headings list | keywords list | title stringlengths 20 281 | id stringlengths 20 20 | toc stringlengths 57 522 ⌀ | sections list | abstract list | summary list | year stringclasses 13
values |
|---|---|---|---|---|---|---|---|---|
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Preferential Binding to Elk-1 by SLE-Associated IL10 Risk Allele Upregulates IL10 Expression | journal.pgen.1003870 | null | [
[
"The gene cluster that includes interleukin 10 ( IL10 ) , IL19 , IL20 and IL24 is located on chromosome 1q31-32 , a genomic region that is linked with susceptibility to systemic lupus erythematosus ( SLE , OMIM 152700 ) [1] , [2] .",
"Recent genome-wide association ( GWA ) and follow-up replication studie... | [
"Immunoregulatory cytokine interleukin-10 ( IL-10 ) is elevated in sera from patients with systemic lupus erythematosus ( SLE ) correlating with disease activity .",
"The established association of IL10 with SLE and other autoimmune diseases led us to fine map causal variant ( s ) and to explore underlying mechan... | [
"Systemic lupus erythematosus ( SLE ) , a debilitating autoimmune disease characterized by the production of pathogenic autoantibodies , has a strong genetic basis .",
"Variants of the IL10 gene , which encodes cytokine interleukin-10 ( IL-10 ) with known function of promoting B cell hyperactivity and autoantibod... | 2013 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"bacteriology",
"antimicrobials",
"gram positive bacteria",
"gram negative bacteria",
"invertebrates",
"medicine and health sciences",
"pathology and laboratory medicine",
"pathogens",
"drugs",
"microbiology",
"animals",
"staphylococcus aureus",
"methicillin-resistant staphylococcus aureus",... | Secondary bacterial infections and antibiotic resistance among tungiasis patients in Western, Kenya | journal.pntd.0005901 | null | [
[
"Tungiasis is a parasitic disease caused by the sand flea Tunga penetrans [1] .",
"The fleas can infest any part of the body .",
"However majority of the cases occur on the feet [2] .",
"Children and the elderly bear the brunt of the infection in endemic areas [3] , [4] .",
"During the transmi... | [
"Tungiasis or jigger infestation is a parasitic disease caused by the female sand flea Tunga penetrans .",
"Secondary infection of the lesions caused by this flea is common in endemic communities .",
"This study sought to shed light on the bacterial pathogens causing secondary infections in tungiasis lesions an... | [
"Secondary bacterial infection of tungiaisis lesions is a threat to jigger infested patients .",
"Once the flea penetrates the skin , it leaves an opening on the skin through which it lays eggs , defecates and breathes throughout it’s life cycle on the host .",
"At the same time , it feeds on the host’s blood h... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Gastrointestinal Infections and Diarrheal Disease in Ghanaian Infants and Children: An Outpatient Case-Control Study | journal.pntd.0003568 | null | [
[
"Diarrheal diseases are the second leading cause of childhood mortality worldwide .",
"In 2010 , diarrhea was responsible for 0 . 8 million deaths of children below the age of five years , accounting for 10 . 5% of all deaths within that age group [1] .",
"Mortality and morbidity patterns differ acros... | [
"Diarrheal diseases are among the most frequent causes of morbidity and mortality in children worldwide , especially in resource-poor areas .",
"This case-control study assessed the associations between gastrointestinal infections and diarrhea in children from rural Ghana .",
"Stool samples were collected from ... | [
"Gastrointestinal infections are frequent in many low-income countries .",
"However , their role in diarrheal diseases is still under discussion .",
"Many epidemiological studies focus on individuals with diarrheal symptoms only , ignoring the fact that infections may progress asymptomatically as well .",
"In... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Contribution of the Two Genes Encoding Histone Variant H3.3 to Viability and Fertility in Mice | journal.pgen.1004964 | null | [
[
"The core histones H2A , H2B , H3 and H4 , package DNA into nucleosomes and modify higher-order chromatin structure .",
"H3 in mammals is represented by three near-identical 135 amino acid isoforms: canonical H3 . 1 and H3 . 2 , and the variant H3 . 3 .",
"Chromatin incorporation is replication-couple... | [
"Histones package DNA and regulate epigenetic states .",
"For the latter , probably the most important histone is H3 .",
"Mammals have three near-identical H3 isoforms: canonical H3 . 1 and H3 . 2 , and the replication-independent variant H3 . 3 .",
"This variant can accumulate in slowly dividing somatic cell... | [
"Histones package DNA and regulate chromosome activity .",
"Histone H3 is particularly important in this regard .",
"The H3 . 3 isoform is unique , among H3 histones , in being able to incorporate into chromosomes independent of DNA replication .",
"Thus , in slowly- or non-dividing somatic cells , H3 . 3 his... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"spiking dynamics",
"schizophrenia",
"attractor networks",
"neuroscience",
"homo (human)",
"neuronal networks"
] | A Dynamical Systems Hypothesis of Schizophrenia | journal.pcbi.0030228 | null | [
[
"Schizophrenia is a major mental illness , which has a great impact on patients and their environment .",
"One of the difficulties in proposing models for schizophrenia is the complexity and heterogeneity of the illness .",
"We propose that part of the reason for the inconsistent symptoms may be a red... | [
"We propose a top-down approach to the symptoms of schizophrenia based on a statistical dynamical framework .",
"We show that a reduced depth in the basins of attraction of cortical attractor states destabilizes the activity at the network level due to the constant statistical fluctuations caused by the stochasti... | [
"One of the hallmarks of schizophrenia is the complexity and heterogeneity of the illness .",
"We propose that part of the reason for the inconsistent symptoms may be a reduced signal-to-noise ratio and increased statistical fluctuations in different cortical brain networks .",
"The novelty of the approach desc... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"cell biology",
"biology and life sciences",
"proteomics",
"microbiology",
"molecular cell biology"
] | A Genome-Wide Tethering Screen Reveals Novel Potential Post-Transcriptional Regulators in Trypanosoma brucei | journal.ppat.1004178 | null | [
[
"Kinetoplastid protists are exposed to environmental challenges in the host and vector , necessitating extensive changes in gene expression .",
"In kinetoplastids , most protein-coding genes are transcribed by RNA polymerase II in unidirectional clusters .",
"Individual mRNAs are excised by 5′ trans s... | [
"In trypanosomatids , gene expression is regulated mainly by post-transcriptional mechanisms , which affect mRNA processing , translation and degradation .",
"Currently , our understanding of factors that regulate either mRNA stability or translation is rather limited .",
"We know that often , the regulators ar... | [
"Survival and adaptation of trypanosomatids to new surroundings requires activation of specific gene networks .",
"This is mainly achieved by post-transcriptional mechanisms , and proteins that bind to specific mRNAs , and influence degradation or translation , are known to be important .",
"However , only few ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"systems biology",
"rna",
"cellular stress responses",
"model organisms",
"molecular cell biology",
"rna processing",
"nucleic acids",
"gene regulation",
"genetics",
"gene expression",
"molecular genetics",
"population genetics",
"biology",
"yeast and fungal models",
"saccharomyces cerev... | A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool | journal.pgen.1004084 | null | [
[
"Messenger RNA translation is a central molecular process in any living cell and is among the most complicated and highly regulated of cellular processes [1] , [2] .",
"The tRNA pool is a fundamental component in that process , serving as the physical link between the nucleotide sequence of mRNAs and the ... | [
"Deciphering the architecture of the tRNA pool is a prime challenge in translation research , as tRNAs govern the efficiency and accuracy of the process .",
"Towards this challenge , we created a systematic tRNA deletion library in Saccharomyces cerevisiae , aimed at dissecting the specific contribution of each t... | [
"Transfer RNAs are an important component of the translation machinery .",
"Despite extensive biochemical investigations , a systems-level investigation of tRNAs' functional roles in physiology , and genetic interactions among them , is lacking .",
"We created a comprehensive tRNA deletion library in yeast and ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"swimming",
"medicine and health sciences",
"brain",
"vertebrates",
"mice",
"neuroscience",
"habits",
"mammals",
"animals",
"biological locomotion",
"animal behavior",
"zoology",
"neuronal dendrites",
"animal cells",
"behavior",
"neostriatum",
"amygdala",
"rodents",
"cellular neu... | Regulation of actions and habits by ventral hippocampal trkB and adolescent corticosteroid exposure | journal.pbio.2003000 | null | [
[
"Goal-directed actions are defined as behaviors directed towards achieving a specific outcome .",
"By contrast , habits are stimulus elicited and insensitive to action–outcome relationships .",
"Individuals who experience early-life stress have an increased incidence of behaviors that can lead to addi... | [
"In humans and rodents , stress promotes habit-based behaviors that can interfere with action–outcome decision-making .",
"Further , developmental stressor exposure confers long-term habit biases across rodent–primate species .",
"Despite these homologies , mechanisms remain unclear .",
"We first report that ... | [
"Stress can impair the ability of individuals to select actions based on their consequences , promoting instead the acquisition of habits—automatic behaviors that are insensitive to action–outcome relationships .",
"Stress in adolescence can have particularly long-lasting consequences , affecting behavior and moo... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"dermatology",
"medicine and health sciences",
"demography",
"tropical diseases",
"geographical locations",
"health care",
"treponematoses",
"bacterial diseases",
"health care providers",
"skin infections",
"global health",
"neglected tropical diseases",
"africa",
"skin diseases",
"publi... | Knowledge, attitudes and practices towards yaws and yaws-like skin disease in Ghana | journal.pntd.0005820 | null | [
[
"Yaws , caused by Treponema pallidum subsp .",
"pertenue , is endemic in Ghana .",
"The disease is reported in all districts but predominantly in the south of the country .",
"The majority of clinical disease is seen in young children , with the organism being transmitted by skin to skin contact w... | [
"Yaws is endemic in Ghana .",
"The World Health Organization ( WHO ) has launched a new global eradication campaign based on total community mass treatment with azithromycin .",
"Achieving high coverage of mass treatment will be fundamental to the success of this new strategy; coverage is dependent , in part , ... | [
"Yaws , a bacterial skin infection , is endemic in Ghana .",
"WHO has launched a campaign to eradicate yaws based on community mass treatment with the antibiotic azithromycin .",
"Community perceptions of disease are an important contributor to participation in mass treatment interventions .",
"This study use... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"carbohydrate metabolism",
"invertebrates",
"gene regulation",
"glucose metabolism",
"animals",
"dna transcription",
"animal models",
"drosophila melanogaster",
"model organisms",
"experimental organism systems",
"chronobiology",
"molecular biology techniques",
"epigenetics",
"chromatin",
... | Genome-wide discovery of the daily transcriptome, DNA regulatory elements and transcription factor occupancy in the monarch butterfly brain | journal.pgen.1008265 | null | [
[
"Organisms have evolved daily and seasonal rhythms in behavior , physiology and metabolism that are driven by biological clocks to adapt to a temporally dynamic environment .",
"The Eastern North American migratory monarch butterfly , Danaus plexippus , has emerged as a new system to study circadian clock... | [
"The Eastern North American monarch butterfly , Danaus plexippus , is famous for its spectacular seasonal long-distance migration .",
"In recent years , it has also emerged as a novel system to study how animal circadian clocks keep track of time and regulate ecologically relevant daily rhythmic activities and se... | [
"With a rich biology that includes a clock-regulated migratory behavior and a circadian clock possessing mammalian clock orthologues , the monarch butterfly is an unconventional system with broad appeal to study circadian and seasonal rhythms .",
"While clockwork mechanisms and rhythmic behavioral outputs have be... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"clinical research design",
"population dynamics",
"immunology",
"tropical diseases",
"census",
"vaccines",
"preventive medicine",
"bacterial diseases",
"research design",
"global health",
"neglected tropical diseases",
"population biology",
"infectious dise... | Highly targeted cholera vaccination campaigns in urban setting are feasible: The experience in Kalemie, Democratic Republic of Congo | journal.pntd.0006369 | null | [
[
"Cholera is endemic [1] in several countries in Africa and Asia [2 , 3] and can also cause large national wide epidemics , often involving several countries [4 , 5] .",
"The World Health Organization ( WHO ) with financial support from GAVI , the Vaccine Alliance , has established an oral cholera vaccine ... | [
"Oral cholera vaccines are primarily recommended by the World Health Organization for cholera control in endemic countries .",
"However , the number of cholera vaccines currently produced is very limited and examples of OCV use in endemic countries , and especially in urban settings , are scarce .",
"A vaccinat... | [
"The oral cholera vaccine , Shanchol , has already been shown as an effective tool in controlling a cholera outbreak .",
"The limited amount of doses , concurrently with the logistic constraints associated with a targeted vaccination campaign are serious difficulties to tackle in order to organize a vaccination c... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"infectious diseases",
"cell biology",
"yeast and fungi",
"microbiology"
] | Als3 Is a Candida albicans Invasin That Binds to Cadherins and Induces Endocytosis by Host Cells | journal.pbio.0050064 | Als3 aids the invasion of the fungal pathogenCandida albicans into human host cells by mimicking human cadherins to induce endocytosis. | [
[
"The fungus Candida albicans causes both hematogenously disseminated and oropharyngeal disease .",
"During the initiation of hematogenously disseminated candidiasis , blood-borne organisms invade the endothelial cell lining of the vasculature to infect deeper tissues .",
"Fungal invasion of the superf... | [
"Candida albicans is the most common cause of hematogenously disseminated and oropharyngeal candidiasis .",
"Both of these diseases are characterized by fungal invasion of host cells .",
"Previously , we have found that C . albicans hyphae invade endothelial cells and oral epithelial cells in vitro by inducing ... | [
"The fungus Candida albicans is usually a harmless colonizer of human mucosal surfaces .",
"In the mouth , it can cause oropharyngeal candidiasis , also called thrush .",
"In hospitalized and immunocompromised patients , C . albicans can enter the blood stream and be carried throughout the body to cause a disse... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"hepatitis c",
"medicine",
"infectious diseases",
"infectious hepatitis",
"hepatitis",
"gastroenterology and hepatology",
"viral diseases",
"infectious disease modeling",
"liver diseases"
] | Quantifying the Diversification of Hepatitis C Virus (HCV) during Primary Infection: Estimates of the In Vivo Mutation Rate | journal.ppat.1002881 | null | [
[
"Hepatitis C virus ( HCV ) is a member of the hepacivirus genus within the flaviviridae family of virus , and it has a single positive stranded RNA molecule ( ∼9500 nucleotides ) as its genome [1]–[3] .",
