protein | journal.ppat.1003059 | null | [
[
"Influenza A viruses ( IAVs ) are highly infectious pathogens that have caused major pandemics and annual epidemics with serious economic and health consequences [1] , [2] .",
"IAVs are naturally maintained in avian species but they also circulate in humans , horses , dogs and pigs [3] .",
"Although m... | [
"Influenza A viruses can adapt to new host species , leading to the emergence of novel pathogenic strains .",
"There is evidence that highly pathogenic viruses encode for non-structural 1 ( NS1 ) proteins that are more efficient in suppressing the host immune response .",
"The NS1 protein inhibits type-I interf... | [
"Influenza viruses cause annual epidemics and occasionally , major global pandemics .",
"To establish productive infection these viruses have mechanisms to evade host immune responses , including the type-I interferon ( IFN ) response .",
"An important component of the IFN system is the helicase RIG-I that reco... | 2012 |
[
"Introduction",
"Model of CML dynamics",
"Treatment optimization problem",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"cancer treatment",
"cell differentiation",
"toxicology",
"oncology",
"optimization",
"toxicity",
"developmental biology",
"mathematics",
"pharmaceutics",
"stem cells",
"animal cells",
"stem cell therapy",
"differential... | Optimized Treatment Schedules for Chronic Myeloid Leukemia | journal.pcbi.1005129 | null | [
[
"Chronic Myeloid Leukemia ( CML ) is an acquired hematopoietic stem cell disorder leading to the over-proliferation of myeloid cells and an increase in cellular output from the bone marrow that is often associated with splenomegaly .",
"The most common driving mutation in CML is a translocation between ch... | [
"Over the past decade , several targeted therapies ( e . g . imatinib , dasatinib , nilotinib ) have been developed to treat Chronic Myeloid Leukemia ( CML ) .",
"Despite an initial response to therapy , drug resistance remains a problem for some CML patients .",
"Recent studies have shown that resistance mutat... | [
"Targeted therapy using imatinib , nilotinib or dasatinib has become standard treatment for chronicle myeloid leukemia .",
"A minority of patients , however , fail to respond to treatment or relapse due to drug resistance .",
"One primary driving factor of drug resistance are point mutations within the driving ... | 2016 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"infectious diseases",
"computer and information sciences",
"medicine and health sciences",
"veterinary diseases",
"livestock",
"pathology and laboratory medicine",
"simulation and modeling",
"agriculture",
"infectious disease epidemiology",
"epidemiology",
"network analysis",
"disease dynamic... | Network analyses to quantify effects of host movement in multilevel disease transmission models using foot and mouth disease in Cameroon as a case study | journal.pcbi.1007184 | null | [
[
"Host movement influences disease dynamics [1–3] .",
"In situations where the population size is too small to sustain long-term chains of transmission , movement of infected hosts can spark local outbreaks and increase incidence counts .",
"Alternatively , migration of susceptible hosts away from outb... | [
"The dynamics of infectious diseases are greatly influenced by the movement of both susceptible and infected hosts .",
"To accurately represent disease dynamics among a mobile host population , detailed movement models have been coupled with disease transmission models .",
"However , a number of different host ... | [
"Epidemics of infectious disease vary geographically and vary through time .",
"A large part of this variation is caused by movement of individuals who are susceptible to the disease or infected with the disease .",
"To study how movement affects epidemics , researchers often combine movement models with transm... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Methods and Materials"
] | [
"bacteriology",
"complement system",
"medicine and health sciences",
"immune physiology",
"enzyme-linked immunoassays",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"bacillus",
"microbiology",
"antibodies",
"immunologic techniques",
"bacteria",
"bacterial pathogens",
"... | Bacillus anthracis Spore Surface Protein BclA Mediates Complement Factor H Binding to Spores and Promotes Spore Persistence | journal.ppat.1005678 | null | [
[
"Persistent colonization of the host by microbial pathogens can cause chronic infections , which are often difficult to treat with conventional antibiotics .",
"It is recognized that persistent infection is a unique phase often involving specific virulence factors and pathogenic mechanisms [1] .",
"Id... | [
"Spores of Bacillus anthracis , the causative agent of anthrax , are known to persist in the host lungs for prolonged periods of time , however the underlying mechanism is poorly understood .",
"In this study , we demonstrated that BclA , a major surface protein of B . anthracis spores , mediated direct binding o... | [
"We discovered an immune modulatory mechanism of Bacillus anthracis mediated by the spore surface protein BclA .",
"We showed for the first time that BclA mediated the binding of complement factor H , a major negative regulator of complement , to the surface of spores .",
"The binding led to the down-regulation... | 2016 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"electroporation",
"neural networks",
"nervous system",
"neuroscience",
"synaptic plasticity",
"computational neuroscience",
"research and analysis methods",
"circuit models",
"specimen preparation and treatment",
"spinal cord",
"developmental neuroscience",
"biophysics",
"neural circuit for... | From Spontaneous Motor Activity to Coordinated Behaviour: A Developmental Model | journal.pcbi.1003653 | null | [
[
"In mammals , the developmental path that links the rudimentary behaviours observed during foetal stages to the full fledged behaviours observed in adults is still beyond our understanding [1] .",
"We observe foetus generate spontaneous motor activity [2] , [3] , we observe newborns react reflexively to e... | [
"In mammals , the developmental path that links the primary behaviours observed during foetal stages to the full fledged behaviours observed in adults is still beyond our understanding .",
"Often theories of motor control try to deal with the process of incremental learning in an abstract and modular way without ... | [
"Mammals display a fascinating behavioural proficiency , which is a remarkable feature given the number of muscles that need to be continuously coordinated .",
"Understanding the processes that give rise to this level of performance has been the main focus of many researchers during the last century , but until n... | 2014 |
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