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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" ]	[ "genetics", "biology", "genetics and genomics", "gene function" ]	Poly(ADP-Ribose) Polymerase 1 (PARP-1) Regulates Ribosomal Biogenesis in Drosophila Nucleoli	journal.pgen.1002442	null	[ [ "The nuclear substructure , nucleolus , is a site commonly associated with translational complex assembly , and thus functions as a major regulator of cell growth [1] .", "The nucleolus is composed of an array of tandem repeated units of ribosomal RNA ( rRNA ) genes , some of which are transcribed , while...	[ "Poly ( ADP-ribose ) polymerase 1 ( PARP1 ) , a nuclear protein , utilizes NAD to synthesize poly ( AD-Pribose ) ( pADPr ) , resulting in both automodification and the modification of acceptor proteins .", "Substantial amounts of PARP1 and pADPr ( up to 50% ) are localized to the nucleolus , a subnuclear organell...	[ "Ribosome assembly happens primarily in the subnuclear organelle nucleolus .", "In the nucleolus , ribosomes are assembled into a multmeric complex , composed of rRNA and ribosomal proteins .", "Although a lot is known about ribosomes and how they function , very little is known about the mechanism that facilit...	2012
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing techniques", "microhomology-mediated end joining", "genome sequencing", "non-homologous end joining", "genome analysis", "bioassays and physiological analysis", "dna", "molecular biology techniques", "research and analysis methods", "genomic libraries", "genome complexity", "chromo...	Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization	journal.pgen.1007780	null	[ [ "Structural variants ( SVs ) contribute to genomic diversity in human [1] and include copy number variants ( CNVs ) ( deletions , duplications ) , as well as copy number neutral ( balanced ) variants ( inversions and translocations ) , and more complex rearrangements , resulting from chromothripsis and/or chr...	[ "Clustered copy number variants ( CNVs ) as detected by chromosomal microarray analysis ( CMA ) are often reported as germline chromothripsis .", "However , such cases might need further investigations by massive parallel whole genome sequencing ( WGS ) in order to accurately define the underlying complex rearran...	[ "Clustered copy number variants ( CNVs ) as detected by chromosomal microarray are often reported as germline chromoanagenesis .", "However , such cases might need further investigation by whole genome sequencing ( WGS ) to accurately resolve the complexity of the structural rearrangement and predict underlying m...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "microbiology", "cell differentiation", "developmental biology", "morphogenesis", "mycology", "cell adhesion", "microbial pathogens", "biology", "pathogenesis", "cell biology", "sexual differentiation", "genetics", "molecular cell biology", "gene networks", "genetics and genomics" ]	The Link between Morphotype Transition and Virulence in Cryptococcus neoformans	journal.ppat.1002765	null	[ [ "Adaptation to the host environment by many eukaryotic pathogens is often companied by transition in cellular morphology [1] , [2] , [3] , [4] , [5] , [6] , [7] , [8] , [9] .", "The ubiquitous fungal pathogen Cryptococcus neoformans causes more than half a million deaths each year [10] .", "It can gro...	[ "Cryptococcus neoformans is a ubiquitous human fungal pathogen .", "This pathogen can undergo morphotype transition between the yeast and the filamentous form and such morphological transition has been implicated in virulence for decades .", "Morphotype transition is typically observed during mating , which is ...	[ "Although morphogenesis and virulence are commonly associated in many eukaryotic pathogens , the nature of such association is often unknown .", "For example , Cryptococcus neoformans , a fungal pathogen that causes cryptococcal meningitis , typically undergoes morphological transition between the yeast and the f...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "cognitive neurology", "medicine and health sciences", "growth restriction", "onchocerca volvulus", "integumentary system", "helminths", "tropical diseases", "parasitic diseases", "animals", "onchocerca", "neuroscience", "pediatrics", "epileptic seizures", "cognitive neu...	Onchocerciasis-associated epilepsy in the Democratic Republic of Congo: Clinical description and relationship with microfilarial density	journal.pntd.0007300	null	[ [ "As early as the 1930s , onchocerciasis was already suspected to cause seizures [1] .", "A meta-analysis has reported a 0 . 4% increase in epilepsy prevalence , for every 10% increase in onchocerciasis prevalence [2] .", "Today , there is increasing evidence that onchocerciasis is a risk factor for ep...	[ "High epilepsy prevalence and incidence were observed in onchocerciasis-endemic villages in the Democratic Republic of Congo ( DRC ) .", "We investigated the clinical characteristics of onchocerciasis-associated epilepsy ( OAE ) , and the relationship between seizure severity and microfilarial density .", "In O...	[ "Several epidemiological surveys suggest that onchocerciasis ( a disease resulting from an infection with the parasite Onchocerca volvulus ) is a cause of epilepsy .", "We conducted a study to describe the clinical characteristics of persons with epilepsy ( PWE ) living in onchocerciasis-endemic villages in the D...	2019
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "medicine and health sciences", "paracrine signaling", "animals", "epithelial cells", "endocrine physiology", "oncology", "animal models", "developmental biology", "drosophila melanogaster", "model organisms", "stem cells", "connective tissue cells", "experimental organism...	Cytoneme-mediated signaling essential for tumorigenesis	journal.pgen.1008415	null	[ [ "Human tumors include transformed tumor cells , blood vessels , immune response cells , and stromal cells that together with the extracellular matrix ( ECM ) constitute a “tumor microenvironment” [1] .", "The tumor microenvironment is essential for oncogenesis , cell survival , tumor progression , invasio...	[ "Communication between neoplastic cells and cells of their microenvironment is critical to cancer progression .", "To investigate the role of cytoneme-mediated signaling as a mechanism for distributing growth factor signaling proteins between tumor and tumor-associated cells , we analyzed EGFR and RET Drosophila ...	[ "The growth of many types of tumors depend on productive interactions with stromal , non-tumor neighbors , and although there is evidence that tumor and stromal cells exchange signaling proteins and growth factors that they produce , the mechanism by which these proteins move between the signaling cells has not bee...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "pathogens", "endocrine tumors", "immunology", "carcinomas", "microbiology", "basic cancer research", "cancers and neoplasms", "biomarkers", "orthomyxoviruses", "cell processes", "oncology", "viruses", "rna viruses", ...	Quantifying critical states of complex diseases using single-sample dynamic network biomarkers	journal.pcbi.1005633	null	[ [ "Biomarkers , which are indicators of physiological states for living things , are commonly used to examine organ functions or disease states in biology or medicine .", "Generally , complex disease progression can be divided into three states , i . e . , normal , pre-disease and disease ( Fig 1A ) [1 , 2]...	[ "Dynamic network biomarkers ( DNB ) can identify the critical state or tipping point of a disease , thereby predicting rather than diagnosing the disease .", "However , it is difficult to apply the DNB theory to clinical practice because evaluating DNB at the critical state required the data of multiple samples o...	[ "The concept of dynamic network biomarkers ( DNB ) was proposed for detecting the critical state or tipping point of a complex disease ( a pre-disease state immediately preceding the disease state ) , and has been applied to study the mechanism of cell fate decision and immune checkpoint blockade .", "But DNB can...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "antimicrobials", "dermatology", "typhus", "medicine and health sciences", "enzyme-linked immunoassays", "drugs", "immunology", "microbiology", "observational studies", "bacterial diseases", "research design", "antibiotics", "pharmacology", "immunologic techniques", "research and analysi...	The validity of diagnostic cut-offs for commercial and in-house scrub typhus IgM and IgG ELISAs: A review of the evidence	journal.pntd.0007158	null	[ [ "Scrub typhus is a neglected tropical disease caused by the obligate intracellular bacterium Orientia tsutsugamushi [1] .", "Transmission of the bacteria to humans occurs via the bite of larval trombiculid mites , known commonly as chiggers [2] .", "It was formerly thought to be confined to the ‘tsuts...	[ "Scrub typhus is a neglected tropical disease that causes acute febrile illness .", "Diagnosis is made based upon serology , or detection of the causative agent–Orientia tsutsugamushi–using PCR or in vitro isolation .", "The enzyme-linked immunosorbent assay ( ELISA ) is an objective and reproducible means of d...	[ "Scrub typhus is a neglected tropical disease that causes acute fever and can cause serious complications without appropriate antibiotic treatment .", "Diagnosis is usually made by the detection of specific antibodies or the causative agent–Orientia tsutsugamushi .", "Specific antibodies can be detected using E...	2019