"After entering a cell this RNA is translated into a single large polyprotein , which is cleaved to p... | [
"Hepatitis C virus ( HCV ) is present in the host with multiple variants generated by its error prone RNA-dependent RNA polymerase .",
"Little is known about the initial viral diversification and the viral life cycle processes that influence diversity .",
"We studied the diversification of HCV during acute infe... | [
"Hepatitis C virus ( HCV ) is a RNA virus that infects over 170 million people across the world .",
"It leads to a chronic infection in the majority of people who are infected ( >70% ) .",
"Most people only discover that they are infected long after initial infection .",
"Thus , it is difficult to study the v... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genomics",
"genetics",
"molecular genetics",
"biology",
"evolutionary biology",
"genetics and genomics"
] | Evaluation of the Role of Functional Constraints on the Integrity of an Ultraconserved Region in the Genus Drosophila | journal.pgen.1002475 | null | [
[
"Collinearity conservation , i . e . conservation of local gene order , across distantly related phyla is often viewed as the result of functional constraints that prevent the occurrence of breaks of chromosomal rearrangements during evolution .",
"The nature of these constraints is still poorly understoo... | [
"Why gene order is conserved over long evolutionary timespans remains elusive .",
"A common interpretation is that gene order conservation might reflect the existence of functional constraints that are important for organismal performance .",
"Alteration of the integrity of genomic regions , and therefore of th... | [
"Eukaryotic genomes have been reshaped by chromosomal rearrangements during evolution .",
"However , the comparison of distantly related species has uncovered unusually large genomic regions with conserved gene organization .",
"A widely accepted explanation is that , in those regions , there exist genes with j... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Human-Mediated Marine Dispersal Influences the Population Structure of Aedes aegypti in the Philippine Archipelago | journal.pntd.0003829 | null | [
[
"Aedes aegypti is the major vector of dengue virus ( DENV ) .",
"An estimated 96 million dengue cases and 300 million asymptomatic infections were reported globally in 2010 [1] .",
"Currently , there is no effective dengue vaccine available and the principal way to prevent the spread of the virus and ... | [
"Dengue virus ( DENV ) is an extraordinary health burden on global scale , but still lacks effective vaccine .",
"The Philippines is endemic for dengue fever , but massive employment of insecticides favored the development of resistance mutations in its major vector , Aedes aegypti .",
"Alternative vector contr... | [
"Dengue fever threatens the health of millions in the tropics and its causative agent , dengue virus , is mainly transmitted by the mosquito Aedes aegypti .",
"To control the spread of the virus , insecticides have been abundantly used but Ae .",
"aegypti has developed a genetic resistance to them .",
"Curren... | 2015 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Development of a Simple Dipstick Assay for Operational Monitoring of DDT | journal.pntd.0004324 | null | [
[
"In India , DDT ( 2 , 2-bis ( p-chlorophenyl ) -1 , 1 , 1 , -trichloroethane ) is used extensively by the Indian National Vector Borne Disease Control Programme ( NVBCDP ) as part of efforts to eliminate VL [1] .",
"VL is caused by Leishmania donovani and is transmitted by the female sand fly Phlebotomus ... | [
"Indoor residual spraying ( IRS ) of DDT is used to control visceral leishmaniasis ( VL ) in India .",
"However , the quality of spraying is severely compromised by a lack of affordable field assays to monitor target doses of insecticide .",
"Our aim was to develop a simple DDT insecticide quantification kit ( ... | [
"Visceral leishmaniasis ( VL ) is a major parasitic disease on the Indian Subcontinent , with 85% of the disease incidence in India .",
"DDT is being used to control the sandfly vector of VL , but the quality of indoor residual spraying ( IRS ) is not routinely assessed due to a lack of practical assays .",
"He... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genomics",
"genetics and genomics/gene discovery",
"genetics and genomics/gene expression",
"genetics and genomics/genetics of the immune system",
"genetics and genomics/complex traits",
"rheumatology/systemic lupus erythematosos",
"genetics and genomics/genetics of disease",
"i... | Genome-Wide Association Study in Asian Populations Identifies Variants in ETS1 and WDFY4 Associated with Systemic Lupus Erythematosus | journal.pgen.1000841 | null | [
[
"Systemic lupus erythematosus ( SLE ) is a prototype autoimmune disease characterized by auto-antibody production and multi-organ damage .",
"Genetic factors are known to play an important role in the disease , with the monozygotic twin concordance rate between 20–59 , and the risk for siblings of affecte... | [
"Systemic lupus erythematosus is a complex and potentially fatal autoimmune disease , characterized by autoantibody production and multi-organ damage .",
"By a genome-wide association study ( 320 patients and 1 , 500 controls ) and subsequent replication altogether involving a total of 3 , 300 Asian SLE patients ... | [
"In this study , we first conducted a genome-wide association study in a Hong Kong Chinese population , followed by replication in three other cohorts from Mainland China and a cohort from Thailand , which totaled 3 , 300 Asian patients and 4 , 200 ethnically and geographically matched controls .",
"We identified... | 2010 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"immunology/antigen processing and recognition",
"biophysics/protein folding",
"biochemistry/protein folding",
"biophysics/theory and simulation",
"pharmacology/drug development",
"molecular biology/bioinformatics",
"biophysics/biomacromolecule-ligand interactions",
"biochemistry/bioinformatics",
"c... | SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models | journal.pcbi.1000644 | null | [
[
"High resolution structures of protein-protein complexes are necessary for understanding mechanisms of protein-protein interactions , analyzing mutations , and manipulating binding affinity [1] .",
"The large gap between the number of experimentally determined complex structures and the available sequence... | [
"High resolution structures of antibody-antigen complexes are useful for analyzing the binding interface and to make rational choices for antibody engineering .",
"When a crystallographic structure of a complex is unavailable , the structure must be predicted using computational tools .",
"In this work , we ill... | [
"Antibodies are proteins that are key elements of the immune system and increasingly used as drugs .",
"Antibodies bind tightly and specifically to antigens to block their activity or to mark them for destruction .",
"Three-dimensional structures of the antibody-antigen complexes are useful for understanding th... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Active Transport of Phosphorylated Carbohydrates Promotes Intestinal Colonization and Transmission of a Bacterial Pathogen | journal.ppat.1005107 | null | [
[
"Competition between host cells and pathogenic bacteria for diverse substrates ranging from metals to vitamins can often influence the outcome of infection .",
"As a result , pathogens have developed a variety of nutrient uptake mechanisms to increase their competitiveness and hence their ability to colon... | [
"Efficient acquisition of extracellular nutrients is essential for bacterial pathogenesis , however the identities and mechanisms for transport of many of these substrates remain unclear .",
"Here , we investigate the predicted iron-binding transporter AfuABC and its role in bacterial pathogenesis in vivo .",
"... | [
"Essentially all Gram-negative pathogens are reliant on specific transport machineries termed binding protein-dependent transporters ( BPDTs ) to transport solutes such as amino acids , sugars and metal ions across their membranes .",
"In this study we investigated AfuABC , a predicted iron-transporting BPDT foun... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | TGF-β Suppression of HBV RNA through AID-Dependent Recruitment of an RNA Exosome Complex | journal.ppat.1004780 | null | [
[
"Hepatitis B virus ( HBV ) is recognized as the major causative factor of severe liver diseases such as cirrhosis and hepatocellular carcinoma .",
"The clinical outcomes and development of hepatocellular carcinoma and cirrhosis are modulated by viral replication and antiviral immunity against HBV [1] .",
... | [
"Transforming growth factor ( TGF ) -β inhibits hepatitis B virus ( HBV ) replication although the intracellular effectors involved are not determined .",
"Here , we report that reduction of HBV transcripts by TGF-β is dependent on AID expression , which significantly decreases both HBV transcripts and viral DNA ... | [
"HBV is one of the causative factors of hepatocellular carcinoma .",
"Recent studies have shown that the members of the APOBEC deaminase family are antiviral factors that suppress the replication of viruses , such as HIV-1 and HBV .",
"APOBEC3G suppresses viral replication by either hypermutation of nascent DNA... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"sequencing techniques",
"complement system",
"medicine and health sciences",
"toxins",
"immune physiology",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"toxicology",
"toxic agents",
"plasmid construction",
"membrane proteins",
"bacterial diseases",
"o... | CdiA Effectors from Uropathogenic Escherichia coli Use Heterotrimeric Osmoporins as Receptors to Recognize Target Bacteria | journal.ppat.1005925 | null | [
[
"Contact-dependent growth inhibition ( CDI ) systems mediate the transfer of protein toxins between Gram-negative bacteria .",
"CDI was first discovered and characterized in Escherichia coli EC93 , which uses CdiBEC93/CdiAEC93 two-partner secretion proteins to inhibit the growth of other E . coli isolates... | [
"Many Gram-negative bacterial pathogens express contact-dependent growth inhibition ( CDI ) systems that promote cell-cell interaction .",
"CDI+ bacteria express surface CdiA effector proteins , which transfer their C-terminal toxin domains into susceptible target cells upon binding to specific receptors .",
"C... | [
"Bacterial pathogens often live in crowded communities where cells reside in close contact with one another .",
"Many of these bacteria possess contact-dependent growth inhibition ( CDI ) systems , which allow cells to touch and inhibit each other using toxic CdiA proteins .",
"CDI+ bacteria also produce immuni... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"cell biology",
"genetics and genomics",
"homo (human)",
"computational biology"
] | A Transcriptional Program Mediating Entry into Cellular Quiescence | journal.pgen.0030091 | null | [
[
"Quiescence , also termed G0 , is defined as reversible cell cycle arrest where cells are poised to re-enter the cell cycle .",
"Most eukaryotic cells spend the majority of their lifespan in the state of quiescence .",
"In response to injury or specific extracellular stimuli , many types of somatic ce... | [
"The balance of quiescence and cell division is critical for tissue homeostasis and organismal health .",
"Serum stimulation of fibroblasts is well studied as a classic model of entry into the cell division cycle , but the induction of cellular quiescence , such as by serum deprivation ( SD ) , is much less under... | [
"Cells constantly sense their environment to decide whether to divide .",
"Many genes that control the entry into cell division are known , and their excessive activation may cause cancer .",
"In contrast , the way that cells cease to divide was thought to be a passive process , where signals for cell division ... | 2007 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"virology/vaccines",
"virology/virion structure, assembly, and egress",
"cell biology/membranes and sorting",
"infectious diseases/hiv infection and aids",
"infectious diseases/viral infections"
] | Ion-Abrasion Scanning Electron Microscopy Reveals Surface-Connected Tubular Conduits in HIV-Infected Macrophages | journal.ppat.1000591 | null | [
[
"Conventional transmission electron microscopy is a powerful tool for investigation of HIV pathogenesis and subcellular organization of viral compartments in infected cells [1] .",
"Insights into cellular ultrastructure using this approach have generally been obtained using thin sections derived from fixe... | [
"HIV-1-containing internal compartments are readily detected in images of thin sections from infected cells using conventional transmission electron microscopy , but the origin , connectivity , and 3D distribution of these compartments has remained controversial .",
"Here , we report the 3D distribution of viruse... | [
"Current treatment regimens for HIV-infected individuals are not capable of eradicating HIV infection , even though combinations of highly potent antiviral drugs are used .",
"Indeed , drug regimens must be periodically altered as the virus resurges from a persistent reservoir .",
"Macrophages , which serve as ... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public health and epidemiology",
"epidemiology",
"biology",
"population biology",
"spatial epidemiology"
] | Determining Treatment Needs at Different Spatial Scales Using Geostatistical Model-Based Risk Estimates of Schistosomiasis | journal.pntd.0001773 | null | [
[
"Schistosomiasis is a snail-borne parasitic disease , which affects more than 200 million people globally based on 2003 population estimates [1] .",
"The main burden is concentrated in sub-Saharan Africa , where schistosomiasis control had been neglected for many decades , and hence country-specific infec... | [
"After many years of neglect , schistosomiasis control is going to scale .",
"The strategy of choice is preventive chemotherapy , that is the repeated large-scale administration of praziquantel ( a safe and highly efficacious drug ) to at-risk populations .",
"The frequency of praziquantel administration is bas... | [
"More than 200 million people are affected by the snailborne disease schistosomiasis .",
"The main strategy to control schistosomiasis is to regularly treat school-aged children with the drug praziquantel .",
"The frequency of praziquantel treatment depends on the average prevalence of schistosomiasis , which c... | 2012 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"evolutionary ecology",
"genome evolution",
"comparative genomics",
"biology",
"genomics",
"evolutionary biology",
"genomic evolution",
"evolutionary genetics"
] | Genomic Analysis of the Kiwifruit Pathogen Pseudomonas syringae pv. actinidiae Provides Insight into the Origins of an Emergent Plant Disease | journal.ppat.1003503 | null | [
[
"Despite considerable improvements in the management of plant diseases , modern agriculture remains vulnerable to losses caused by microbial pathogens .",
"Plant diseases conservatively account for the loss of at least 10% of annual global food production [1] .",
"The intensive cultivation of clonally... | [
"The origins of crop diseases are linked to domestication of plants .",
"Most crops were domesticated centuries – even millennia – ago , thus limiting opportunity to understand the concomitant emergence of disease .",
"Kiwifruit ( Actinidia spp . ) is an exception: domestication began in the 1930s with outbreak... | [
"Despite considerable scientific advances in plant protection during the last century , agricultural crops remain vulnerable to infection by pathogens .",
"The intensive cultivation particularly of clonally propagated crop plants increases the potential for the emergence and rapid spread of new diseases .",
"Ps... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"infectious diseases/neglected tropical diseases",
"microbiology/parasitology",
"cell biology/cell signaling"
] | Kinome-Wide RNAi Screen Implicates at Least 5 Host Hepatocyte Kinases in Plasmodium Sporozoite Infection | journal.ppat.1000201 | null | [
[
"Although malaria has long been a devastating killer for the most vulnerable populations in countries of sub-Saharan Africa and other developing nations , our understanding of the early host-parasite interactions underlying this infectious disease remains far from complete .",
"In fact , the first stage o... | [
"Plasmodium sporozoites , the causative agent of malaria , are injected into their vertebrate host through the bite of an infected Anopheles mosquito , homing to the liver where they invade hepatocytes to proliferate and develop into merozoites that , upon reaching the bloodstream , give rise to the clinical phase ... | [
"During a mammalian malaria infection , Plasmodium sporozoites injected by an infected mosquito travel to the liver where they invade hepatocytes and multiply into thousands of new parasites .",
"These newly formed merozoites are then released into the bloodstream where they infect red blood cells and cause the s... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genetics and genomics/genomics",
"genetics and genomics/gene expression",
"genetics and genomics/complex traits",
"genetics and genomics/bioinformatics",
"genetics and genomics/disease models",
"diabetes and endocrinology/obesity",
"genetics and genomics/genetics of disease",
"biochemistry/bioinforma... | Genetic Networks of Liver Metabolism Revealed by Integration of Metabolic and Transcriptional Profiling | journal.pgen.1000034 | null | [
[
"Genetic linkage and association studies have the power to establish a causal link between gene loci and physiological traits .",
"These studies can make novel connections between biological processes that would not otherwise be predictable based on current knowledge .",
"The pace of gene discovery ha... | [
"Although numerous quantitative trait loci ( QTL ) influencing disease-related phenotypes have been detected through gene mapping and positional cloning , identification of the individual gene ( s ) and molecular pathways leading to those phenotypes is often elusive .",
"One way to improve understanding of geneti... | [
"Although numerous quantitative trait loci ( QTL ) influencing disease-related phenotypes have been detected through gene mapping and positional cloning , identifying individual genes and their potential roles in molecular pathways leading to disease remains a challenge .",
"In this study , we include transcripti... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics and genomics/gene function",
"genetics and genomics/gene expression"
] | A Regulated Response to Impaired Respiration Slows Behavioral Rates and Increases Lifespan in Caenorhabditis elegans | journal.pgen.1000450 | null | [
[
"Mitochondria generate most of the cell's energy as well as its reactive oxygen species ( ROS ) , and mitochondrial dysfunction can cause disease and accelerate aging .",
"Paradoxically , mitochondrial dysfunction can also increase longevity .",
"Yeast petite mutants , which lack mitochondrial DNA and... | [
"When mitochondrial respiration or ubiquinone production is inhibited in Caenorhabditis elegans , behavioral rates are slowed and lifespan is extended .",
"Here , we show that these perturbations increase the expression of cell-protective and metabolic genes and the abundance of mitochondrial DNA .",
"This resp... | [
"Mitochondrial respiration generates energy in the form of adenosine triphospate ( ATP ) , a molecule that powers many cellular processes .",
"When respiration is inhibited in C . elegans , rates of behavior and growth are slowed and , interestingly , lifespan is extended .",
"In this study , we investigated th... | 2009 |
[
"Introduction",
"Models",
"Results",
"Discussion"
] | [
"physics",
"statistical mechanics",
"biophysic al simulations",
"computational neuroscience",
"neural networks",
"biophysics simulations",
"biophysics theory",
"biology",
"computational biology",
"biophysics",
"neuroscience"
] | Complementarity of Spike- and Rate-Based Dynamics of Neural Systems | journal.pcbi.1002560 | null | [
[
"The brain is a multiscale system , whose dynamics spans from microscale structures , such as ion-channels and synapses , to emergent behavior , such as oscillations at the whole-brain scale .",
"The problem then arises of how to simultaneously incorporate these diverse scales to make predictions about br... | [
"Relationships between spiking-neuron and rate-based approaches to the dynamics of neural assemblies are explored by analyzing a model system that can be treated by both methods , with the rate-based method further averaged over multiple neurons to give a neural-field approach .",
"The system consists of a chain ... | [
"We develop and demonstrate a model that allows us to examine how the predictions of spiking and rate-based models of neurons and their interactions are related .",
"First , the behavior of a chain of neurons is explored by simulating each spiking neuron and spike-mediated interactions between neurons individuall... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"genome evolution",
"evolutionary selection",
"epistasis",
"genome sequencing",
"biology",
"adaptation",
"natural selection",
"heredity",
"genetics",
"genomics",
"evolutionary biology",
"genomic evolution",
"evolutionary processes",
"genetics and genomics"
] | Reciprocal Sign Epistasis between Frequently Experimentally Evolved Adaptive Mutations Causes a Rugged Fitness Landscape | journal.pgen.1002056 | null | [
[
"Introduced by Wright , the fitness landscape describes the possible mutational trajectories by which lineages evolve in a stepwise manner from genotypes that lie in regions of low fitness to ones of higher fitness [1] , [2] .",
"When viewed as a whole , this metaphorical landscape represents a species' p... | [
"The fitness landscape captures the relationship between genotype and evolutionary fitness and is a pervasive metaphor used to describe the possible evolutionary trajectories of adaptation .",
"However , little is known about the actual shape of fitness landscapes , including whether valleys of low fitness create... | [
"How organisms adapt to their environment is of central importance in biology , but the molecular underpinnings of adaptation are difficult to discover .",
"Fitness landscapes illustrate possible steps adaptive evolution can take to increase the evolutionary fitness of individuals within a population , and the sh... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Models"
] | [] | The Shape of an Auxin Pulse, and What It Tells Us about the Transport Mechanism | journal.pcbi.1004487 | null | [
[
"Auxin is the key integrating signal in plants [1 , 2] , and the dynamics of its movement within the plant is crucial to understanding development [3–9] and a multitude of physiological responses [10–12] .",
"A traditional way to observe these dynamics in stems or coleoptiles is to apply a pulse of radioa... | [
"Auxin underlies many processes in plant development and physiology , and this makes it of prime importance to understand its movements through plant tissues .",
"In stems and coleoptiles , classic experiments showed that the peak region of a pulse of radio-labelled auxin moves at a roughly constant velocity down... | [
"Auxin is one of the most important signalling molecules in plants .",
"It is a key player in the development of veins and plant organs , and in responses that the plant makes to light and gravity .",
"Yet we have a rather limited understanding of how auxin moves around plant tissues .",
"I show here that a c... | 2015 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"ecology/behavioral ecology"
] | Wolbachia Infection Reduces Blood-Feeding Success in the Dengue Fever Mosquito, Aedes aegypti | journal.pntd.0000516 | null | [
[
"A number of the major mosquito vectors of disease , including the various anopheline species that transmit malaria and Aedes aegypti that transmits dengue and other arboviruses , do not naturally carry the common insect endosymbiont Wolbachia pipientis .",
"Recently , A . aegypti was artificially transin... | [
"The mosquito Aedes aegypti was recently transinfected with a life-shortening strain of the endosymbiont Wolbachia pipientis ( wMelPop ) as the first step in developing a biocontrol strategy for dengue virus transmission .",
"In addition to life-shortening , the wMelPop-infected mosquitoes also exhibit increased ... | [
"The primary mosquito vector of dengue virus , Aedes aegypti , has recently been artificially infected with a symbiotic bacterium called Wolbachia pipientis .",
"This bacterium occurs naturally inside the cells of ∼66% of insect species .",
"The Wolbachia used to infect A . aegypti shortens the insect's lifespa... | 2009 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"sequencing techniques",
"invertebrates",
"rna interference",
"vertebrates",
"animals",
"mammals",
"dogs",
"viruses",
"rna viruses",
"epigenetics",
"molecular biology techniques",
"rna sequencing",
"echinoderms",
"starfish",
"plants",
"research and analysis methods",
"genetic interfe... | Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes | journal.pgen.1007533 | null | [
[
"RNA interference-related ( RNAi ) pathways provide an important line of defence against parasitic nucleic acids in plants , fungi , and most animals [1–5] .",
"In plants and fungi , which lack a distinct germline , Dicer and Argonaute-dependent RNAi responses suppress the expression and replication of vi... | [
"RNA interference ( RNAi ) -related pathways target viruses and transposable element ( TE ) transcripts in plants , fungi , and ecdysozoans ( nematodes and arthropods ) , giving protection against infection and transmission .",
"In each case , this produces abundant TE and virus-derived 20-30nt small RNAs , which... | [
"The presence of abundant virus-derived small RNAs in infected plants , fungi , nematodes , and arthropods suggests that Dicer-dependent antiviral RNAi is an ancient and conserved defence .",
"Using metagenomic sequencing from wild-caught organisms we find that antiviral RNAi is variable across animals .",
"We ... | 2018 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion and conclusions",
"Model properties"
] | [
"death rates",
"livestock",
"morocco",
"medicine and health sciences",
"ruminants",
"demography",
"geographical locations",
"tropical diseases",
"vertebrates",
"animals",
"mammals",
"animal slaughter",
"bacterial diseases",
"animal management",
"infectious disease control",
"africa",
... | Transmission dynamics and elimination potential of zoonotic tuberculosis in morocco | journal.pntd.0005214 | null | [
[
"Bovine tuberculosis ( BTB ) is a zoonotic bacterial infection caused by Mycobacterium bovis .",
"It belongs to a group of well-known and newer mycobacteria , together with Mycobacterium tuberculosis , all of which derive from a common ancestor forming the Mycobacterium tuberculosis complex ( MTBC ) [1–4]... | [
"Bovine tuberculosis ( BTB ) is an endemic zoonosis in Morocco caused by Mycobacterium bovis , which infects many domestic animals and is transmitted to humans through consumption of raw milk or from contact with infected animals .",
"The prevalence of BTB in Moroccan cattle is estimated at 18% , and 33% at the i... | [
"Tuberculosis is a disease of humans and animals which mainly affects the lungs but can also manifest in other organs .",
"A variety of tuberculosis bacteria cause the disease and are usually transmitted through air , i . e . inhalation of aerosols .",
"Bovine tuberculosis ( BTB ) occurs predominantly among dom... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"chemistry",
"veterinary science",
"biology"
] | Structure of the Membrane Anchor of Pestivirus Glycoprotein Erns, a Long Tilted Amphipathic Helix | journal.ppat.1003973 | null | [
[
"The genus Pestivirus belongs to the family Flaviviridae , together with the genera Hepacivirus , Flavivirus and Pegivirus .",
"It represents a group of economically important animal viruses like classical swine fever virus ( CSFV ) and bovine viral diarrhea virus ( BVDV ) [1] .",
"The economical dama... | [
"Erns is an essential virion glycoprotein with RNase activity that suppresses host cellular innate immune responses upon being partially secreted from the infected cells .",
"Its unusual C-terminus plays multiple roles , as the amphiphilic helix acts as a membrane anchor , as a signal peptidase cleavage site , an... | [
"The Erns protein ( envelope protein , RNase , secreted ) of pestiviruses represents one of the most fascinating proteins in virology .",
"Erns is not only an essential structural component of the virus particle but also an unspecific RNase .",
"The latter activity is dispensable for pestivirus replication but ... | 2014 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biophysic al simulations",
"protein folding",
"biology",
"computational biology",
"biophysics simulations",
"biophysics"
] | Binding of Two Intrinsically Disordered Peptides to a Multi-Specific Protein: A Combined Monte Carlo and Molecular Dynamics Study | journal.pcbi.1002682 | null | [
[
"It has become clear that many functional proteins do not fold into unique three-dimensional structures , as expected from the classical view of proteins , but remain highly conformationally dynamic under native conditions .",
"These intrinsically disordered proteins ( IDPs ) are now estimated to represen... | [
"The unique ability of intrinsically disordered proteins ( IDPs ) to fold upon binding to partner molecules makes them functionally well-suited for cellular communication networks .",
"For example , the folding-binding of different IDP sequences onto the same surface of an ordered protein provides a mechanism for... | [
"A substantial fraction of our proteins are believed to be partly or completely disordered , meaning that they contain regions that lack a stable folded structure under typical physiological conditions .",
"This is a feature which plays a key role in their functions .",
"For example , it allows them to have man... | 2012 |
[
"Introduction",
"Results and discussion",
"Conclusion",
"Materials and methods"
] | [
"fungal spores",
"meiosis",
"cell cycle and cell division",
"cell processes",
"fungi",
"model organisms",
"fungal evolution",
"experimental organism systems",
"dna",
"fungal reproduction",
"homologous recombination",
"saccharomyces",
"research and analysis methods",
"mycology",
"chromoso... | Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts | journal.pgen.1006917 | null | [
[
"Accurate chromosome segregation at the first meiotic division often requires crossovers ( COs ) between homologous chromosomes [1] .",
"Meiotic COs result from the repair of programmed DNA double strand breaks ( DSBs ) by homologous recombination , that can yield gene conversions through non reciprocal t... | [
"Meiotic recombination is a major factor of genome evolution , deeply characterized in only a few model species , notably the yeast Saccharomyces cerevisiae .",
"Consequently , little is known about variations of its properties across species .",
"In this respect , we explored the recombination landscape of Lac... | [
"Meiotic recombination promotes accurate chromosome segregation and genetic diversity .",
"To date , the mechanisms and rules lying behind recombination were dissected using model organisms such as the budding yeast Saccharomyces cerevisiae .",
"To assess the conservation and variation of this process over a br... | 2017 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"genome expression analysis",
"parasitic diseases",
"parasitology",
"dna transcription",
"neglected tropical diseases",
"zoology",
"infectious diseases",
"gene expression",
"biology",
"helminthology",
"opisthorchiasis",
"genetics",
"genomics",
"computational biology",
"gene... | Molecular Changes in Opisthorchis viverrini (Southeast Asian Liver Fluke) during the Transition from the Juvenile to the Adult Stage | journal.pntd.0001916 | null | [
[
"Parasitic worms of humans and other animals cause diseases of major socio-economic importance around the world .",
"In spite of their significance , many of them have been substantially neglected in terms of research and their control [1] .",
"Among parasitic flukes ( i . e . , trematodes ) , the foo... | [
"The Southeast Asian liver fluke ( Opisthorchis viverrini ) chronically infects and affects tens of millions of people in regions of Asia , leading to chronic illness and , importantly , inducing malignant cancer ( = cholangiocarcinoma ) .",
"In spite of this , little is known , at the molecular level , about the... | [
"Opistorchis viverrini is an important and neglected parasite affecting ∼9 million people in South-east Asia .",
"The parasite has a complex life-cycle which involves an intermediate phase in cyprinoid fishes .",