[ "Introduction", "Models", "Results", "Discussion" ]	[ "systems biology", "computer and information sciences", "biology and life sciences", "computational biology", "computerized simulations" ]	BiP Clustering Facilitates Protein Folding in the Endoplasmic Reticulum	journal.pcbi.1003675	null	[ [ "Protein homeostasis , or proteostasis , is characterized by the integration of biological pathways that modulate protein biogenesis , maturation , transport , and degradation .", "As a critical element to cell survival , networks of molecular chaperones , foldases , and quality control components minimiz...	[ "The chaperone BiP participates in several regulatory processes within the endoplasmic reticulum ( ER ) : translocation , protein folding , and ER-associated degradation .", "To facilitate protein folding , a cooperative mechanism known as entropic pulling has been proposed to demonstrate the molecular-level unde...	[ "The misfolding of proteins carries important implications for diseases such as Alzheimer's , Parkinson's , cancer , and diabetes .", "Once misfolded , proteins tend to associate into aggregates that pose a toxic threat to the cell .", "Chaperones are proteins that rescue the cell from an accumulation of these ...	2014
[ "Introduction", "Materials and Methods", "Results/Discussion" ]	[ "physics", "computer science", "medicinal chemistry", "computational chemistry", "computer modeling", "chemistry", "biology", "computational biology", "computerized simulations", "biophysics" ]	Identification of Potent EGFR Inhibitors from TCM Database@Taiwan	journal.pcbi.1002189	null	[ [ "Target-specific therapies have generated much attention in addition to conventional cancer treatments [1]–[3] .", "By targeting key molecules essential for cellular function , replication , or tumorigenesis , such therapies may exert cytostatic or cytotoxic effects on tumors while minimizing nonspecific ...	[ "Overexpression of epidermal growth factor receptor ( EGFR ) has been associated with cancer .", "Targeted inhibition of the EGFR pathway has been shown to limit proliferation of cancerous cells .", "Hence , we employed Traditional Chinese Medicine Database ( TCM Database@Taiwan ) ( http://tcm . cmu . edu . tw ...	[ "Tumor growth is associated with overexpression of epidermal growth factors receptors .", "Targeted control of EGFR by EGFR inhibitors is an attractive therapy alternative to conventional cancer treatment that offers specificity and reduced adverse effects .", "The purpose of this study was to identify natural ...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "genome expression analysis", "microbial metabolism", "functional genomics", "genome evolution", "gene regulation", "microbiology", "dna transcription", "gene function", "microbial evolution", "molecular genetics", "microbial physiology", "gene expression", "biology", "sy...	Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses	journal.pgen.1002929	null	[ [ "Transcriptional responses to stress are critical to cell growth and survival .", "In bacteria , stress responses are often controlled by alternative σ factors that direct RNA polymerase to transcribe promoters different from those recognized by the primary σ factor [1] , [2] .", "Therefore , identify...	[ "Cells often mount transcriptional responses and activate specific sets of genes in response to stress-inducing signals such as heat or reactive oxygen species .", "Transcription factors in the RpoH family of bacterial alternative σ factors usually control gene expression during a heat shock response .", "Inter...	[ "An important property of living systems is their ability to survive under conditions of stress such as increased temperature or the presence of reactive oxygen species .", "Central to the function of these stress responses are transcription factors that activate specific sets of genes needed for this response ."...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "immunology/cellular microbiology and pathogenesis", "cell biology/cell growth and division", "microbiology/microbial evolution and genomics", "cell biology/microbial growth and development", "infectious diseases/bacterial infections", "microbiology/microbial physiology and metabolism", "microbiology/ce...	Polar Localization of Virulence-Related Esx-1 Secretion in Mycobacteria	journal.ppat.1000285	null	[ [ "Mycobacteria , and in particular M . tuberculosis , represent a major human health problem globally [1] .", "The Esx-1 secretion system [early secreted antigen 6 kilodaltons ( Esat-6 ) secretion system 1] , which is primarily encoded by genes within , and adjacent to , the region of difference 1 ( RD1 ) ...	[ "The Esx-1 ( type VII ) secretion system is critical for virulence of both Mycobacterium tuberculosis and Mycobacterium marinum , and is highly conserved between the two species .", "Despite its importance , there has been no direct visualization of Esx-1 secretion until now .", "In M . marinum , we show that s...	[ "Mycobacteria represent a major human health problem globally , and there is a pressing need to identify novel processes and mechanisms including therapeutic targets .", "The Esx-1 secretion system is required for both Mycobacterium tuberculosis and Mycobacterium marinum to cause disease , and is absent from vacc...	2009
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "plant anatomy", "plant growth and development", "membrane proteins", "developmental biology", "protein expression", "plant science", "seedlings", "molecular biology techniques", "plants", "cellular structures and organelles", "research and analysis methods", "protein kinase signaling cascade"...	BRASSINOSTEROID-SIGNALING KINASE 3, a plasma membrane-associated scaffold protein involved in early brassinosteroid signaling	journal.pgen.1007904	null	[ [ "Brassinosteroids ( BRs ) are steroid hormones that are essential for plant growth and development .", "BRs regulate a wide range of cellular , physiological , and developmental processes , including cell expansion , cell division , stem elongation , root development , leaf growth , organ boundary formati...	[ "Brassinosteroids ( BRs ) are steroid hormones essential for plant growth and development .", "The BR signaling pathway has been studied in some detail , however , the functions of the BRASSINOSTEROID-SIGNALING KINASE ( BSK ) family proteins in the pathway have remained elusive .", "Through forward genetics , w...	[ "Steroid hormones exist in both animals and plants .", "Brassinosteroids ( BRs ) are steroid hormones that regulate numerous growth and developmental processes throughout the plant life cycle .", "Discovered in 2008 , the BRASSINOSTEROID-SIGNALING KINASE ( BSK ) protein family is composed of twelve members .", ...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "helminths", "animals", "invertebrate genomics", "ascaris", "ascaris lumbricoides", "genome analysis", "molecular biology techniques", "extraction techniques", "research and analysis methods", "sequence analysis", "artificial gene amplification and extension", "bioinformatic...	Targeting a highly repeated germline DNA sequence for improved real-time PCR-based detection of Ascaris infection in human stool	journal.pntd.0007593	null	[ [ "Believed responsible for more than 800 million global infections , Ascaris lumbricoides is the most prevalent of the human-infecting soil transmitted helminths ( STH ) [1–2] .", "As recently as 2017 , infections with this parasite were believed to result in approximaely 861 , 000 disability adjusted life...	[ "With the expansion of soil transmitted helminth ( STH ) intervention efforts and the corresponding decline in infection prevalence , there is an increased need for sensitive and specific STH diagnostic assays .", "Previously , through next generation sequencing ( NGS ) -based identification and targeting of non-...	[ "With an at-risk population in the billions , Ascaris lumbricoides is a pathogen of great global importance .", "In recent years , efforts to control the spread of this parasitic helminth have expanded , resulting in declining infection rates and worm burdens in some regions .", "While immeasurably important fo...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "animal models", "biochemistry", "medicine and health sciences", "model organisms", "biology and life sciences", "bioenergetics", "mouse models", "energy-producing organelles", "research and analysis methods", "mitochondrial diseases", "clinical genetics" ]	Loss of UCP2 Attenuates Mitochondrial Dysfunction without Altering ROS Production and Uncoupling Activity	journal.pgen.1004385	null	[ [ "Mitochondria are organelles found in almost every eukaryotic cell .", "They produce the bulk of cellular energy in the form of ATP , which is required for numerous processes in the cell .", "Still , mitochondrial energy production comes with a cost , the generation of reactive oxygen species ( ROS ) ...	[ "Although mitochondrial dysfunction is often accompanied by excessive reactive oxygen species ( ROS ) production , we previously showed that an increase in random somatic mtDNA mutations does not result in increased oxidative stress .", "Normal levels of ROS and oxidative stress could also be a result of an activ...	[ "Mitochondria produce the majority of the energy needed for numerous cell functions through oxidative phosphorylation .", "However , this comes with the cost in the form of potentially harmful reactive oxygen species ( ROS ) that could damage all kinds of biological macromolecules .", "Changes in mitochondrial ...	2014