"Consumption of raw or under-cooked fish infected with the metacercarial ( larval ) stage of O . vi... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"dimers (chemical physics)",
"crystal structure",
"condensed matter physics",
"crystals",
"membrane receptor signaling",
"materials science",
"crystallography",
"g protein coupled receptors",
"materials by structure",
"physical chemistry",
"chemical properties",
"lipids",
"solid state physic... | Dynamic Cholesterol-Conditioned Dimerization of the G Protein Coupled Chemokine Receptor Type 4 | journal.pcbi.1005169 | null | [
[
"Signaling across cell barriers by G protein coupled receptors ( GPCRs ) is increasingly associated with GPCR dimerization or more general oligomerization [1] .",
"While G protein coupling was shown for many GPCRs to not necessarily depend on dimerization , a direct coupling of function with homo- or hete... | [
"G protein coupled receptors ( GPCRs ) allow for the transmission of signals across biological membranes .",
"For a number of GPCRs , this signaling was shown to be coupled to prior dimerization of the receptor .",
"The chemokine receptor type 4 ( CXCR4 ) was reported before to form dimers and their functionali... | [
"The G protein coupled C-X-C chemokine receptor type 4 ( CXCR4 ) is a transmembrane receptor that plays an essential role in the human immune system .",
"However , overexpression of CXCR4 has been shown to lead to metastasis of breast and lung cancer cells .",
"Furthermore , the HI-Virus infects T-cells through... | 2016 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"diagnostic radiology",
"tractography",
"nervous system",
"brain",
"vertebrates",
"neuroscience",
"animals",
"mammals",
"magnetic resonance imaging",
"primates",
"brain morphometry",
"brain mapping",
"neuroimaging",
"old world monkeys",
"research and ana... | The missing link: Predicting connectomes from noisy and partially observed tract tracing data | journal.pcbi.1005374 | null | [
[
"Recent years have seen a surge in research effort devoted to obtaining the human connectome , a map of all the connections in the human brain at the level of macroscopic brain regions [1 , 2] .",
"Technological advances , in particular diffusion-weighted MRI ( dMRI ) , have enabled bundles of white-matte... | [
"Our understanding of the wiring map of the brain , known as the connectome , has increased greatly in the last decade , mostly due to technological advancements in neuroimaging techniques and improvements in computational tools to interpret the vast amount of available data .",
"Despite this , with the exception... | [
"Tract tracing is a highly accurate procedure for identifying animal brain connectivity .",
"However , the technique is labor intensive and requires the sacrifice of animal subjects .",
"In our work , we describe a computational method that is able to predict the presence or absence of unobserved connections , ... | 2017 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"invertebrates",
"medicine and health sciences",
"china",
"immunology",
"geographical locations",
"animals",
"seasons",
"insect vectors",
"infectious diseases",
"south america",
"aedes aegypti",
"disease vectors",
"brazil",
"insects",
"arthropoda",
"people and places",
"seasonal vari... | Seasonal temperature variation influences climate suitability for dengue, chikungunya, and Zika transmission | journal.pntd.0006451 | null | [
[
"Over the last 30–40 years , arboviral outbreaks have dominated the public health landscape globally [1] .",
"These viruses , most notably dengue ( DENV ) , chikungunya ( CHIKV ) , and Zika ( ZIKV ) , can cause symptoms ranging from rash , arthralgia , and fever to hemorrhagic fever ( DENV ) , long-term a... | [
"Dengue , chikungunya , and Zika virus epidemics transmitted by Aedes aegypti mosquitoes have recently ( re ) emerged and spread throughout the Americas , Southeast Asia , the Pacific Islands , and elsewhere .",
"Understanding how environmental conditions affect epidemic dynamics is critical for predicting and re... | [
"Mosquito-borne viruses like dengue , Zika , and chikungunya have recently caused large epidemics that are partly driven by temperature .",
"Using a mathematical model built from laboratory experimental data for Aedes aegypti mosquitoes and dengue virus , we examine the impact of variation in seasonal temperature... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"molecular biology/rna splicing",
"genetics and genomics/cancer genetics",
"cell biology/gene expression",
"cardiovascular disorders/peripheral vascular disease"
] | Expression of Linear and Novel Circular Forms of an INK4/ARF-Associated Non-Coding RNA Correlates with Atherosclerosis Risk | journal.pgen.1001233 | null | [
[
"Atherosclerotic vascular disease ( ASVD ) is a leading cause of human mortality worldwide [1] .",
"While there are well-recognized risk factors for ASVD such as tobacco use , obesity and hyperlipidemia , the identification of common genetic variants associated with the disease has proven difficult despit... | [
"Human genome-wide association studies have linked single nucleotide polymorphisms ( SNPs ) on chromosome 9p21 . 3 near the INK4/ARF ( CDKN2a/b ) locus with susceptibility to atherosclerotic vascular disease ( ASVD ) .",
"Although this locus encodes three well-characterized tumor suppressors , p16INK4a , p15INK4b... | [
"Unbiased studies of the human genome have identified strong genetic determinants of atherosclerotic vascular disease ( ASVD ) on chromosome 9p21 . 3 .",
"This region of the genome does not encode genes previously linked to ASVD , but does contain the INK4/ARF tumor suppressor locus .",
"Products of the INK4/AR... | 2010 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"genetics and genomics/genomics",
"molecular biology",
"cell biology/gene expression",
"infectious diseases/protozoal infections"
] | Leishmania-Specific Surface Antigens Show Sub-Genus Sequence Variation and Immune Recognition | journal.pntd.0000829 | null | [
[
"Kinetoplastid parasites of the genus Leishmania cause a diverse spectrum of infectious diseases , the leishmaniases , in tropical and subtropical regions of the world ( reviewed in [1] ) .",
"Mammalian-infective Leishmania species are divided into two subgenera , Leishmania ( Leishmania ) and Leishmania ... | [
"A family of hydrophilic acylated surface ( HASP ) proteins , containing extensive and variant amino acid repeats , is expressed at the plasma membrane in infective extracellular ( metacyclic ) and intracellular ( amastigote ) stages of Old World Leishmania species .",
"While HASPs are antigenic in the host and c... | [
"Single-celled Leishmania parasites , transmitted by sand flies , infect humans and other mammals in many tropical and sub-tropical regions , giving rise to a spectrum of diseases called the leishmaniases .",
"Species of parasite within the Leishmania genus can be divided into two groups ( referred to as sub-gene... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"pathology and laboratory medicine",
"toxoplasma gondii",
"social sciences",
"parasitic diseases",
"neuroscience",
"parasitic protozoans",
"protozoans",
"signs and symptoms",
"toxoplasma",
"pharmaceutics",
"vision",
"eyes",
"lesions",
"protozoan infections... | Toxoplasmic Retinochoroiditis: Clinical Characteristics and Visual Outcome in a Prospective Study | journal.pntd.0004685 | null | [
[
"Ocular involvement by Toxoplasma gondii may cause severe visual impairment and is the main etiology of posterior uveitis in many parts of the world , however questions about the course of the disease remain unanswered .",
"[1–3] Up to this day there is no consensus on treatment effectiveness and risk fac... | [
"To ascertain the clinical features and visual outcome of toxoplasma retinochoroiditis in a large series of cases .",
"Two hundred and thirty subjects diagnosed with active toxoplasma retinochoroiditis were prospectively followed for periods ranging from 269 to 1976 days .",
"All patients presented with active ... | [
"Ocular toxoplasmosis affects millions of people worldwide and is a cause of severe vision loss .",
"Prospective studies on the disease are rare and require long and expensive follow-ups .",
"A network of intricate host and parasite factors can influence its evolution and its treatment is still subject of discu... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"medicine",
"biology"
] | EBV Tegument Protein BNRF1 Disrupts DAXX-ATRX to Activate Viral Early Gene Transcription | journal.ppat.1002376 | null | [
[
"Epstein-Barr virus ( EBV ) is a member of the human gammaherpesvirus subfamily that infects over 90% of the global adult population [1] , [2] .",
"EBV preferentially establishes latent infection in B-lymphocytes but can also infect epithelial cells [3] , [4] .",
"EBV primary infection is one of the m... | [
"Productive infection by herpesviruses involve the disabling of host-cell intrinsic defenses by viral encoded tegument proteins .",
"Epstein-Barr Virus ( EBV ) typically establishes a non-productive , latent infection and it remains unclear how it confronts the host-cell intrinsic defenses that restrict viral gen... | [
"Persistent infection by Epstein-Barr virus ( EBV ) is associated with a variety of diseases , including lymphoid and epithelial tumors .",
"Despite a wealth of information on the mechanism of viral persistence , relatively little is known about the early steps of EBV infection and viral gene activation .",
"Ho... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"insulin",
"endocrine system",
"biology",
"anatomy and physiology",
"electrophysiology",
"computational biology",
"endocrine physiology"
] | Mathematical Modeling of Heterogeneous Electrophysiological Responses in Human β-Cells | journal.pcbi.1003389 | null | [
[
"Glucose-stimulated insulin secretion from human pancreatic -cells relies on the same major signaling cascade as their rodent counterparts , with electrical activity playing a pivotal role .",
"Following metabolism of the sugar , ATP-sensitive potassium channels ( K ( ATP ) -channels ) close in response t... | [
"Electrical activity plays a pivotal role in glucose-stimulated insulin secretion from pancreatic -cells .",
"Recent findings have shown that the electrophysiological characteristics of human -cells differ from their rodent counterparts .",
"We show that the electrophysiological responses in human -cells to a r... | [
"Insulin is a glucose-lowering hormone secreted from the pancreatic -cells in response to raised plasma glucose levels , and it is now well-established that defective insulin secretion plays a pivotal role in the development of diabetes .",
"The -cells are electrically active , and use electrical activity to tran... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine and health sciences",
"immune physiology",
"enzyme-linked immunoassays",
"viral transmission and infection",
"engineering and technology",
"immunology",
"microbiology",
"vertebrates",
"animals",
"mammals",
"animal models",
"vaccines",
"experimental organism systems",
"infectious ... | Vaccine-induced antibodies to herpes simplex virus glycoprotein D epitopes involved in virus entry and cell-to-cell spread correlate with protection against genital disease in guinea pigs | journal.ppat.1007095 | null | [
[
"Nearly one half-billion people worldwide are infected with herpes simplex virus type 2 ( HSV-2 ) and another one-quarter billion have genital infection caused by herpes simplex virus type 1 ( HSV-1 ) [1 , 2] .",
"The disease manifestations vary from asymptomatic genital infection to severe , recurrent ul... | [
"Herpes simplex virus type 2 ( HSV-2 ) glycoprotein D ( gD2 ) subunit antigen is included in many preclinical candidate vaccines .",
"The rationale for including gD2 is to produce antibodies that block crucial gD2 epitopes involved in virus entry and cell-to-cell spread .",
"HSV-2 gD2 was the only antigen in th... | [
"Herpes simplex virus type 2 ( HSV-2 ) glycoprotein D ( gD2 ) mediates virus entry and cell-to-cell spread .",
"We hypothesized that an effective gD2 vaccine needs to block these activities .",
"Neutralizing titers , which assess blocking virus entry , correlated with protection against HSV-2 genital lesions in... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell binding",
"cell physiology",
"molecular probe techniques",
"gene regulation",
"cell cycle and cell division",
"cell processes",
"immunoblotting",
"green fluorescent protein",
"dna-binding proteins",
"luminescent proteins",
"dna replication",
"immunoprecipitation",
"dna",
"molecular b... | The Cdk8/19-cyclin C transcription regulator functions in genome replication through metazoan Sld7 | journal.pbio.2006767 | null | [
[
"Eukaryotic cells must faithfully replicate their genomic DNA exactly once before each cell division in order to ensure genetic homeostasis through successive cell generations .",
"Initiation of DNA replication is a major step of replication control by the cell cycle and the DNA damage checkpoint , ensuri... | [
"Accurate genome duplication underlies genetic homeostasis .",
"Metazoan Mdm2 binding protein ( MTBP ) forms a main regulatory platform for origin firing together with Treslin/TICRR and TopBP1 ( Topoisomerase II binding protein 1 ( TopBP1 ) –interacting replication stimulating protein/TopBP1-interacting checkpoin... | [
"Efficient and well-regulated DNA replication origin firing is central to ensure complete and accurate genome duplication before cell division .",
"We here use bioinformatics and cultured human cells to understand the role of the essential origin firing factor Mdm2 binding protein ( MTBP ) .",
"We prove that MT... | 2019 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"pharmacology",
"microbiology/medical microbiology",
"biochemistry/membrane proteins and energy transduction",
"infectious diseases/antimicrobials and drug resistance"
] | Requirement for Ergosterol in V-ATPase Function Underlies Antifungal Activity of Azole Drugs | journal.ppat.1000939 | null | [
[
"Pathogenic fungal species , including Aspergillus , Candida , Histoplasma and Cryptococcus among others , cause infections ranging from mucocutaneous disorders to life-threatening invasive diseases that can involve any organ .",
"In the past two decades , expanding populations of immunocompromised patien... | [
"Ergosterol is an important constituent of fungal membranes .",
"Azoles inhibit ergosterol biosynthesis , although the cellular basis for their antifungal activity is not understood .",
"We used multiple approaches to demonstrate a critical requirement for ergosterol in vacuolar H+-ATPase function , which is kn... | [
"Systemic fungal infections impose a significant threat to public health and therapeutic options to treat these diseases remain limited .",
"Azoles represent the largest category of anti-fungal drugs and repress fungal growth by inhibiting biosynthesis of ergosterol , an important constituent of fungal membranes ... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cell death",
"medicine and health sciences",
"autophagic cell death",
"neurochemistry",
"pathology and laboratory medicine",
"gene regulation",
"endothelial cells",
"pathogens",
"cell processes",
"microbiology",
"neuroscience",
"salmonellosis",
"epithelial cells",
"bacterial diseases",
... | Endothelial cells are intrinsically defective in xenophagy of Streptococcus pyogenes | journal.ppat.1006444 | null | [
[
"Streptococcus pyogenes , also known as group A Streptococcus ( GAS ) , is a common human pathogen that causes a variety of illnesses , ranging from mild self-limiting infections to severe invasive diseases .",
"Pathogenesis involves various virulence factors for adhesion , invasion , colonization , and d... | [
"Group A Streptococcus ( GAS ) is deleterious pathogenic bacteria whose interaction with blood vessels leads to life-threatening bacteremia .",
"Although xenophagy , a special form of autophagy , eliminates invading GAS in epithelial cells , we found that GAS could survive and multiply in endothelial cells .",
... | [
"Autophagy is an intracellular bulk degradation system to survive within starved condition , which is one of the most common threats limiting organism’s expansion .",
"By the system , cells digest their own cytoplasmic compartments that are sequestered by double membrane structure called autophagosome .",
"It i... | 2017 |
[
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biomacromolecule-ligand interactions",
"physics",
"statistical mechanics",
"protein folding",
"macromolecular assemblies",
"biophysics theory",
"chemistry",
"biology",
"computational chemistry",
"biophysics simulations",
"biophysics"
] | Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1 | journal.pcbi.1003114 | null | [
[
"The plant hormone abscisic acid ( ABA ) controls seed development , germination , dormancy and stress response [1] , [2] .",
"Using combined molecular , biophysical and genetic techniques many details of ABA signal transduction have been elucidated [3]–[5] .",
"In particular , under abiotic stress , ... | [
"The pyrabactin resistance 1 ( PYR1 ) /PYR1-like ( PYL ) /regulatory component of abscisic acid ( ABA ) response ( RCAR ) proteins comprise a well characterized family of ABA receptors .",
"Recent investigations have revealed two subsets of these receptors that , in the absence of ABA , either form inactive homod... | [
"Protein pyrabactin resistance 1 ( PYR1 ) belongs to a group of PYR1-like ( PYL ) proteins that regulate plant development and responses to conditions of drought and salinity .",
"Recent studies have reported characterization of their molecular structures as well as elucidation of important aspects of their funct... | 2013 |
[
"Introduction",
"Materials and methods",
"Results",
"Discussion"
] | [
"schistosoma",
"invertebrates",
"schistosoma mansoni",
"medicine and health sciences",
"diagnostic radiology",
"ultrasound imaging",
"helminths",
"tropical diseases",
"fibrosis",
"parasitic diseases",
"animals",
"liver diseases",
"developmental biology",
"hepatitis",
"gastroenterology an... | Liver ultrasound elastography for the evaluation of periportal fibrosis in schistosomiasis mansoni: A cross-sectional study | journal.pntd.0006868 | null | [
[
"Schistosomiasis is considered a public health problem in many parts of the world and one of the most frequent causes of liver fibrosis worldwide [1] .",
"In Brazil , schistosomiasis mansoni infection affects 1 . 5 millions of people , particularly in the Northeastern region [2] .",
"The state of Pern... | [
"ARFI elastrography has been used as a noninvasive method to assess the severity of liver fibrosis in viral hepatitis , although with few studies in schistosomiasis mansoni .",
"We aimed to evaluate the performance of point shear wave elastography ( pSWE ) for predicting significant periportal fibrosis ( PPF ) in... | [
"In the developing world , over 207 million people are infected with parasitic Schistosoma worms .",
"Among the species of Schistosoma that infect humans Schistosoma mansoni is one of the most common causes of illness .",
"Here , we investigated the performance of point shear wave elastography ( pSWE ) for pred... | 2018 |
[
"Discussion"
] | [
"computational biology/systems biology"
] | Protein Interaction Networks—More Than Mere Modules | journal.pcbi.1000659 | null | [
[
"Using a suited algorithm , any network can be separated into cohesive groups of nodes with more internal than external connections .",
"Accordingly , protein-protein interaction networks can also be divided into relatively independent units as putative functional modules [4] .",
"Do these modules rea... | [
"It is widely believed that the modular organization of cellular function is reflected in a modular structure of molecular networks .",
"A common view is that a “module” in a network is a cohesively linked group of nodes , densely connected internally and sparsely interacting with the rest of the network .",
"M... | [
"Cellular function is widely believed to be organized in a modular fashion .",
"On all scales and at all levels of complexity , relatively independent sub-units perform relatively independent sub-tasks .",
"This functional modularity must be reflected in the topology of molecular networks .",
"But how a funct... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | CD44 Plays a Functional Role in Helicobacter pylori-induced Epithelial Cell Proliferation | journal.ppat.1004663 | null | [
[
"The major cause of chronic inflammation in the stomach is Helicobacter pylori ( H . pylori ) [1] , and it is widely accepted that chronic inflammation is a trigger for the development of gastric cancer [2] .",
"The severity and localization of the inflammation that results from H . pylori infection is be... | [
"The cytotoxin-associated gene ( Cag ) pathogenicity island is a strain-specific constituent of Helicobacter pylori ( H . pylori ) that augments cancer risk .",
"CagA translocates into the cytoplasm where it stimulates cell signaling through the interaction with tyrosine kinase c-Met receptor , leading cellular p... | [
"Chronic gastric inflammation , typically caused by Helicobacter pylori ( H . pylori ) , is the most consistent lesion leading to cancer .",
"During a well-choreographed interaction between H . pylori and the host , the progression from chronic inflammation to cancer involves gastric epithelial changes with evide... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"genetics",
"biology",
"molecular cell biology",
"neuroscience",
"genetics and genomics"
] | A Regulatory Loop Involving PAX6, MITF, and WNT Signaling Controls Retinal Pigment Epithelium Development | journal.pgen.1002757 | null | [
[
"The vertebrate retinal pigment epithelium or RPE is a monolayer of melanin-containing cells that are intimately juxtaposed to the photoreceptor layer of the retina where they function as light screen and provide metabolic support for the retina's photoreceptors .",
"Like the retina , the RPE is developme... | [
"The separation of the optic neuroepithelium into future retina and retinal pigment epithelium ( RPE ) is a critical event in early eye development in vertebrates .",
"Here we show in mice that the transcription factor PAX6 , well-known for its retina-promoting activity , also plays a crucial role in early pigmen... | [
"The retinal pigment epithelium or RPE in the back of the eye is critical for the normal function of the retina , and its abnormalities can lead to retinal disorders such as adult-onset macular degeneration .",
"Insights into the pathogenesis of such disorders , and potential therapies , may come from using RPE c... | 2012 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | A Viral Genome Landscape of RNA Polyadenylation from KSHV Latent to Lytic Infection | journal.ppat.1003749 | null | [
[
"Kaposi sarcoma-associated herpesvirus ( KSHV ) , also referred as human herpesvirus 8 ( HHV-8 ) , is a member of gammaherpervirus subfamily [1] .",
"KSHV infection in healthy individuals is well-controlled by host immune system and other host factors , and hence , it is usually asymptomatic .",
"Howe... | [
"RNA polyadenylation ( pA ) is one of the major steps in regulation of gene expression at the posttranscriptional level .",
"In this report , a genome landscape of pA sites of viral transcripts in B lymphocytes with Kaposi sarcoma-associated herpesvirus ( KSHV ) infection was constructed using a modified PA-seq s... | [
"A genome-wide polyadenylation landscape in the expression of human herpesviruses has not been reported .",
"In this study , we provide the first genome landscape of viral RNA polyadenylation sites in B cells from KSHV latent to lytic infection by using a modified PA-seq protocol and selectively validated by 3′ R... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious diseases",
"epidemiology"
] | Strong Association between Serological Status and Probability of Progression to Clinical Visceral Leishmaniasis in Prospective Cohort Studies in India and Nepal | journal.pntd.0002657 | null | [
[
"Visceral leishmaniasis ( VL ) is a vector borne infectious disease that is endemic in parts of Asia , Africa , South America and Europe , and is caused by different species of the genus Leishmania .",
"In South America and the Mediterranean region , the disease is mainly caused by Leishmania infantum , w... | [
"Asymptomatic persons infected with the parasites causing visceral leishmaniasis ( VL ) usually outnumber clinically apparent cases by a ratio of 4–10 to 1 .",
"We assessed the risk of progression from infection to disease as a function of DAT and rK39 serological titers .",
"We used available data on four coho... | [
"To study the association between positive serology for VL among asymptomatic persons and progression to disease , we analyzed combined data from two different cohort studies in which over 32 , 000 subjects were enrolled .",
"All subjects were screened for presence of antibodies to L . donovani with DAT and rK39 ... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Experimental Procedures"
] | [
"biology"
] | Effects of Resveratrol and SIRT1 on PGC-1α Activity and Mitochondrial Biogenesis: A Reevaluation | journal.pbio.1001603 | Feeding resveratrol to rodents has no effect on mitochondrial biogenesis, and deacetylation of PGC-1α results in a decrease, not an increase, in its coactivator activity. | [
[
"Resveratrol has been reported to have a number of remarkable effects in mice .",
"These include protection against high-fat-diet-induced obesity and insulin resistance [1]–[3] , marked improvements in running endurance and maximal oxygen uptake capacity ( VO2max ) [3] , increased muscle strength [3] , im... | [
"It has been reported that feeding mice resveratrol activates AMPK and SIRT1 in skeletal muscle leading to deacetylation and activation of PGC-1α , increased mitochondrial biogenesis , and improved running endurance .",
"This study was done to further evaluate the effects of resveratrol , SIRT1 , and PGC-1α deace... | [
"Studies on cultured muscle cells have shown that treatment with resveratrol , a chemical famously found in the skin of red grapes , stimulates the manufacture of new mitochondria .",
"This has been attributed to the activation of the deacetylase SIRT1 either directly by resveratrol or indirectly via the activati... | 2013 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood cells",
"cell physiology",
"medicine and health sciences",
"enzyme-linked immunoassays",
"immune cells",
"immune physiology",
"pathology and laboratory medicine",
"pathogens",
"immunology",
"microbiology",
"viruses",
"filoviruses",
"rna viruses",
"cytotoxic t cells",
"infectious d... | A modified anthrax toxin-based enzyme-linked immunospot assay reveals robust T cell responses in symptomatic and asymptomatic Ebola virus exposed individuals | journal.pntd.0006530 | null | [
[
"Ebola viruses including the five antigenically distinct species , Bundibugyo ebolavirus ( BDBV ) , Reston ebolavirus ( RESTV ) , Tai Forest ebolavirus ( TAFV ) , Sudan ebolavirus ( SUDV ) , and Zaire ebolavirus ( EBOV ) , are enveloped filamentous viruses belonging to the family Filoviridae [1–3] .",
"Th... | [
"Ebola virus ( EBOV ) caused more than 11 , 000 deaths during the 2013–2016 epidemic in West Africa without approved vaccines or immunotherapeutics .",
"Despite its high lethality in some individuals , EBOV infection can produce little to no symptoms in others .",
"A better understanding of the immune responses... | [
"The 2013–2016 West African Ebola virus ( EBOV ) outbreak is the largest on record with over 28 , 000 reported symptomatic cases and more than 11 , 000 deaths .",
"We developed a simple and inexpensive modified anthrax toxin-based ELISPOT assay to detect and characterize the T cell responses elicited by prior exp... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/immune response",
"immunology/innate immunity",
"microbiology/parasitology",
"infectious diseases/protozoal infections",
"immunology/immunity to infections"
] | Leishmania-Induced Inactivation of the Macrophage Transcription Factor AP-1 Is Mediated by the Parasite Metalloprotease GP63 | journal.ppat.1001148 | null | [
[
"Parasites of the Leishmania genus are the causative agent of leishmaniasis; a disease distributed worldwide affecting more than 12 million people in 88 countries [1] .",
"Leishmaniasis is a complex of diseases ranging from self-healing cutaneous lesions to lethal visceral afflictions [2] .",
"In its ... | [
"Leishmania parasites have evolved sophisticated mechanisms to subvert macrophage immune responses by altering the host cell signal transduction machinery , including inhibition of JAK/STAT signalling and other transcription factors such as AP-1 , CREB and NF-κB .",
"AP-1 regulates pro-inflammatory cytokines , ch... | [
"Leishmaniasis is a tropical disease affecting more than 12 million people around the world .",
"The disease is caused by the Leishmania parasites that are transmitted to the mammalian host by a sandfly vector when it takes a blood meal .",
"The parasites are able to survive and multiply inside of cells that co... | 2010 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"immunology",
"biology",
"computational biology"
] | Models of Self-Peptide Sampling by Developing T Cells Identify Candidate Mechanisms of Thymic Selection | journal.pcbi.1003102 | null | [
[
"Conventional T cells ( T ) and T regulatory cells ( T ) are essential components of the adaptive immune system .",
"Conventional T cells develop effector function in response to foreign antigens , while natural T regulatory cells produced in the thymus play a key role in the maintenance of tolerance to s... | [
"Conventional and regulatory T cells develop in the thymus where they are exposed to samples of self-peptide MHC ( pMHC ) ligands .",
"This probabilistic process selects for cells within a range of responsiveness that allows the detection of foreign antigen without excessive responses to self .",
"Regulatory T ... | [
"T cells develop in the thymus , where they are vetted – they must respond weakly to self-antigens , but not so strongly as to risk causing autoimmunity .",
"This selection process involves developing T cells being exposed to a large sample of self-peptides presented on specialised cells in the thymus , and decid... | 2013 |
[
"Introduction",
"Materials and Methods",
"Results and Discussion"
] | [
"medicine and health sciences",
"microcephaly",
"pathology and laboratory medicine",
"gene regulation",
"pathogens",
"microbiology",
"database searching",
"human genomics",
"viruses",
"developmental biology",
"micrornas",
"rna viruses",
"genome analysis",
"morphogenesis",
"thermodynamics... | ZIKV – CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms | journal.pntd.0004817 | null | [
[
"Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus , first isolated in 1947 from the serum of a pyrexial rhesus monkey caged in the Zika Forest ( Uganda/Africa ) [1] .",
"In 2007 , ZIKV was reported linked to an outbreak of relatively mild disease , characterized by rash , arthralgia , and conj... | [
"In early 2015 , a ZIKA Virus ( ZIKV ) infection outbreak was recognized in northeast Brazil , where concerns over its possible links with infant microcephaly have been discussed .",
"Providing a causal link between ZIKV infection and birth defects is still a challenge .",
"MicroRNAs ( miRNAs ) are small noncod... | [
"The potential interaction between ZIKA Virus ( ZIKV ) infection and infant brain defects still has no explanatory mechanism .",
"The mechanism of action for several other viruses have been described , and are often related to the control or production of sncRNA ( small noncoding RNA ) molecules , which regulate ... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | ATPaseTb2, a Unique Membrane-bound FoF1-ATPase Component, Is Essential in Bloodstream and Dyskinetoplastic Trypanosomes | journal.ppat.1004660 | null | [
[
"Trypanosomes are unicellular flagellates from the order Kinetoplastida , which is comprised of some of the most devastating human pathogens in the world .",
"For example , in sub-Saharan Africa , infection from Trypanosoma brucei gambiense and T .",
"b . rhodesiense causes Human African Trypanosomias... | [
"In the infectious stage of Trypanosoma brucei , an important parasite of humans and livestock , the mitochondrial ( mt ) membrane potential ( Δψm ) is uniquely maintained by the ATP hydrolytic activity and subsequent proton pumping of the essential FoF1-ATPase .",
"Intriguingly , this multiprotein complex contai... | [
"The presence of the FoF1-ATP synthase in every aerobic organism suggests that evolution has settled on a basic blueprint for the complex rotary motor capable of synthesizing life’s universal energy currency—ATP .",
"However , compared to yeast and mammalian models of the FoF1-ATP synthase , several recent studie... | 2015 |
[