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	The Effect of In Vitro Cultivation on the Transcriptome of Adult Brugia malayi	journal.pntd.0004311	null	[ [ "Lymphatic filariasis ( LF ) is a neglected tropical disease caused by three filarial nematodes: Wuchereria bancrofti , Brugia malayi , and Brugia timori , which are transmitted by several species of mosquitoes [1] .", "LF is presently endemic in 60 countries , mainly in subtropical and tropical regions o...	[ "Filarial nematodes cause serious and debilitating infections in human populations of tropical countries , contributing to an entrenched cycle of poverty .", "Only one human filarial parasite , Brugia malayi , can be maintained in rodents in the laboratory setting .", "It has been a widely used model organism i...	[ "Infections with filarial worms cause serious physical impairment and affect tens of millions of people in tropical and subtropical countries .", "To better understand the biology and pharmacology of these parasites , Brugia malayi is often used as a model .", "This parasite can be maintained in the laboratory ...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	A Neuron-Specific Antiviral Mechanism Prevents Lethal Flaviviral Infection of Mosquitoes	journal.ppat.1004848	null	[ [ "Mosquitoes transmit many human pathogens of medical importance throughout the world .", "Flaviviruses , such as West Nile ( WNV ) , Japanese Encephalitis ( JEV ) , Dengue ( DENV ) and Yellow Fever ( YFV ) viruses that are transmitted by mosquitoes are the etiologic agents of human hemorrhagic fever , enc...	[ "Mosquitoes are natural vectors for many etiologic agents of human viral diseases .", "Mosquito-borne flaviviruses can persistently infect the mosquito central nervous system without causing dramatic pathology or influencing the mosquito behavior and lifespan .", "The mechanism by which the mosquito nervous sys...	[ "The central nervous system plays a predominant role in organisms associated with cognition and higher-order functions , which is key to their normal behavior and successful survival .", "Many mosquito-borne flaviviruses particularly invade the central nervous system in vertebrates , resulting in dramatic neural ...	2015
[ "Introduction", "Methods", "Results", "", "", "Discussion" ]	[ "public health and epidemiology/health policy", "public health and epidemiology/social and behavioral determinants of health", "infectious diseases/helminth infections", "public health and epidemiology/infectious diseases", "public health and epidemiology/health services research and economics" ]	Neglected Patients with a Neglected Disease? A Qualitative Study of Lymphatic Filariasis	journal.pntd.0000128	null	[ [ "Recently , the profile of the “neglected diseases” [1] , [2] has been enhanced by a renewed interest by policymakers , including the new Director-General of the World Health Organization ( WHO ) .", "These diseases cause long-term morbidity , rather than high mortality , but have been overshadowed by hig...	[ "Lymphatic filariasis ( LF ) is a so-called neglected tropical disease , currently overshadowed by higher-profile efforts to address malaria , tuberculosis , and HIV/AIDS .", "Despite recent successes in arresting transmission , some 40 million people who already have the disease have been largely neglected .", ...	[ "Lymphatic filariasis ( LF ) is a tropical disease causing extreme swelling of the limbs and male genitals .", "Despite recent successes in preventing transmission of the disease , some 40 million people worldwide who already have the disease have been largely neglected .", "We aimed to increase understanding o...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "influenza", "viral diseases", "infectious disease control" ]	Multidrug Resistant 2009 A/H1N1 Influenza Clinical Isolate with a Neuraminidase I223R Mutation Retains Its Virulence and Transmissibility in Ferrets	journal.ppat.1002276	null	[ [ "Two classes of antiviral drugs are approved for prophylaxis and therapy of influenza virus infected patients [1] .", "Antiviral therapy against the new ( swine-origin ) 2009 pandemic A/H1N1 influenza virus relies on the neuraminidase inhibitor ( NAI ) class of antiviral drugs only , because this subtype ...	[ "Only two classes of antiviral drugs , neuraminidase inhibitors and adamantanes , are approved for prophylaxis and therapy against influenza virus infections .", "A major concern is that influenza virus becomes resistant to these antiviral drugs and spreads in the human population .", "The 2009 pandemic A/H1N1 ...	[ "Recently , a 2009 pandemic A/H1N1 influenza virus was isolated from an immune compromised patient , with antiviral resistance to the neuraminidase inhibitor class of drugs .", "This virus had an amino acid change in the viral neuraminidase enzyme; an isoleucine at position 223 was substituted for an arginine ( I...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "ecology and environmental sciences", "population dynamics", "tropical diseases", "geographical locations", "parasitic diseases", "health care", "data management", "filariasis", "tanzania", "urban environments", "neglected tropical diseases", "population biolo...	Lymphatic filariasis patient identification in a large urban area of Tanzania: An application of a community-led mHealth system	journal.pntd.0005748	null	[ [ "Lymphatic filariasis ( LF ) is a neglected tropical disease ( NTD ) that can have a devastating impact on affected individuals , with clinical symptoms such as acute dermatolymphangioadenitis ( ADLA , “acute attacks” ) , lymphoedema and elephantiasis , and hydrocoele , causing physical , mental and economic ...	[ "Lymphatic filariasis ( LF ) is best known for the disabling and disfiguring clinical conditions that infected patients can develop; providing care for these individuals is a major goal of the Global Programme to Eliminate LF .", "Methods of locating these patients , knowing their true number and thus providing c...	[ "Lymphatic filariasis ( LF ) can cause disabling conditions in infected patients including lymphoedema-elephantiasis ( LE ) and hydrocoele .", "Identifying the number and locations of these patients is the first step towards ensuring that these patients receive the care they require , however there is currently n...	2017
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public health and epidemiology/epidemiology", "public health and epidemiology/global health", "public health and epidemiology/infectious diseases", "infectious diseases/epidemiology and control of infectious diseases" ]	Evaluation of Mammalian and Intermediate Host Surveillance Methods for Detecting Schistosomiasis Reemergence in Southwest China	journal.pntd.0000987	null	[ [ "The success of disease control programs in reducing schistosomiasis infections and morbidity have prompted consideration of the elimination of human schistosomiasis [1] , [2] .", "Dramatic declines in Schistosoma haematobium and S . mansoni have been observed following widespread distribution of the anti...	[ "Schistosomiasis has reemerged in China , threatening schistosomiasis elimination efforts .", "Surveillance methods that can identify locations where schistosomiasis has reemerged are needed to prevent the further spread of infections .", "We tested humans , cows , water buffalo and the intermediate host snail ...	[ "Schistosomiasis has reemerged in China in regions where it was previously controlled .", "As reductions in schistosomiasis , a water-born parasitic infection , prompt consideration of schistosomiasis elimination , surveillance strategies that can signal reemergence and prevent further lapses in control are neede...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "ecology", "biology and life sciences", "microbiology", "molecular biology", "parasitology" ]	Investigating the Role of Free-living Amoebae as a Reservoir for Mycobacterium ulcerans	journal.pntd.0003148	null	[ [ "Mycobacterium ulcerans is a slow growing environmental pathogen responsible for a necrotizing cutaneous infection called Buruli ulcer ( BU ) .", "The disease has been reported in over 30 countries worldwide mainly in tropical and subtropical climates and emerged as an increasing cause of morbidity in end...	[ "The reservoir and mode of transmission of Mycobacterium ulcerans , the causative agent of Buruli ulcer , still remain a mystery .", "It has been suggested that M . ulcerans persists with difficulty as a free-living organism due to its natural fragility and inability to withstand exposure to direct sunlight , and...	[ "Mycobacterium ulcerans , the causative agent of Buruli ulcer ( BU ) is an environmental pathogen known to reside in aquatic habitat .", "However , the reservoir and modes of transmission to humans still remain unknown .", "M . ulcerans can probably not live freely due to its natural fragility and inability to ...	2014
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Harnessing Diversity towards the Reconstructing of Large Scale Gene Regulatory Networks	journal.pcbi.1003361	null	[ [ "Most genes do not exert their functions in isolation [1] , but make their functions through regulations among them .", "Such regulatory interactions are in the same cell , between different cells , and even between different organs , forming large-scale gene regulatory networks ( GRNs ) .", "The impa...	[ "Elucidating gene regulatory network ( GRN ) from large scale experimental data remains a central challenge in systems biology .", "Recently , numerous techniques , particularly consensus driven approaches combining different algorithms , have become a potentially promising strategy to infer accurate GRNs .", "...	[ "Elucidating gene regulatory networks is crucial to understand disease mechanisms at the system level .", "A large number of algorithms have been developed to infer gene regulatory networks from gene-expression datasets .", "If you remember the success of IBM's Watson in ”Jeopardy !", "„ quiz show , the criti...	2013
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "mosquitoes", "rna viruses", "emerging infectious diseases", "vector biology", "virology", "viral classification", "emerging viral diseases", "biology", "microbiology", "viral vectors" ]	Zika Virus in Gabon (Central Africa) – 2007: A New Threat from Aedes albopictus?	journal.pntd.0002681	null	[ [ "Zika virus ( ZIKV ) is a mosquito-borne flavivirus phylogenetically related to dengue viruses .", "Following its first isolation in 1947 from a sentinel monkey placed in the Zika forest in Uganda [1] , serological surveys and viral isolations ( reviewed in [2] ) suggested that ZIKV", "( i ) ranged wi...	[ "Chikungunya and dengue viruses emerged in Gabon in 2007 , with large outbreaks primarily affecting the capital Libreville and several northern towns .", "Both viruses subsequently spread to the south-east of the country , with new outbreaks occurring in 2010 .", "The mosquito species Aedes albopictus , that wa...	[ "Not previously considered an important human arboviral pathogen , the epidemic capacity of Zika virus ( ZIKV , a dengue-related flavivirus ) was revealed by the Micronesia outbreak in 2007 , which affected about 5000 persons .", "Widely distributed throughout tropical areas of Asia and Africa , ZIKV is transmitt...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "american samoa", "medicine and health sciences", "infectious disease epidemiology", "disease eradication", "spatial epidemiology", "vector-borne diseases", "tropical diseases", "geographical locations", "parasitic diseases", "health care", "plant science", "filariasis", "global health", "...	Seroprevalence and Spatial Epidemiology of Lymphatic Filariasis in American Samoa after Successful Mass Drug Administration	journal.pntd.0003297	null	[ [ "Lymphatic filariasis ( LF ) is a neglected tropical disease of global importance , with an estimated 1 . 4 billion people in 73 countries at risk of infection .", "Over 120 million people worldwide are currently affected by lymphatic filariasis and 40 million are disfigured and disabled [1] .", "Infe...	[ "As part of the Global Programme to Eliminate Lymphatic Filariasis ( LF ) , American Samoa conducted mass drug administration ( MDA ) from 2000–2006 , and passed transmission assessment surveys in 2011–2012 .", "We examined the seroprevalence and spatial epidemiology of LF post-MDA to inform strategies for ongoin...	[ "Lymphatic filariasis ( LF ) is caused by infection with filarial worms that are transmitted by mosquito bites .", "Globally , 120 million people are affected , and 40 million are disfigured and disabled by complications such as severe swelling of the legs ( elephantiasis ) .", "The Global Programme to Eliminat...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "death rates", "invertebrates", "medicine and health sciences", "deer", "ixodes", "pathology and laboratory medicine", "ruminants", "infectious disease epidemiology", "demography", "vector-borne diseases", "vertebrates", "animals", "mammals", "population biology", "ticks", "infectious ...	Modeling Relapsing Disease Dynamics in a Host-Vector Community	journal.pntd.0004428	null	[ [ "An important development in the study of infectious diseases is the application of mathematical models to understand the interplay between various factors that determine epidemiological processes .", "Many systems show a rich variety of dynamics that arise from nonlinear interactions ( due to the mixing ...	[ "Vector-borne diseases represent a threat to human and wildlife populations and mathematical models provide a means to understand and control epidemics involved in complex host-vector systems .", "The disease model studied here is a host-vector system with a relapsing class of host individuals , used to investiga...	[ "An important development in the study of infectious diseases is the application of mathematical models to understand the interplay between various factors that determine epidemiological processes .", "Vector-borne diseases are additionally complex with interactions between multiple host and vector species .", ...	2016
[ "Introduction", "Results", "Discussion", "Material and Methods" ]	[ "virology" ]	Distinct DNA Exit and Packaging Portals in the Virus Acanthamoeba polyphaga mimivirus	journal.pbio.0060114	The mechanisms that promote genome delivery and packaging in the giant virus Mimivirus call into question the conventional distinction between viruses and single-celled organisms.	[ [ "The prevailing model for genome translocations in icosahedral viruses entails a molecular motor that is localized at a single vertex and comprises a packaging ATPase and a portal complex [1–5] .", "The particular structural features revealed by the vertex-portal assembly have been argued to facilitate bo...	[ "Icosahedral double-stranded DNA viruses use a single portal for genome delivery and packaging .", "The extensive structural similarity revealed by such portals in diverse viruses , as well as their invariable positioning at a unique icosahedral vertex , led to the consensus that a particular , highly conserved v...	[ "Two fundamental events in viral life cycles are the delivery of viral genomes into host cells and the packaging of these genomes into viral protein capsids .", "In bacteriophages and herpesviruses , these processes occur linearly along the genome , base pair after base pair , through a single portal located at a...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "neurobiology of disease and regeneration", "neuroscience", "gene function", "animal models", "drosophila melanogaster", "model organisms", "molecular genetics", "huntington disease", "biology", "mouse", "genetic screens", "neurology", "neurological disorders", "genetics", ...	A Genome-Scale RNA–Interference Screen Identifies RRAS Signaling as a Pathologic Feature of Huntington's Disease	journal.pgen.1003042	null	[ [ "Huntington's disease ( HD ) is a dominantly-inherited , invariably fatal , familial neurodegenerative disease caused by an expansion in the polyglutamine encoding CAG tract in the huntingtin gene ( Htt ) [1] .", "HD manifests with severe motor and psychiatric impairments caused by neuronal dysfunction an...	[ "A genome-scale RNAi screen was performed in a mammalian cell-based assay to identify modifiers of mutant huntingtin toxicity .", "Ontology analysis of suppressor data identified processes previously implicated in Huntington's disease , including proteolysis , glutamate excitotoxicity , and mitochondrial dysfunct...	[ "Huntington's disease ( HD ) is an inherited disorder caused by mutation of the gene that encodes the huntingtin protein .", "The specific mutation that results in disease is an increase in the copies of the amino acid glutamine in a stretch of repeated glutamines at the amino-terminus of the protein .", "This ...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Clustering and Negative Feedback by Endocytosis in Planar Cell Polarity Signaling Is Modulated by Ubiquitinylation of Prickle	journal.pgen.1005259	null	[ [ "PCP is the tissue-level organization of cells in the plane of an epithelium , resulting from the coordinated acquisition of cellular polarity orthogonal to the apical-basal axis .", "PCP signaling controls the polarity of numerous epithelial cells in both Drosophila and vertebrates .", "In Drosophila...	[ "The core components of the planar cell polarity ( PCP ) signaling system , including both transmembrane and peripheral membrane associated proteins , form asymmetric complexes that bridge apical intercellular junctions .", "While these can assemble in either orientation , coordinated cell polarization requires t...	[ "Many epithelial cells display a level of organization in which cellular structures or appendages are positioned asymmetrically within the cell along an axis perpendicular to the apical-basal axis of the cell .", "When the direction of this polarization is coordinated within the plane of the epithelium , this phe...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Replicative DNA Polymerase δ but Not ε Proofreads Errors in Cis and in Trans	journal.pgen.1005049	null	[ [ "Unlike prokaryotes , eukaryotic cells have multiple DNA polymerases involved in chromosomal replication .", "It was first demonstrated in Saccharomyces cerevisiae [1] and then in human cells [2] that Pol α , Pol δ , and Pol ε were necessary for normal replication .", "It was subsequently found that t...	[ "It is now well established that in yeast , and likely most eukaryotic organisms , initial DNA replication of the leading strand is by DNA polymerase ε and of the lagging strand by DNA polymerase δ .", "However , the role of Pol δ in replication of the leading strand is uncertain .", "In this work , we use a re...	[ "Many DNA polymerases are able to proofread their errors: after incorporation of a wrong base , the resulting mispair invokes an exonuclease activity of the polymerase that removes the mispaired base and allows replication to continue .", "Elimination of the proofreading activity thus results in much higher mutat...	2015
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "infectious diseases", "veterinary diseases", "medicine and health sciences", "veterinary epidemiology", "epidemiology", "global health", "biology and life sciences", "veterinary science" ]	New Insights in Cysticercosis Transmission	journal.pntd.0003247	null	[ [ "Cysticercosis affects humans following the ingestion of Taenia solium eggs , generally by fecal-oral contamination .", "Once ingested , T . solium eggs turn into cysticerci .", "In humans , cysticerci establish primarily in the central nervous system and is the main cause of epilepsy in adults in end...	[ "Taenia solium infection causes severe neurological disease in humans .", "Even though infection and exposure to swine cysticercosis is scattered throughout endemic villages , location of the tapeworm only explains some of the nearby infections and is not related to location of seropositive pigs .", "Other play...	[ "In endemic areas , pigs acquire cysticercosis when ingesting Taenia solium eggs that have been released into the environment in the feces of a person infected with T . solium .", "The present study has found evidence that players , such as dung beetles , might be involved in further dissemination of the parasite...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "uterus", "meiosis", "medicine and health sciences", "reproductive system", "caenorhabditis", "cell cycle and cell division", "cell processes", "neuroscience", "animals", "reproductive physiology", "germ cells", "animal models", "caenorhabditis elegans", "model organisms...	Chemosensory and hyperoxia circuits in C. elegans males influence sperm navigational capacity	journal.pbio.2002047	null	[ [ "Animals employ sexual reproduction to increase genetic diversity critical for adapting to changing environments [1–3] .", "An essential process is fertilization , the merging of sperm and oocyte [4 , 5] .", "The motile spermatozoa ( referred to as sperm ) is a highly specialized cell built for findin...	[ "The sperm’s crucial function is to locate and fuse with a mature oocyte .", "Under laboratory conditions , Caenorhabditis elegans sperm are very efficient at navigating the hermaphrodite reproductive tract and locating oocytes .", "Here , we identify chemosensory and oxygen-sensing circuits that affect the spe...	