"Introduction",
"Methods",
"Discussion"
] | [] | Brucellosis and Coxiella burnetii Infection in Householders and Their Animals in Secure Villages in Herat Province, Afghanistan: A Cross-Sectional Study | journal.pntd.0004112 | null | [
[
"Brucellosis and coxiellosis are known to be endemic in ruminant populations throughout Afghanistan but information about their prevalence and factors that affect prevalence in householders and livestock under diverse husbandry systems and pastoral settings is sparse .",
"Brucellosis in animals results in... | [
"Brucellosis and coxiellosis are known to be endemic in ruminant populations throughout Afghanistan , but information about their prevalence and factors that affect prevalence in householders and livestock under diverse husbandry systems and pastoral settings is sparse .",
"We conducted a cross-sectional survey t... | [
"Our study alerted authorities to a hitherto unrecognised high prevalence of C . burnetii infections , acted as a catalyst for the introduction of a national vaccination programme for protection of sheep and goats from brucellosis using Rev1 vaccine , demonstrated the benefits of a coordinated approach and fostered... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology"
] | Antagonism of LIN-17/Frizzled and LIN-18/Ryk in Nematode Vulva Induction Reveals Evolutionary Alterations in Core Developmental Pathways | journal.pbio.1001110 | null | [
[
"Biological diversity in metazoans is basically generated by two principles , the evolution of novelty and the modification of already existing structures .",
"Many case studies in recent years have shown that the evolution of novelty often depends on the co-option of developmental control genes in new ce... | [
"Most diversity in animals and plants results from the modification of already existing structures .",
"Many organ systems , for example , are permanently modified during evolution to create developmental and morphological diversity , but little is known about the evolution of the underlying developmental mechani... | [
"Diversity of biological form in animals can be generated by the modification of already existing developmental and morphological structures .",
"One major challenge in evolutionary biology is to identify the molecular and genetic changes associated with such morphological modifications .",
"A decade ago , the ... | 2011 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"cellular stress responses",
"caulobacter",
"enzymes",
"cell processes",
"enzymology",
"mutation",
"prokaryotic models",
"dna replication",
"experimental organism systems",
"gene types",
"dna",
"molecular biology techniques",
"bacteria",
"research and analysis methods",
"heat shock respo... | An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus | journal.pgen.1007148 | null | [
[
"Hsp70 proteins play a key role in thermal stress adaptation by assisting the folding and refolding of client proteins , thereby preventing and reversing the accumulation of toxic protein aggregates [1] .",
"In addition to this chaperoning activity these proteins can play critical roles in regulating gene... | [
"Hsp70 chaperones are well known for their important functions in maintaining protein homeostasis during thermal stress conditions .",
"In many bacteria the Hsp70 homolog DnaK is also required for growth in the absence of stress .",
"The molecular reasons underlying Hsp70 essentiality remain in most cases uncle... | [
"Molecular chaperones of the Hsp70 family belong to the most conserved cellular machineries throughout the tree of life .",
"These proteins play key roles in maintaining protein homeostasis , especially under heat stress conditions .",
"In diverse bacteria the Hsp70 homolog DnaK is essential for growth even in ... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data | journal.pcbi.1003314 | null | [
[
"Determining the functions of proteins is a central goal of genetics , fundamental for understanding the molecular basis of diverse genetic diseases [1]–[7] .",
"During the past few decades , significant efforts have been made to integrate and develop diverse machine learning algorithms for gene function ... | [
"Integrating large-scale functional genomic data has significantly accelerated our understanding of gene functions .",
"However , no algorithm has been developed to differentiate functions for isoforms of the same gene using high-throughput genomic data .",
"This is because standard supervised learning requires... | [
"In mammalian genomes , a single gene can be alternatively spliced into multiple isoforms which greatly increase the functional diversity of the genome .",
"In the human , more than 95% of multi-exon genes undergo alternative splicing .",
"It is hard to computationally differentiate the functions for the splice... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetic networks",
"neural networks",
"engineering and technology",
"neuroscience",
"logic circuits",
"network analysis",
"genome analysis",
"computer and information sciences",
"animal cells",
"evolutionary genetics",
"cellular neuroscience",
"cell biology",
"gene regulatory networks",
"... | The Evolutionary Origins of Hierarchy | journal.pcbi.1004829 | null | [
[
"Hierarchy is an important organizational property in many biological and man-made systems , ranging from neural [1 , 2] , ecological [3] , metabolic [4] , and genetic regulatory networks [5] , to the organization of companies [6] , cities [7] , societies [8] , and the Internet [9 , 10] .",
"There are man... | [
"Hierarchical organization—the recursive composition of sub-modules—is ubiquitous in biological networks , including neural , metabolic , ecological , and genetic regulatory networks , and in human-made systems , such as large organizations and the Internet .",
"To date , most research on hierarchy in networks ha... | [
"Hierarchy is a ubiquitous organizing principle in biology , and a key reason evolution produces complex , evolvable organisms , yet its origins are poorly understood .",
"Here we demonstrate for the first time that hierarchy evolves as a result of the costs of network connections .",
"We confirm a previous fin... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood serum",
"complement system",
"medicine and health sciences",
"parasite groups",
"immune physiology",
"body fluids",
"immunology",
"parasitic diseases",
"parasitic protozoans",
"parasitology",
"parasitemia",
"animal models",
"apicomplexa",
"model organisms",
"protozoans",
"experi... | Plasmodium-specific antibodies block in vivo parasite growth without clearing infected red blood cells | journal.ppat.1007599 | null | [
[
"Clinical symptoms of malaria occur during the erythrocytic phase of infection , when Plasmodium parasites mature and replicate asexually in red blood cells ( RBC ) [1] .",
"A key feature of the asexual life-cycle in RBC is the capacity for rapid population growth , because each parasite can produce many ... | [
"Plasmodium parasites invade and multiply inside red blood cells ( RBC ) .",
"Through a cycle of maturation , asexual replication , rupture and release of multiple infective merozoites , parasitised RBC ( pRBC ) can reach very high numbers in vivo , a process that correlates with disease severity in humans and ex... | [
"Malaria occurs when Plasmodium parasites replicate inside red blood cells , with the number of parasitised cells ( pRBC ) correlating with disease severity .",
"Antibodies are highly effective at controlling pRBC numbers in the bloodstream , and yet we know very little about how they function in vivo .",
"Huma... | 2019 |
[
"Introduction",
"Results and discussion",
"Materials and methods"
] | [
"biotechnology",
"medicine and health sciences",
"methods and resources",
"crystal structure",
"chemical compounds",
"small molecules",
"nmr spectroscopy",
"immunology",
"condensed matter physics",
"organic compounds",
"crystals",
"materials science",
"centrifugation",
"materials physics",... | Insight into small molecule binding to the neonatal Fc receptor by X-ray crystallography and 100 kHz magic-angle-spinning NMR | journal.pbio.2006192 | null | [
[
"In order to discover new chemical drugs , fragment screening followed by structure-based design is an efficient way to sample chemical space and find hits for challenging target classes such as protein-protein interactions [1–3] .",
"In addition to discovering orthosteric ligands , fragment screening has... | [
"Aiming at the design of an allosteric modulator of the neonatal Fc receptor ( FcRn ) –Immunoglobulin G ( IgG ) interaction , we developed a new methodology including NMR fragment screening , X-ray crystallography , and magic-angle-spinning ( MAS ) NMR at 100 kHz after sedimentation , exploiting very fast spinning ... | [
"In drug design , a detailed characterization of structural changes induced by drug binding is useful for further optimizing lead compounds .",
"In many cases , structural alterations are distant from the compound binding site , potentially acting through allosteric effects .",
"These allosteric effects are oft... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"neuroscience",
"homo (human)"
] | Gamma Oscillations in Human Primary Somatosensory Cortex Reflect Pain Perception | journal.pbio.0050133 | Magnetoencephalography reveals that gamma oscillations in the somatosensory cortex correlate with the subjective rating of pain and are stronger for laser stimuli that cause pain, compared with the same stimuli when no pain is perceived. | [
[
"Within the continuous flow of sensory information , a huge number of events compete for neural representation and perception .",
"This sensory overflow requires the selection and preferential processing of relevant information in order to optimize the utilization of cerebral processing resources .",
... | [
"Successful behavior requires selection and preferred processing of relevant sensory information .",
"The cortical representation of relevant sensory information has been related to neuronal oscillations in the gamma frequency band .",
"Pain is of invariably high behavioral relevance and , thus , nociceptive st... | [
"Pain is a highly subjective sensation of inherent behavioral importance and is therefore expected to receive enhanced processing in relevant brain regions .",
"We show that painful stimuli induce high-frequency oscillations in the electrical activity of the human primary somatosensory cortex .",
"Amplitudes of... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"physics",
"biochemistry",
"protein interactions",
"theoretical biology",
"interdisciplinary physics",
"molecular biology",
"biophysics theory",
"synthetic biology",
"biology",
"computational biology",
"metabolic networks",
"biophysics",
"proteomics"
] | Genetic Co-Occurrence Network across Sequenced Microbes | journal.pcbi.1002340 | null | [
[
"An important challenge in biology is to understand the relationships between an organism's genotype and its phenotype , involving dissection of myriad interdependencies among various cellular components , such as genes , proteins , and small molecules [1] , [2] .",
"Recent efforts to map protein-protein ... | [
"The phenotype of any organism on earth is , in large part , the consequence of interplay between numerous gene products encoded in the genome , and such interplay between gene products affects the evolutionary fate of the genome itself through the resulting phenotype .",
"In this regard , contemporary genomes ca... | [
"Genes in organisms have a number of interactions with one another in their biological contexts .",
"For example , proteins produced from one gene may interact with other proteins produced from another gene to perform together a particular biological task , and such pairs of cooperative genes may often reside tog... | 2011 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"ecology and environmental sciences",
"parasite groups",
"plasmodium",
"atmospheric science",
"tropical diseases",
"geographical locations",
"india",
"parasitic diseases",
"parasitic protozoans",
"parasitology",
"seasons",
"apicomplexa",
"plasmodium vivax",
... | Population Density, Climate Variables and Poverty Synergistically Structure Spatial Risk in Urban Malaria in India | journal.pntd.0005155 | null | [
[
"Addressing health problems associated with urban growth will be one of the major challenges of the 21st century , especially for the developing world [1] .",
"City life is associated with significant variation in socioeconomic and environmental conditions of potential relevance to vector-borne diseases [... | [
"The world is rapidly becoming urban with the global population living in cities projected to double by 2050 .",
"This increase in urbanization poses new challenges for the spread and control of communicable diseases such as malaria .",
"In particular , urban environments create highly heterogeneous socio-econo... | [
"Urbanization and environmental change are the main driving forces of ecological and social change around the globe , specifically in developing countries and for human health .",
"Cities in developing countries exhibit rapid and unplanned urbanization which creates heterogeneous environmental and socio-economic ... | 2016 |
[
"Introduction",
"Recent Applications Made Possible by Hardware and Algorithmic Advancements",
"Categorization by Algorithmic Frameworks",
"Conclusions"
] | [
"applied mathematics",
"simulation and modeling",
"algorithms",
"review",
"mathematics",
"protein structure prediction",
"protein structure",
"macromolecules",
"thermodynamics",
"research and analysis methods",
"polymer chemistry",
"proteins",
"chemistry",
"biophysics",
"molecular biolog... | Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics | journal.pcbi.1004619 | null | [
[
"A detailed understanding of how fundamental biological macromolecules , such as proteins and nucleic acids , carry out their biological functions is central to obtaining a detailed and complete picture of molecular mechanisms in the healthy and diseased cell .",
"Furthering our understanding of macromole... | [
"Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell .",
"Significant advances have been made toward this end in silico , with a growing number of computational methods proposed yearly to study and simulate various aspects... | [
"This paper provides an overview of recent advancements in computational methods for modeling macromolecular structure and dynamics .",
"The focus is on methods aimed at providing efficient representations of macromolecular structure spaces for the purpose of characterizing equilibrium dynamics .",
"The overvie... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"blood cells",
"cell physiology",
"medicine and health sciences",
"immune cells",
"immune physiology",
"pathology and laboratory medicine",
"body fluids",
"spleen",
"pathogens",
"293t cells",
"immunology",
"biological cultures",
"microbiology",
"rna extraction",
"retroviruses",
"viruse... | PDZ domain-binding motif of Tax sustains T-cell proliferation in HTLV-1-infected humanized mice | journal.ppat.1006933 | null | [
[
"HTLV-1 ( Human T-cell leukemia virus , type 1 ) is the etiological agent of adult T-cell leukemia/lymphoma ( ATLL ) , an aggressive and fatal form of leukemia characterized by the malignant expansion of activated CD4+ T-cells [1] .",
"Among several non-structural regulatory proteins encoded by HTLV-1 , T... | [
"Human T-cell leukemia virus type 1 ( HTLV-1 ) is the etiological agent of adult T-cell leukemia/lymphoma ( ATLL ) , an aggressive malignant proliferation of activated CD4+ T lymphocytes .",
"The viral Tax oncoprotein is critically involved in both HTLV-1-replication and T-cell proliferation , a prerequisite to t... | [
"The viral Tax oncoprotein is a critical contributor to the development of adult T-cell leukemia/lymphoma , an aggressive malignant proliferation of T lymphocytes .",
"Tax contains a PDZ domain-binding motif ( PBM ) that favors the interaction with several cellular PDZ proteins .",
"Here , we compare the in viv... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Conclusion",
"Methods"
] | [
"genome-wide association studies",
"applied mathematics",
"brassica",
"quantitative traits",
"simulation and modeling",
"algorithms",
"model organisms",
"mathematics",
"statistics (mathematics)",
"genome analysis",
"experimental organism systems",
"plants",
"arabidopsis thaliana",
"researc... | Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies | journal.pcbi.1005357 | null | [
[
"Genome-wide association study ( GWAS ) focuses on associations between single nucleotide polymorphism ( SNP ) and traits of interest in order to investigate the genetic foundation of these traits [1 , 2] .",
"In GWAS , hundreds of thousands of SNPs are genotyped for several hundreds of individuals .",
... | [
"Genome-wide association study ( GWAS ) entails examining a large number of single nucleotide polymorphisms ( SNPs ) in a limited sample with hundreds of individuals , implying a variable selection problem in the high dimensional dataset .",
"Although many single-locus GWAS approaches under polygenic background a... | [
"Genome-wide association study is concerned with the associations between markers and traits of interest so as to identify all the significantly associated markers .",
"In genome-wide association studies , hundreds of thousands of markers are genotyped for several hundreds of individuals .",
"Usually , only a v... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"medicine and health sciences",
"kidney development",
"marker genes",
"precursor cells",
"developmental biology",
"organism development",
"stem cells",
"nephrons",
"molecular biology techniques",
"kidneys",
"research and analysis methods",
"specimen preparation and treatment",
"staining",
... | Single-cell transcriptomics reveals gene expression dynamics of human fetal kidney development | journal.pbio.3000152 | A detailed transcriptomic characterization of the human fetal kidney at the single-cell level allows the identification of 22 cell types and a host of novel marker genes, revealing heterogeneity in the nephrogenic niche and localized podocyte precursors. | [
[
"Mammalian kidney development initiates in the intermediate mesoderm through crosstalk between the metanephric mesenchyme ( MM ) and the ureteric bud ( UB ) .",
"The UB originates from the nephric duct , invades the MM , and starts to subdivide progressively into multiple ramifications .",
"The UB tip... | [
"The current understanding of mammalian kidney development is largely based on mouse models .",
"Recent landmark studies revealed pervasive differences in renal embryogenesis between mouse and human .",
"The scarcity of detailed gene expression data in humans therefore hampers a thorough understanding of human ... | [
"Regenerative medicine offers an exciting avenue to potential cures of kidney disease .",
"However , a detailed knowledge of the structure and embryonic development of the kidney is crucial , both for stimulating regeneration in the body and for growing healthy kidney tissue in a dish .",
"Most of such knowledg... | 2019 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | Direct Measurements of Local Coupling between Myosin Molecules Are Consistent with a Model of Muscle Activation | journal.pcbi.1004599 | null | [
[
"Muscle contraction underlies most voluntary and involuntary motion of multicellular animals .",
"The last 100 years have revolutionized our understanding of this process .",
"Advances in light microscopy in the early 20th century culminated in the sliding filament theory , the discovery that muscle c... | [
"Muscle contracts due to ATP-dependent interactions of myosin motors with thin filaments composed of the proteins actin , troponin , and tropomyosin .",
"Contraction is initiated when calcium binds to troponin , which changes conformation and displaces tropomyosin , a filamentous protein that wraps around the act... | [
"Despite decades of study , there is no clear connection between muscle contraction at the molecular and the macroscopic scale .",
"For example , we cannot yet predict how a genetic defect in a muscle protein will result in a physiological change in the heart .",
"This multi-scale understanding is difficult , i... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"infectious diseases",
"medicine and health sciences",
"viral transmission and infection",
"virology",
"biology and life sciences",
"microbiology",
"viral diseases",
"viral structure",
"rubella"
] | Rubella Virus: First Calcium-Requiring Viral Fusion Protein | journal.ppat.1004530 | null | [
[
"Rubella virus ( RuV ) is the causative agent of “German measles” , an airborne , relatively mild childhood disease [for review] , [ see 1 , 2] .",
"However , RuV infection of pregnant women can have very serious consequences due to transplacental infection of the fetus , causing first trimester miscarria... | [
"Rubella virus ( RuV ) infection of pregnant women can cause fetal death , miscarriage , or severe fetal malformations , and remains a significant health problem in much of the underdeveloped world .",
"RuV is a small enveloped RNA virus that infects target cells by receptor-mediated endocytosis and low pH-depend... | [
"Rubella virus ( RuV ) is a small enveloped RNA virus causing mild disease in children .",
"However , infection of pregnant women can produce fetal death or congenital rubella syndrome , a constellation of severe birth defects including cataracts , hearing loss , heart disease and developmental delays .",
"Whil... | 2014 |
[
"Introduction",
"Materials and Methods",
"Results",
"Discussion"
] | [
"medicine",
"biochemistry",
"infectious diseases",
"diagnostic medicine",
"immunology",
"biology",
"microbiology",
"proteomics"
] | Proteomic Selection of Immunodiagnostic Antigens for Human African Trypanosomiasis and Generation of a Prototype Lateral Flow Immunodiagnostic Device | journal.pntd.0002087 | null | [
[
"Human African Trypanosomiasis ( HAT ) , also known as Sleeping Sickness , is a disease caused by Trypanosoma brucei gambiense and T . b .",
"rhodesiense [1] , [2] , [3] .",
"The parasites are transmitted in sub-Saharan Africa by the bite from an infected tsetse fly .",
"HAT is of great public hea... | [
"The diagnosis of Human African Trypanosomiasis relies mainly on the Card Agglutination Test for Trypanosomiasis ( CATT ) .",
"While this test is successful , it is acknowledged that there may be room for improvement .",
"Our aim was to develop a prototype lateral flow test based on the detection of antibodies ... | [
"Human African Trypanosomiasis is caused by infection with Trypanosoma brucei gambiense or T . b .",
"rhodesiense .",
"Preliminary diagnosis of T . b .",
"gambiense infection relies mainly on a Card Agglutination Test for Trypanosomiasis ( CATT ) , which has acknowledged limitations .",
"New approaches are ... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"diabetes mellitus type 2",
"drugs and devices",
"endocrinology",
"pharmacogenetics",
"diabetic endocrinology",
"pharmacology",
"diabetes and endocrinology"
] | Genetic Modulation of Lipid Profiles following Lifestyle Modification or Metformin Treatment: The Diabetes Prevention Program | journal.pgen.1002895 | null | [
[
"Dyslipidemia is a strong risk factor for atherosclerotic heart disease [1]–[3] , has a well-defined genetic basis [4] , and is modifiable through therapeutic lifestyle changes and weight-loss interventions [5] , [6] .",
"Individuals at risk for diabetes are also at high risk of cardiovascular disease [7]... | [
"Weight-loss interventions generally improve lipid profiles and reduce cardiovascular disease risk , but effects are variable and may depend on genetic factors .",
"We performed a genetic association analysis of data from 2 , 993 participants in the Diabetes Prevention Program to test the hypotheses that a geneti... | [
"The study included 2 , 993 participants from the Diabetes Prevention Program , a randomized clinical trial of intensive lifestyle intervention , metformin treatment , and placebo control .",
"We examined associations between 32 gene variants that have been reproducibly associated with dyslipidemia and concentrat... | 2012 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods"
] | [
"evolutionary biology",
"drosophila 1"
] | Repetitive Element-Mediated Recombination as a Mechanism for New Gene Origination in Drosophila | journal.pgen.0040003 | null | [
[
"Gene duplication followed by the acquisition of novel molecular function is a fundamental process underlying biological diversity .",
"It has been theoretically and empirically demonstrated that functionally distinct duplicates are capable of evolving through a neofunctionalization process in which there... | [
"Previous studies of repetitive elements ( REs ) have implicated a mechanistic role in generating new chimerical genes .",
"Such examples are consistent with the classic model for exon shuffling , which relies on non-homologous recombination .",
"However , recent data for chromosomal aberrations in model organi... | [
"In numerous organisms , many new genes have been found to originate through dispersed gene duplication and exon/domain shuffling .",
"What recombination mechanisms were involved in the duplication and the shuffling processes ?",
"Lack of the intermediate products of recombination that share adequate sequence i... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biochemistry",
"plant science",
"model organisms",
"pest control",
"genetics",
"biology",
"microbiology",
"molecular cell biology",
"agriculture"
] | The Late Endosomal HOPS Complex Anchors Active G-Protein Signaling Essential for Pathogenesis in Magnaporthe oryzae | journal.ppat.1003527 | null | [
[
"Eukaryotes , ranging from yeasts to multicellular metazoans , interact with their environment , constantly sampling it for physico-chemical signals or cues for proper growth and development .",
"Extracellular ligands or stimuli detected by membrane bound GPCR ( G- protein coupled receptors ) are transmit... | [
"In Magnaporthe oryzae , the causal ascomycete of the devastating rice blast disease , the conidial germ tube tip must sense and respond to a wide array of requisite cues from the host in order to switch from polarized to isotropic growth , ultimately forming the dome-shaped infection cell known as the appressorium... | [
"Magnaporthe oryzae , a filamentous fungus , causes the devastating and economically important blast disease in rice and related species .",
"It produces asexual spores , conidia , which can switch to a disease-causing mode of development in response to host and environmental cues .",
"Activation of a highly co... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"signal transduction",
"immunity",
"mechanisms of signal transduction",
"innate immunity",
"immunology",
"biology",
"molecular cell biology"
] | A Distinct Role of Riplet-Mediated K63-Linked Polyubiquitination of the RIG-I Repressor Domain in Human Antiviral Innate Immune Responses | journal.ppat.1003533 | null | [
[
"The innate immune system is essential for controlling virus infections , and several viruses have evolved strategies to evade host innate immune responses .",
"Cytoplasmic viral RNA is recognized by RIG-I-like receptors , including RIG-I and MDA5 [1] , [2] .",
"The RIG-I protein comprises N-terminal ... | [
"The innate immune system is essential for controlling viral infections , but several viruses have evolved strategies to escape innate immunity .",
"RIG-I is a cytoplasmic viral RNA sensor that triggers the signal to induce type I interferon production in response to viral infection .",
"RIG-I activation is reg... | [
"The cytoplasmic viral RNA sensor RIG-I recognizes various types of pathogenic viruses and evokes innate immune responses , whereas several viruses have evolved strategies to escape the host innate immune responses .",
"RIG-I triggers a signal to induce type I interferon and inflammatory cytokines .",
"RIG-I ac... | 2013 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"biology and life sciences",
"immunology"
] | CD160-Associated CD8 T-Cell Functional Impairment Is Independent of PD-1 Expression | journal.ppat.1004380 | null | [
[
"Co-stimulatory and co-inhibitory molecules play a major role in the regulation of antigen-specific T-cell responses [1] .",
"Following T-cell receptor ( TCR ) engagement , activation or inhibition of T-cell responses depends upon the balance between stimulatory and inhibitory signals , on the type of mol... | [
"Expression of co-inhibitory molecules is generally associated with T-cell dysfunction in chronic viral infections such as HIV or HCV .",
"However , their relative contribution in the T-cell impairment remains unclear .",
"In the present study , we have evaluated the impact of the expression of co-inhibitory mo... | [
"T-cell immune response is regulated by a variety of molecules known as co-inhibitory receptors .",
"The over expression of co-inhibitory receptors has been observed in several chronic viral infections such as HIV disease , and is found to be associated with severe T-cell dysfunction .",
"Recent studies have de... | 2014 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"immunology/antigen processing and recognition",
"gastroenterology and hepatology/hepatology",
"immunology/immune response",
"virology/immune evasion",
"immunology/immunity to infections",
"infectious diseases/gastrointestinal infections"
] | Coexpression of PD-1, 2B4, CD160 and KLRG1 on Exhausted HCV-Specific CD8+ T Cells Is Linked to Antigen Recognition and T Cell Differentiation | journal.ppat.1000947 | null | [
[
"Virus-specific CD8+ T cells play a central role in the outcome of HCV infection .",
"Indeed , several human and animal studies have shown associations between strong and multispecific T cell responses and viral clearance [1] .",
"During chronic HCV infection , viral escape and an impairment of HCV-sp... | [
"Exhausted CD8+ T cell responses during chronic viral infections are defined by a complex expression pattern of inhibitory receptors .",
"However , very little information is currently available about the coexpression patterns of these receptors on human virus-specific CD8+ T cells and their correlation with anti... | [
"About 170 million people are infected with hepatitis C virus ( HCV ) , which may cause severe liver disease and liver cancer .",
"Upon acute infection , only about 30% of patients are able to eliminate the virus spontaneously while about 70% of patients develop chronic infection .",
"It is known that a success... | 2010 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"cell biology"
] | Redundant Mechanisms Recruit Actin into the Contractile Ring in Silkworm Spermatocytes | journal.pbio.0060209 | How is actin recruited to assemble a contractile ring during cytokinesis? Combining micromanipulation with pharmacological perturbation, this comprehensive study elegantly documents the contributions of two complementary mechanisms within one cell. | [
[
"The contractile ring is a dynamic , actomyosin-based structure whose constriction generates a cleavage furrow , ultimately producing two daughter cells .",
"To ensure accurate distribution of chromosomes to each cell , the location of the division plane and the timing of cleavage must be tightly regulate... | [
"Cytokinesis is powered by the contraction of actomyosin filaments within the newly assembled contractile ring .",
"Microtubules are a spindle component that is essential for the induction of cytokinesis .",
"This induction could use central spindle and/or astral microtubules to stimulate cortical contraction a... | [
"In animal cells , the last step of cell division , or cytokinesis , requires the action of a contractile ring—composed largely of actin and myosin filaments—that cleaves the cell in two .",
"Before the cell divides , it first duplicates its genome and separates the chromosomes into the two newly forming daughter... | 2008 |
[
"Introduction",
"Results/Discussion",
"Materials and Methods",
"Supporting Information"
] | [
"infectious diseases",
"genetics and genomics",
"microbiology",
"eubacteria"
] | Meningococcal Genetic Variation Mechanisms Viewed through Comparative Analysis of Serogroup C Strain FAM18 | journal.pgen.0030023 | null | [
[
"N . meningitidis ( the meningococcus ) colonizes the nonciliated columnar mucosal cells of the human nasopharynx as a harmless commensal organism and , as such , is carried by five to ten percent of the adult population [1 , 2] .",
"Some strains are able to cross the mucosa into the bloodstream from wher... | [
"The bacterium Neisseria meningitidis is commonly found harmlessly colonising the mucosal surfaces of the human nasopharynx .",
"Occasionally strains can invade host tissues causing septicaemia and meningitis , making the bacterium a major cause of morbidity and mortality in both the developed and developing worl... | [