[ "Habitat loss , disease , climate change , and pollution are thought to negatively affect animal fertility .", "Sperm are a potential target , but the molecular mechanisms are not understood .", "The nematode C . elegans is a powerful genetic model to investigate the relationship between environment and male fe...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/plant genomes and evolution", "cell biology", "genetics and genomics/plant genetics and gene expression", "genetics and genomics/chromosome biology" ]	Mutations in AtPS1 (Arabidopsis thaliana Parallel Spindle 1) Lead to the Production of Diploid Pollen Grains	journal.pgen.1000274	null	[ [ "Polyploidy , the condition of organisms having more than two sets of chromosomes , has had a considerable impact on the evolution of many fungi , invertebrate , and vertebrate lineages and is particularly prominent in plants [1] , [2] .", "It is estimated that 95% of ferns are polyploids [3] and that alm...	[ "Polyploidy has had a considerable impact on the evolution of many eukaryotes , especially angiosperms .", "Indeed , most—if not all—angiosperms have experienced at least one round of polyploidy during the course of their evolution , and many important crop plants are current polyploids .", "The occurrence of 2...	[ "In the life cycle of sexual organisms , meiosis reduces the number of chromosomes from two sets ( 2n ) to one set ( n ) , while fertilization restores the original chromosome number .", "However , in case of failure of meiosis to reduce the chromosome number , the fecundation involving the obtained 2n gametes ca...	2008
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "population genetics", "genetic mapping", "evolutionary adaptation", "population biology", "molecular biology techniques", "genotyping", "research and analysis methods", "genetic polymorphism", "molecular biology", "evolutionary genetics", "genetic drift", "population metrics", "haplotypes",...	Slower environmental change hinders adaptation from standing genetic variation	journal.pgen.1007731	null	[ [ "With human activities contributing to climate change [1] , it has become urgent to pinpoint the ecological and evolutionary mechanisms by which natural populations adapt at different rates of environmental change .", "It is generally accepted that lower rates of environmental change allow more time for b...	[ "Evolutionary responses to environmental change depend on the time available for adaptation before environmental degradation leads to extinction .", "Explicit tests of this relationship are limited to microbes where adaptation usually depends on the sequential fixation of de novo mutations , excluding standing va...	[ "Adaptation under environmental change is expected to depend on the time available for the sequential fixation of mutations , but also on standing variation in genotype-by-environment fitness interactions .", "In the later circumstances , some genotypes might be initially favored but then disfavored and overtaken...	2018
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/vaccines", "virology/diagnosis", "infectious diseases/neglected tropical diseases", "virology/animal models of infection", "virology", "virology/emerging viral diseases", "infectious diseases/viral infections", "public health and epidemiology/infectious diseases" ]	Evolutionary History of Rabies in Ghana	journal.pntd.0001001	null	[ [ "Viruses belonging to the genus Lyssavirus , family Rhabdoviridae , cause the disease rabies .", "Rabies virus ( RABV ) is enzootic throughout Africa with the domestic dog ( Canis familiaris ) being the principal vector [1] .", "Sylvatic rabies is also reported in a number of wildlife hosts , particul...	[ "Rabies virus ( RABV ) is enzootic throughout Africa , with the domestic dog ( Canis familiaris ) being the principal vector .", "Dog rabies is estimated to cause 24 , 000 human deaths per year in Africa , however , this estimate is still considered to be conservative .", "Two sub-Saharan African RABV lineages ...	[ "Rabies virus ( RABV ) is widespread throughout Africa , with the domestic dog being the principal vector .", "Dog rabies is estimated to cause 24 , 000 human deaths per year in Africa , however , this estimate is still considered to be conservative .", "Two sub-Saharan African RABV lineages ( Africa 1 and 2 ) ...	2011
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "bacteriology", "innate immune system", "medicine and health sciences", "immune cells", "immune physiology", "pathology and laboratory medicine", "cytokines", "pathogens", "immunology", "microbiology", "physiological processes", "developmental biology", "secretion systems", ...	Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence	journal.ppat.1006363	null	[ [ "A key to the pathogenic success of Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis ( TB ) , is the capacity to survive within host macrophages .", "Although several Mtb factors required for this survival have been identified [1] , a comprehensive knowledge of such factors and how...	[ "A key to the pathogenic success of Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis , is the capacity to survive within host macrophages .", "Although several factors required for this survival have been identified , a comprehensive knowledge of such factors and how they work together to ...	[ "Tuberculosis ( TB ) remains a significant global health problem .", "One barrier to developing novel approaches to preventing and treating TB is an incomplete understanding of the strategies that the causative bacterium , Mycobacterium tuberculosis ( Mtb ) , uses to survive and cause disease in the host .", "T...	2017
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "immune physiology", "enzyme-linked immunoassays", "pathology and laboratory medicine", "pathogens", "immunology", "microbiology", "viruses", "preventive medicine", "immunologic adjuvants", "rna viruses", "antibodies", "immunologic techniques", "vaccination ...	Boosting subdominant neutralizing antibody responses with a computationally designed epitope-focused immunogen	journal.pbio.3000164	A computationally designed epitope-focused immunogen presenting a single neutralization epitope from Respiratory Syncytial Virus elicits superior epitope-specific responses compared to the viral fusion protein. Furthermore, epitope-focused immunogens can reshape established antibody hierarchies.	[ [ "The development of vaccines has proven to be one of the most successful medical interventions to reduce the burden of infectious diseases [1] , and their correlate of protection is the induction of neutralizing antibodies ( nAbs ) that block infection [2] .", "In recent years , advances in high-throughpu...	[ "Throughout the last several decades , vaccination has been key to prevent and eradicate infectious diseases .", "However , many pathogens ( e . g . , respiratory syncytial virus [RSV] , influenza , dengue , and others ) have resisted vaccine development efforts , largely because of the failure to induce potent a...	[ "Vaccines are one of the most valuable instruments to prevent and control infectious diseases .", "Their primary correlate of protection is the level of induction of neutralizing antibodies that target critical antigenic sites and thereby block infection .", "Natural infections with pathogens such as the respir...	2019
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "medicine and health sciences", "decision making", "brain", "social sciences", "vertebrates", "neuroscience", "animals", "mammals", "motor neurons", "primates", "cognitive psychology", "cognition", "amniotes", "vision", "monkeys", "animal cells", "basal ganglia", "cellular neurosci...	Covert spatial selection in primate basal ganglia	journal.pbio.2005930	null	[ [ "The basal ganglia are known to govern behavior by disinhibiting desired actions and inhibiting undesired actions [1] .", "The basal ganglia have also been implicated in perceptual and cognitive functions [2] , such as the encoding of object values [3] and action values [4] , and signals related to visual...	[ "The basal ganglia are important for action selection .", "They are also implicated in perceptual and cognitive functions that seem far removed from motor control .", "Here , we tested whether the role of the basal ganglia in selection extends to nonmotor aspects of behavior by recording neuronal activity in th...	[ "The ability to respond selectively to sensory inputs is a crucial brain function , one that is implicated in variety of high-level brain disorders .", "The basal ganglia are a set of evolutionarily ancient structures best known for their role in controlling motor actions and more recently implicated in nonmotor ...	2018
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "pest control", "drugs and devices", "global health", "chemistry", "biology", "genomics", "neuroscience", "genetics and genomics", "agriculture" ]	A “Genome-to-Lead” Approach for Insecticide Discovery: Pharmacological Characterization and Screening of Aedes aegypti D1-like Dopamine Receptors	journal.pntd.0001478	null	[ [ "Mosquitoes ( Class Insecta; Order Diptera; Family Culicidae ) vector multiple neglected tropical diseases ( NTDs ) affecting human health , including malaria , yellow-fever , dengue and filariasis .", "Historically , insecticides employed against arthropod disease vectors have reduced the impact of NTDs ...	[ "Many neglected tropical infectious diseases affecting humans are transmitted by arthropods such as mosquitoes and ticks .", "New mode-of-action chemistries are urgently sought to enhance vector management practices in countries where arthropod-borne diseases are endemic , especially where vector populations have...	[ "Mosquitoes and other arthropods transmit important disease-causing agents affecting human health worldwide .", "There is an urgent need to discover new chemistries to control these pests in order to reduce or eliminate arthropod-borne diseases .", "We describe an approach to identify and evaluate potential ins...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/effects of virus infection on host gene expression", "virology/virulence factors and mechanisms", "virology/animal models of infection" ]	Genomic Analysis Reveals a Potential Role for Cell Cycle Perturbation in HCV-Mediated Apoptosis of Cultured Hepatocytes	journal.ppat.1000269	null	[ [ "Hepatitis C virus ( HCV ) , a member of the Flaviviridae family , is a blood-borne pathogen which currently infects approximately 170 million people worldwide .", "Exposure to HCV typically results in a persistent infection and approximately 30% of chronically infected patients will develop progressive l...	[ "The mechanisms of liver injury associated with chronic HCV infection , as well as the individual roles of both viral and host factors , are not clearly defined .", "However , it is becoming increasingly clear that direct cytopathic effects , in addition to immune-mediated processes , play an important role in li...	[ "Chronic HCV infection is associated with progressive liver injury and subsequent development of fibrosis/cirrhosis .", "The cellular mechanisms by which HCV replication , and subsequent virus–host interactions , may mediate liver injury are unclear .", "Microarray experiments were performed to characterize the...	2009
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics", "virology/immunodeficiency viruses", "immunology/immune response", "virology/antivirals, including modes of action and resistance", "computational biology/evolutionary modeling", "infectious diseases/hiv infection and aids", "infectious diseases/antimicrobials and drug resistance", "vir...	Treatment-Mediated Alterations in HIV Fitness Preserve CD4+ T Cell Counts but Have Minimal Effects on Viral Load	journal.pcbi.1001012	null	[ [ "Antiretroviral therapy has been used to successfully treat HIV-1 infection .", "However , a subset of patients develops drug resistance followed by an observable increase in plasma HIV viral load .", "This “virological failure” usually triggers a change in the drug regimen .", "Here we examine a ...	[ "For most HIV-infected patients , antiretroviral therapy controls viral replication .", "However , in some patients drug resistance can cause therapy to fail .", "Nonetheless , continued therapy with a failing regimen can preserve or even lead to increases in CD4+ T cell counts .", "To understand the biologic...	[ "The impact of antiretroviral drug-resistance on viral load , CD4+ T cells , and clinical outcomes is complex .", "We used mathematical models to evaluate the benefits of HIV drug therapy in the presence of drug-resistant virus .", "As an example , we considered resistance to enfuvirtide , the first FDA-approve...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	Natural, Persistent Oscillations in a Spatial Multi-Strain Disease System with Application to Dengue	journal.pcbi.1003308	null	[ [ "Mathematical models based upon the various derivatives of the classic susceptible-infected-recovered ( SIR ) framework have greatly improved our understanding of the transmission and population dynamics of many important pathogens [1] , [2] .", "Common to this class of models is their propensity to exhib...	[ "Many infectious diseases are not maintained in a state of equilibrium but exhibit significant fluctuations in prevalence over time .", "For pathogens that consist of multiple antigenic types or strains , such as influenza , malaria or dengue , these fluctuations often take on the form of regular or irregular epi...	[ "The population dynamics of multi-strain pathogens are often characterized by persistent and irregular fluctuations in disease incidence and strain prevalence levels over time .", "Previous theoretical approaches have often evoked strong immunological interactions between individual strains , such as cross-immuni...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "oncology", "medicine", "endocrinology", "biology", "genomics", "diabetes and endocrinology", "genetics and genomics" ]	PBX1 Genomic Pioneer Function Drives ERα Signaling Underlying Progression in Breast Cancer	journal.pgen.1002368	null	[ [ "The implementation of transcriptional programs is central to the commitment of pluripotent cells occurring throughout development [1] , [2] .", "Likewise , diseases commonly arise from altered transcriptional programs .", "This requires active reprogramming characterized by chromatin remodeling and a...	[ "Altered transcriptional programs are a hallmark of diseases , yet how these are established is still ill-defined .", "PBX1 is a TALE homeodomain protein involved in the development of different types of cancers .", "The estrogen receptor alpha ( ERα ) is central to the development of two-thirds of all breast c...	[ "Approximately two-thirds of breast cancers depend on the estrogen receptor alpha ( ERα ) for their growth .", "Its capacity to act as a transcription factor binding DNA following estrogen stimulation is central to promote a pro-tumorigenic transcriptional response .", "Importantly , different classes of ERα-po...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "public health and epidemiology/infectious diseases", "microbiology/microbial evolution and genomics", "infectious diseases/antimicrobials and drug resistance" ]	Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam	journal.pntd.0000929	null	[ [ "The Mekong river delta is located in the south of Vietnam ( Figure 1 ) in an area of 40 , 000 square kilometres ( 12% of Vietnam's land mass ) and is home to over 20% of Vietnam's population .", "It is the area where the Mekong river divides into multiple channels and drains into the South China sea .", ...	[ "Typhoid fever remains a public health problem in Vietnam , with a significant burden in the Mekong River delta region .", "Typhoid fever is caused by the bacterial pathogen Salmonella enterica serovar Typhi ( S . Typhi ) , which is frequently multidrug resistant with reduced susceptibility to fluoroquinolone-bas...	[ "Typhoid fever remains a serious public health issue in some parts of Vietnam , including the Mekong delta region .", "Typhoid is caused by the bacterium Salmonella Typhi , which is frequently multidrug resistant and shows reduced susceptibility to fluoroquinolone-based drugs .", "We assayed single nucleotide v...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "pathology and laboratory medicine", "gene regulation", "pathogens", "immunology", "microbiology", "viruses", "regulator genes", "gene types", "small interfering rnas", "medical microbiology", "gene expression", "microbial pathogens", "viral replication", ...	Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens	journal.pcbi.1005013	null	[ [ "To combat infections from diverse pathogens , mammalian immune systems must be able to mount appropriate and specific responses to pathogenic infections .", "A key challenge in current infectious disease research is to understand the molecular mechanisms that make the host immune system more or less susc...	[ "Mammalian host response to pathogenic infections is controlled by a complex regulatory network connecting regulatory proteins such as transcription factors and signaling proteins to target genes .", "An important challenge in infectious disease research is to understand molecular similarities and differences in ...	[ "An important challenge in infectious disease research is to understand how the human immune system responds to different types of pathogenic infections .", "An important component of mounting proper response is the transcriptional regulatory network that specifies the context-specific gene expression program in ...	2016
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	Cortical Hierarchies Perform Bayesian Causal Inference in Multisensory Perception	journal.pbio.1002073	The human brain uses Bayesian Causal Inference to integrate and segregate information by encoding multiple estimates of spatial relationships at different levels of the auditory and visual processing hierarchies. Read the accompanying Primer.	[ [ "Our senses are constantly bombarded with many different signals .", "Imagine you are crossing a street and suddenly hear a loud motor noise .", "Is that motor noise coming from the car on the opposite side of the street or from a rapidly approaching car that you have not yet spotted ?", "To locat...	[ "To form a veridical percept of the environment , the brain needs to integrate sensory signals from a common source but segregate those from independent sources .", "Thus , perception inherently relies on solving the “causal inference problem . ”", "Behaviorally , humans solve this problem optimally as predicte...	[ "How can the brain integrate signals into a veridical percept of the environment without knowing whether they pertain to same or different events ?", "For example , I can hear a bird and I can see a bird , but is it one bird singing on the branch , or is it two birds ( one sitting on the branch and the other sing...	2015