"Human surface tissues , including the skin and gut lining , are host to many different species of bacteria .",
"N . meningitidis is a species of bacteria that is only found in humans where it is able to colonise mucosal surfaces of the nasopharynx ( nose and throat ) .",
"This association is normally harmless ... | 2007 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"machine learning algorithms",
"medicine and health sciences",
"immune physiology",
"pathology and laboratory medicine",
"pathogens",
"applied mathematics",
"immunology",
"microbiology",
"retroviruses",
"viruses",
"immunodeficiency viruses",
"algorithms",
"simulation and modeling",
"mathem... | Exploiting glycan topography for computational design of Env glycoprotein antigenicity | journal.pcbi.1006093 | null | [
[
"Env glycoproteins on the surface of enveloped viruses , such as HIV [1–4] , Dengue [5 , 6] , Ebola [7] , hepatitis C [8] , influenza [9] , Lassa [10] , and Zika [6 , 11] , are the primary vaccine targets for the induction of protective , broadly neutralizing antibodies ( bNAbs ) .",
"However , many of th... | [
"Mounting evidence suggests that glycans , rather than merely serving as a “shield” , contribute critically to antigenicity of the HIV envelope ( Env ) glycoprotein , representing critical antigenic determinants for many broadly neutralizing antibodies ( bNAbs ) .",
"While many studies have focused on defining th... | [
"Carbohydrates on the HIV Env glycoprotein , previously often considered as a “shield” permitting immune evasion , can themselves represent targets for broadly neutralizing antibody ( bNAb ) recognition .",
"Efforts to define the impact of individual glycans on bNAb recognition have clearly illustrated the critic... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"virology/vaccines",
"infectious diseases/viral infections",
"immunology/immune response",
"virology/host antiviral responses"
] | Maturation of West Nile Virus Modulates Sensitivity to Antibody-Mediated Neutralization | journal.ppat.1000060 | null | [
[
"Flaviviruses are a group of positive-stranded RNA viruses that are of global significance due to their widespread distribution and their ability to cause a variety of diseases in humans [1] .",
"West Nile virus ( WNV ) is a mosquito-borne member of this genus and is the etiologic agent of West Nile encep... | [
"West Nile virions incorporate 180 envelope ( E ) proteins that orchestrate the process of virus entry and are the primary target of neutralizing antibodies .",
"The E proteins of newly synthesized West Nile virus ( WNV ) are organized into trimeric spikes composed of pre-membrane ( prM ) and E protein heterodime... | [
"West Nile virus ( WNV ) virions incorporate 180 envelope ( E ) proteins that are the primary target of neutralizing antibodies .",
"As newly formed WNV virions are released from infected cells , the E proteins undergo a significant organizational change associated with maturation into an infectious virus .",
"... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"plant science",
"plant evolution",
"plant biology",
"gene expression",
"genetics",
"plant genetics",
"population genetics",
"biology",
"evolutionary biology",
"plant ecology",
"evolutionary genetics",
"genetics and genomics",
"plant-environment interactions"
] | The Genetic Basis of Pollinator Adaptation in a Sexually Deceptive Orchid | journal.pgen.1002889 | null | [
[
"Understanding the genetic basis of adaptation is of great interest to evolutionary biologists .",
"For over a century , it has been debated whether adaptations are likely caused by a large number of mutations of small phenotypic effect or by very few genetic changes of large effect [1]–[3] .",
"To ad... | [
"In plants , pollinator adaptation is considered to be a major driving force for floral diversification and speciation .",
"However , the genetic basis of pollinator adaptation is poorly understood .",
"The orchid genus Ophrys mimics its pollinators' mating signals and is pollinated by male insects during matin... | [
"In plants , the extraordinary floral diversity has been suggested to be a consequence of divergent adaptation .",
"However , the genetic basis of this process is poorly understood .",
"In this study , we take advantage of the high specificity of plant-pollinator interactions in the sexually deceptive orchid ge... | 2012 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine and health sciences",
"disabilities",
"tropical diseases",
"geographical locations",
"census",
"geoinformatics",
"health care",
"bacterial diseases",
"research design",
"neglected tropical diseases",
"spatial analysis",
"research and analysis methods",
"public and occupational heal... | Spatial clustering and local risk of leprosy in São Paulo, Brazil | journal.pntd.0005381 | null | [
[
"Leprosy is a chronic infectious-contagious disease caused by Mycobacterium Leprae , an obligate intracellular bacillus that affects the skin and the peripheral nervous system [1] .",
"Leprosy is characterized as a slowly advancing disease and , due to the characteristics of the bacillus , presents high i... | [
"Although the detection rate is decreasing , the proportion of new cases with WHO grade 2 disability ( G2D ) is increasing , creating concern among policy makers and the Brazilian government .",
"This study aimed to identify spatial clustering of leprosy and classify high-risk areas in a major leprosy cluster usi... | [
"Brazil has still not achieved the goal of leprosy elimination established by the World Health Organization .",
"The diagnosis and treatment of leprosy are available and the country is striving to fully integrate leprosy services into the existing general health services .",
"Access to information , diagnosis a... | 2017 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/comparative sequence analysis",
"computational biology/evolutionary modeling",
"molecular biology/bioinformatics",
"computational biology/macromolecular sequence analysis",
"evolutionary biology/bioinformatics",
"genetics and genomics/bioinformatics"
] | Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate | journal.pcbi.1000413 | null | [
[
"Different proteins evolve at drastically different rates [1] .",
"Some proteins are highly conserved across distantly diverged species , such as the ribosomal and histone proteins in eukaryotes [2] .",
"Other proteins evolve much more quickly , often to the point where they occur in one species but c... | [
"Rates of evolution differ widely among proteins , but the causes and consequences of such differences remain under debate .",
"With the advent of high-throughput functional genomics , it is now possible to rigorously assess the genomic correlates of protein evolutionary rate .",
"However , dissecting the corre... | [
"Proteins encoded within a given genome are known to evolve at drastically different rates .",
"Through recent large-scale studies , researchers have measured a wide variety of properties for all proteins in yeast .",
"We are interested to know how these properties relate to one another and to what extent they ... | 2009 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"sequencing techniques",
"dehydration (medicine)",
"medicine and health sciences",
"pathology and laboratory medicine",
"enzymes",
"enzymology",
"serine proteases",
"signs and symptoms",
"protein structure",
"lyases",
"molecular biology techniques",
"research and analysis methods",
"sequence... | Isofunctional Protein Subfamily Detection Using Data Integration and Spectral Clustering | journal.pcbi.1005001 | null | [
[
"Despite the best research efforts , a substantial and ever-increasing amount of predicted proteins still lack functional annotation [1] .",
"Indeed , the unprecedented increase in the number of new protein sequences being produced by genomics and proteomics projects , as well as the copious amounts of st... | [
"As increasingly more genomes are sequenced , the vast majority of proteins may only be annotated computationally , given experimental investigation is extremely costly .",
"This highlights the need for computational methods to determine protein functions quickly and reliably .",
"We believe dividing a protein ... | [
"The knowledge of protein functions is central for understanding life at a molecular level and has huge biochemical and pharmaceutical implications .",
"However , despite best research efforts , a substantial and ever-increasing number of proteins predicted by genome sequencing projects still lack functional anno... | 2016 |
[
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational biology/evolutionary modeling",
"evolutionary biology/bioinformatics"
] | Facilitated Variation: How Evolution Learns from Past Environments To Generalize to New Environments | journal.pcbi.1000206 | null | [
[
"The origin of the ability to generate novelty is one of the main mysteries in evolution .",
"Pioneers of evolutionary theory , including Baldwin [1] , Simpson [2] , and Waddington [3] , [4] , suggested how useful novelty might be enhanced by physiological adaptations and by the robustness of the developm... | [
"One of the striking features of evolution is the appearance of novel structures in organisms .",
"Recently , Kirschner and Gerhart have integrated discoveries in evolution , genetics , and developmental biology to form a theory of facilitated variation ( FV ) .",
"The key observation is that organisms are desi... | [
"One of the striking features of evolution is the appearance of novel structures in organisms .",
"The origin of the ability to generate novelty is one of the main mysteries in evolutionary theory .",
"The molecular mechanisms that enhance the evolution of novelty were recently integrated by Kirschner and Gerha... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"cell biology",
"molecular biology",
"genetics and genomics"
] | Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast | journal.pbio.0060326 | During nutritional adaptation, transcriptional activation in yeast produces noncoding RNAs that allow the formation of a positive-feedback regulatory loop. | [
[
"When environmental conditions change , the budding yeast Saccharomyces cerevisiae , like other microorganisms , makes a decision about growth , cell division , and which responses to elicit in a coordinated fashion .",
"Starvation for nutrients , alterations in temperature or salt concentration , and the... | [
"The budding yeast Saccharomyces cerevisiae alters its gene expression profile in response to a change in nutrient availability .",
"The PHO system is a well-studied case in the transcriptional regulation responding to nutritional changes in which a set of genes ( PHO genes ) is expressed to activate inorganic ph... | [
"How does a microorganism adapt to changes in its environment ?",
"Phosphate metabolism in the budding yeast Saccharomyces cerevisiae serves as a model for investigating mechanisms involved in physiological adaptation .",
"The nutrient inorganic phosphate ( Pi ) is essential for building nucleic acids and phosp... | 2008 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [] | Hyperdiverse Gene Cluster in Snail Host Conveys Resistance to Human Schistosome Parasites | journal.pgen.1005067 | null | [
[
"Schistosomiasis is by far the most important helminth parasitic disease of humans .",
"Schistosomes infect over 200 million people worldwide [1 , 2] , causing a chronic , debilitating disease that can lead to lifelong disability [3 , 4] .",
"The disability-adjusted-life years lost to this disease are... | [
"Schistosomiasis , a neglected global pandemic , may be curtailed by blocking transmission of the parasite via its intermediate hosts , aquatic snails .",
"Elucidating the genetic basis of snail-schistosome interaction is a key to this strategy .",
"Here we map a natural parasite-resistance polymorphism from a ... | [
"Schistosomes are water-borne blood-flukes that are transmitted by snail vectors .",
"They infect over 200 million people in more than 70 countries and cause severe and chronic disability .",
"Snails naturally vary in resistance to this parasite even within species , so bolstering snail resistance in the wild w... | 2015 |
[
"Introduction",
"Results",
"Discussion",
"Materials and methods"
] | [
"b vitamins",
"chemical compounds",
"biotin",
"gene regulation",
"organic compounds",
"notch signaling",
"cell differentiation",
"developmental biology",
"regulator genes",
"genome analysis",
"gene types",
"genomics",
"gene expression",
"chemistry",
"vitamins",
"signal transduction",
... | Ikaros cooperates with Notch activation and antagonizes TGFβ signaling to promote pDC development | journal.pgen.1007485 | null | [
[
"Dendritic cells ( DCs ) are essential modulators of the immune response [1] .",
"They can be broadly divided into conventional DCs ( cDC ) , which are required for antigen presentation , and plasmacytoid DCs ( pDC ) , which secrete high quantities of type-I interferon ( IFN-α , -β , -ω ) upon certain vir... | [
"Plasmacytoid and conventional dendritic cells ( pDCs and cDCs ) arise from monocyte and dendritic progenitors ( MDPs ) and common dendritic progenitors ( CDPs ) through gene expression changes that remain partially understood .",
"Here we show that the Ikaros transcription factor is required for DC development a... | [
"Dendritic cells ( DCs ) are an important component of the immune system , and exist as two major subtypes: conventional DCs ( cDCs ) which present antigen via major histocompatibility class II molecules , and plasmacytoid DCs ( pDCs ) which act mainly as producers of type-I interferon in response to viral infectio... | 2018 |
[
"Introduction",
"Results",
"Discussion",
"Materials and Methods"
] | [
"developmental biology",
"paleontology",
"biology and life sciences",
"evolutionary biology",
"zoology"
] | New Developmental Evidence Clarifies the Evolution of Wrist Bones in the Dinosaur–Bird Transition | journal.pbio.1001957 | A new study that integrates developmental and paleontological data reveals previously unsuspected evolutionary transformations during the emergence of the bird wrist, consistent with its derivation from non-avian dinosaurs. | [
[
"The wing of birds is highly derived , having reduced the number of ossifications present in the wrist .",
"Early dinosaurs had as many as nine ossifications ( Figure 1A ) [1] , whereas in birds , only four carpal ossifications remain , two distal and two proximal ( Figure 1B ) [2] .",
"The two distal... | [
"From early dinosaurs with as many as nine wrist bones , modern birds evolved to develop only four ossifications .",
"Their identity is uncertain , with different labels used in palaeontology and developmental biology .",
"We examined embryos of several species and studied chicken embryos in detail through a ne... | [
"When birds diverged from nonavian dinosaurs , one of the key adaptations for flight involved a remodelling of the bones of the wrist .",
"However , the correspondence between bird and dinosaur wrist bones is controversial .",
"To identify the bones in the bird wrist , data can be drawn from two radically diffe... | 2014 |
[
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"computer and information sciences",
"natural language processing",
"network analysis",
"regulatory networks",
"biology and life sciences",
"information technology",
"computational biology"
] | Augmenting Microarray Data with Literature-Based Knowledge to Enhance Gene Regulatory Network Inference | journal.pcbi.1003666 | null | [
[
"Previous computational models used to reconstruct gene regulatory networks from microarray data have employed techniques such as Hidden Markov , Bayesian network , and stochastic differential equation models [11]–[15] .",
"In a Hidden Markov Model , the real states of genes are treated as hidden variable... | [
"Gene regulatory networks are a crucial aspect of systems biology in describing molecular mechanisms of the cell .",
"Various computational models rely on random gene selection to infer such networks from microarray data .",
"While incorporation of prior knowledge into data analysis has been deemed important , ... | [
"We have developed a methodology that combines standard computational analysis of gene expression data with knowledge in the literature to identify pathways of gene and protein interactions .",
"We extract the knowledge from PubMed citations using a tool ( SemRep ) that identifies specific relationships between g... | 2014 |
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