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious diseases", "infectious disease epidemiology", "epidemiology", "disease dynamics", "population dynamics", "population biology", "biology", "epidemiological methods", "infectious disease control", "infectious disease modeling" ]	Estimation of Vaccine Efficacy and Critical Vaccination Coverage in Partially Observed Outbreaks	journal.pcbi.1003061	null	[ [ "Mass vaccination programs for childhood diseases have been highly successful in reducing the incidence and public health impact of the targeted diseases .", "Nevertheless , with the exception of smallpox , eradication has not been achieved , and outbreaks continue to occur even in highly vaccinated popul...	[ "Classical approaches to estimate vaccine efficacy are based on the assumption that a person's risk of infection does not depend on the infection status of others .", "This assumption is untenable for infectious disease data where such dependencies abound .", "We present a novel approach to estimating vaccine e...	[ "Less than two decades ago , it was generally believed that in developed countries infectious diseases such as measles , mumps , and pertussis were under firm control via vaccination .", "Nowadays , it is increasingly recognized that this picture has been overly optimistic .", "A central question is whether rec...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine", "infectious diseases", "fungal diseases", "aspergillosis" ]	Aspergillus Galactosaminogalactan Mediates Adherence to Host Constituents and Conceals Hyphal β-Glucan from the Immune System	journal.ppat.1003575	null	[ [ "The incidence of invasive mold infections due to the fungus Aspergillus fumigatus has increased dramatically in hematology patients receiving intensive cytotoxic chemotherapy or undergoing hematopoietic stem cell transplantation [1] .", "Despite the advent of new antifungal therapies , the mortality of i...	[ "Aspergillus fumigatus is the most common cause of invasive mold disease in humans .", "The mechanisms underlying the adherence of this mold to host cells and macromolecules have remained elusive .", "Using mutants with different adhesive properties and comparative transcriptomics , we discovered that the gene ...	[ "Invasive aspergillosis is the most common mold infection in humans , predominately affecting immunocompromised patients .", "The mechanisms by which the mold Aspergillus fumigatus adheres to host tissues and causes disease are poorly understood .", "In this report , we compared mutants of Aspergillus with diff...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "bacteriology", "population genetics", "evolutionary selection", "microbiology", "genome sequencing", "mutation", "effective population size", "microbial evolution", "staphylococci", "bacterial pathogens", "forms of evolution", "genetic polymorphism", "microbial pathogens", "comparative ge...	The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones	journal.ppat.1002129	null	[ [ "The populations of many pathogenic bacterial species exist as a collection of discrete clonal complexes , many of which have emerged recently and exhibit specific resistance or virulence attributes .", "For example , molecular techniques such as multilocus sequence typing ( MLST ) [1] have identified a s...	[ "The development of next-generation sequencing platforms is set to reveal an unprecedented level of detail on short-term molecular evolutionary processes in bacteria .", "Here we re-analyse genome-wide single nucleotide polymorphism ( SNP ) datasets for recently emerged clones of methicillin resistant Staphylococ...	[ "As bacteria diversify , many of the nucleotide changes that emerge will render the cell slightly less competitive , and these mutations will tend to be removed by natural selection .", "However , this purging process does not happen instantaneously , and this delay allows deleterious mutations to survive in the ...	2011
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "pathology and laboratory medicine", "education", "chikungunya infection", "pathogens", "sociology", "tropical diseases", "microbiology", "social sciences", "animals", "viruses", "rna viruses", "neglected tropical diseases", "infectious di...	Mitigating Diseases Transmitted by Aedes Mosquitoes: A Cluster-Randomised Trial of Permethrin-Impregnated School Uniforms	journal.pntd.0005197	null	[ [ "Aedes is a genus of mosquitoes originally found in tropical and subtropical zones , but which is now widespread in most continents .", "The current geographical distribution is the widest ever recorded and there is potential for further spread [1] .", "Over 50% of the world’s population live in areas...	[ "Viral diseases transmitted via Aedes mosquitoes are on the rise , such as Zika , dengue , and chikungunya .", "Novel tools to mitigate Aedes mosquitoes-transmitted diseases are urgently needed .", "We tested whether commercially insecticide-impregnated school uniforms can reduce dengue incidence in school chil...	[ "Viral diseases transmitted via Aedes mosquitoes are on the rise , such as Zika , dengue , and chikungunya .", "Novel tools to mitigate Aedes mosquitoes-transmitted diseases are urgently needed .", "We tested whether commercially available insecticide-impregnated school uniforms can reduce dengue incidence in s...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/human evolution", "evolutionary biology/bioinformatics", "evolutionary biology/genomics" ]	Chromosomal Redistribution of Male-Biased Genes in Mammalian Evolution with Two Bursts of Gene Gain on the X Chromosome	journal.pbio.1000494	Two bursts of gene gains occurred on the mammalian X chromosome contribute to an age-dependent chromosomal distribution of male-biased genes.	[ [ "In mammals and Drosophila , the X chromosome usually differs dramatically from autosomes since it is hemizygous in males [1] .", "Sexual antagonism ( beneficial for one sex , but deleterious for the other ) enriches male-biased genes on the X chromosome , if alleles are generally recessive , and on the a...	[ "Mammalian X chromosomes evolved under various mechanisms including sexual antagonism , the faster-X process , and meiotic sex chromosome inactivation ( MSCI ) .", "These forces may contribute to nonrandom chromosomal distribution of sex-biased genes .", "In order to understand the evolution of gene content on ...	[ "Some evolutionary theories predict that the X chromosome will be enriched for genes with male functions .", "However , recent studies showed there had been gene traffic in which autosomal male-biased genes were retroposed from X-linked parental genes .", "A question remains about whether this pattern also hold...	2010
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "virology/emerging viral diseases", "virology/animal models of infection", "virology" ]	Domestic Pigs Have Low Susceptibility to H5N1 Highly Pathogenic Avian Influenza Viruses	journal.ppat.1000102	null	[ [ "The genus Influenzavirus A ( i . e . influenza A virus ) contains individual virus strains which have infected a broad spectrum of avian and mammalian species .", "While wild aquatic birds are the primordial reservoirs for all influenza A virus genes and subtypes , distinct genetic lineages have become e...	[ "Genetic reassortment of H5N1 highly pathogenic avian influenza viruses ( HPAI ) with currently circulating human influenza A strains is one possibility that could lead to efficient human-to-human transmissibility .", "Domestic pigs which are susceptible to infection with both human and avian influenza A viruses ...	[ "Highly pathogenic avian influenza A viruses of H5N1 subtype have spread through Eurasia and Africa with continuing cases of human infection , suggesting the potential to become a pandemic influenza virus .", "Pigs which are susceptible to infection with both human and avian influenza A viruses are one of the nat...	2008
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "chemical bonding", "medicine and health sciences", "vesicles", "crystal structure", "pathology and laboratory medicine", "pathogens", "condensed matter physics", "microbiology", "viral structure", "neuroscience", "viruses", "membrane fusion", "hantavirus", "rna viruses", "ganglion cells...	Mechanistic Insight into Bunyavirus-Induced Membrane Fusion from Structure-Function Analyses of the Hantavirus Envelope Glycoprotein Gc	journal.ppat.1005813	null	[ [ "Hantaviruses are a small group of zoonotic viruses of rodents , bats and insectivores such as moles and shrews [1] .", "They are often transmitted to humans by persistently infected rodents , causing serious outbreaks of pulmonary syndrome or of hemorrhagic disease with renal syndrome [2 , 3] .", "Th...	[ "Hantaviruses are zoonotic viruses transmitted to humans by persistently infected rodents , giving rise to serious outbreaks of hemorrhagic fever with renal syndrome ( HFRS ) or of hantavirus pulmonary syndrome ( HPS ) , depending on the virus , which are associated with high case fatality rates .", "There is onl...	[ "Hantaviruses belong to the Bunyaviridae family of enveloped viruses .", "This family englobes in total five established genera: Tospovirus ( infecting plants ) , and Phlebovirus , Orthobunyavirus , Nairovirus and Hantavirus infecting animals , some of which cause serious disease in humans .", "An important cha...	2016
[ "Introduction", "Discussion" ]	[]	Social Pathways for Ebola Virus Disease in Rural Sierra Leone, and Some Implications for Containment	journal.pntd.0003567	null	[ [ "The present outbreak of Ebola Virus Disease ( EVD ) in Upper West Africa is the worst ever recorded .", "As of late December 2014 there were 6808 confirmed EVD cases [1] and there are no clear signs of the disease coming under control .", "The international community is alarmed , and resources are be...	[ "The current outbreak of Ebola Virus Disease in Upper West Africa is the largest ever recorded .", "Molecular evidence suggests spread has been almost exclusively through human-to-human contact .", "Social factors are thus clearly important to understand the epidemic and ways in which it might be stopped , but ...	[ "Ebola virus disease is a disease of social intimacy .", "The main infection pathways are through nursing of the sick and through preparation of corpses for burial .", "In African rural communities these are activities mainly undertaken by close family members .", "Infection thus spreads to those most intimat...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "veterinary immunology", "veterinary diseases", "veterinary diagnostics", "zoonotic diseases", "leishmaniasis", "parasitic diseases", "veterinary science", "veterinary medicine" ]	Antigenicity and Protective Efficacy of a Leishmania Amastigote-specific Protein, Member of the Super-oxygenase Family, against Visceral Leishmaniasis	journal.pntd.0002148	null	[ [ "Visceral leishmaniasis ( VL ) caused by Leishmania donovani and L . infantum/L .", "chagasi represents an important disease in the world , leading to nearly 500 , 000 new cases and 50 , 000 deaths annually .", "The first choice of treatment for all forms of leishmaniasis is still based on the use of ...	[ "The present study aimed to evaluate a hypothetical Leishmania amastigote-specific protein ( LiHyp1 ) , previously identified by an immunoproteomic approach performed in Leishmania infantum , which showed homology to the super-oxygenase gene family , attempting to select a new candidate antigen for specific serodia...	[ "Life-long immunity to leishmaniasis in recovered patients has inspired the development of vaccines against disease .", "The present study aimed to evaluate a non-described hypothetical Leishmania amastigote-specific protein , identified by an immunoproteomic approach in L . infantum , attempting to select a new ...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "blood cells", "medicine and health sciences", "immune cells", "cytokines", "immunity to infections", "immunology", "microbiology", "bacterial diseases", "developmental biology", "yersinia", "molecular development", "yersinia pseudotuberculosis", "vaccination and immunization", "bacterial ...	TNFα and IFNγ but Not Perforin Are Critical for CD8 T Cell-Mediated Protection against Pulmonary Yersinia pestis Infection	journal.ppat.1004142	null	[ [ "Plague , one of the world's most deadly infectious diseases , has killed hundreds of millions of humans during three major pandemics [1] .", "It is caused by the Gram-negative facultative intracellular bacterium Yersinia pestis , which is naturally maintained in rodent reservoirs .", "Fleas transmit ...	[ "Septic pneumonias resulting from bacterial infections of the lung are a leading cause of human death worldwide .", "Little is known about the capacity of CD8 T cell-mediated immunity to combat these infections and the types of effector functions that may be most effective .", "Pneumonic plague is an acutely le...	[ "Bacterial pneumonia is one of the most common causes of death worldwide .", "Pulmonary infection of bacterium Yersinia pestis , the causative agent of plague , results in pneumonic plague and is extremely lethal .", "Mouse models of pulmonary Y . pestis infection are considered translational tools for the deve...	2014
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[]	RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium	journal.ppat.1005262	null	[ [ "Salmonella enterica ( S . enterica ) is a food and water-borne pathogen responsible for widespread disease in humans and other animals .", "The serovars responsible for typhoid fever kill more than 250 , 000 people per year , while an estimated 94 million cases of Salmonella-mediated gastroenteritis caus...	[ "Salmonella enterica serovar Typhimurium is arguably the world’s best-understood bacterial pathogen .", "However , crucial details about the genetic programs used by the bacterium to survive and replicate in macrophages have remained obscure because of the challenge of studying gene expression of intracellular pa...	[ "The burden of Salmonellosis remains unacceptably high throughout the world and control measures have had limited success .", "Because Salmonella bacteria can be transmitted from the wider environment to animals and humans , the bacteria encounter diverse environments that include food , water , plant surfaces an...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "sequence analysis", "systems biology", "genomics", "chromosome biology", "biophysic al simulations", "regulatory networks", "biology", "epigenomics", "computational biology", "chromatin" ]	Nucleosome Free Regions in Yeast Promoters Result from Competitive Binding of Transcription Factors That Interact with Chromatin Modifiers	journal.pcbi.1003181	null	[ [ "The genomes of all eukaryotic organisms are packaged into nucleosomes , which are the fundamental units of chromatin , each composed of approximately 147 base pairs ( bp ) of DNA wrapped around a histone octamer .", "Recent developments in technologies for measuring chromatin marks by chromatin immunopre...	[ "Because DNA packaging in nucleosomes modulates its accessibility to transcription factors ( TFs ) , unraveling the causal determinants of nucleosome positioning is of great importance to understanding gene regulation .", "Although there is evidence that intrinsic sequence specificity contributes to nucleosome po...	[ "The DNA of all eukaryotic organisms is packaged into nucleosomes , which cover roughly of the genome .", "As nucleosome positioning profoundly affects DNA accessibility to other DNA binding proteins such as transcription factors ( TFs ) , it plays an important role in transcription regulation .", "However , to...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "public and occupational health", "infectious diseases", "medicine and health sciences", "epidemiology", "global health", "biology and life sciences", "microbiology" ]	Defining the Geographical Range of the Plasmodium knowlesi Reservoir	journal.pntd.0002780	null	[ [ "The Plasmodium knowlesi parasite , found in wild monkey populations , is a serious public health concern yet almost nothing is known about its geographical extent .", "It is known to cause severe and fatal disease in humans [1]–[4] and is the most common cause of clinical malaria in high transmission reg...	[ "The simian malaria parasite , Plasmodium knowlesi , can cause severe and fatal disease in humans yet it is rarely included in routine public health reporting systems for malaria and its geographical range is largely unknown .", "Because malaria caused by P . knowlesi is a truly neglected tropical disease , there...	[ "Plasmodium knowlesi is a malaria parasite found in monkeys which can infect humans via mosquito bites .", "People infected with the P . knowlesi parasite can suffer severe disease and death yet this disease has often been misdiagnosed as a different malaria type and its geographical distribution is largely unkno...	2014
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "medicine and health sciences", "nucleic acid synthesis", "microbial mutation", "pathology and laboratory medicine", "nucleases", "enzymes", "pathogens", "microbiology", "dna-binding proteins", "viral structure", "enzymology", "plasmid construction", "retroviruses", "viruses", "immunodef...	A high rate of polymerization during synthesis of mouse mammary tumor virus DNA alleviates hypermutation by APOBEC3 proteins	journal.ppat.1007533	null	[ [ "Reverse transcription ( RTN ) is an essential step in the life cycle of all retroviruses and retrotransposons .", "It is catalyzed by retroviral reverse transcriptase ( RT ) that converts single-stranded ( ss ) plus-sense viral RNA genomes to double-stranded viral DNA .", "RTN is a vulnerable step in...	[ "Retroviruses have evolved multiple means to counteract host restriction factors such as single-stranded DNA-specific deoxycytidine deaminases ( APOBEC3s , A3s ) .", "These include exclusion of A3s from virions by an A3-unreactive nucleocapsid or expression of an A3-neutralizing protein ( Vif , Bet ) .", "Howev...	[ "Retroviruses have evolved multiple means for evading host restriction factors such as APOBEC3 proteins that lethally deaminate the intermediate product of reverse transcription reaction–single-stranded cDNA .", "Mouse mammary tumor virus ( MMTV ) , although it does not encode an APOBEC3-neutralizing gene product...	2019
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine and health sciences", "action potentials", "neural networks", "engineering and technology", "signal processing", "membrane potential", "electrophysiology", "neuroscience", "signal filtering", "mathematics", "algebra", "network analysis", "computer and information sciences", "anim...	Low-dimensional spike rate models derived from networks of adaptive integrate-and-fire neurons: Comparison and implementation	journal.pcbi.1005545	null	[ [ "There is prominent evidence that information in the brain , about a particular stimulus for example , is contained in the collective neuronal spiking activity averaged over populations of neurons with similar properties ( population spike rate code ) [1 , 2] .", "Although these populations can comprise a...	[ "The spiking activity of single neurons can be well described by a nonlinear integrate-and-fire model that includes somatic adaptation .", "When exposed to fluctuating inputs sparsely coupled populations of these model neurons exhibit stochastic collective dynamics that can be effectively characterized using the ...	[ "Characterizing the dynamics of biophysically modeled , large neuronal networks usually involves extensive numerical simulations .", "As an alternative to this expensive procedure we propose efficient models that describe the network activity in terms of a few ordinary differential equations .", "These systems ...	2017
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "protein structure", "biology", "computational biology", "macromolecular structure analysis" ]	Insights into the Fold Organization of TIM Barrel from Interaction Energy Based Structure Networks	journal.pcbi.1002505	null	[ [ "Proteins are amino–acid polymers capable of folding into unique three–dimensional functional states .", "The information for the structure formation is contained within their amino–acid sequence [1] .", "With an enormous amount of data available on genomic sequences in organisms and the structures of...	[ "There are many well-known examples of proteins with low sequence similarity , adopting the same structural fold .", "This aspect of sequence-structure relationship has been extensively studied both experimentally and theoretically , however with limited success .", "Most of the studies consider remote homology...	[ "Proteins are polymers of amino-acids that fold into unique three-dimensional structures to perform cellular functions .", "This structure formation has been shown to depend on the amino-acid sequences .", "But examples of proteins with diverse sequences retaining a similar structural fold are quite substantial...	2012
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "algorithms", "systems biology", "computer science", "signaling networks", "biology", "computational biology" ]	A Network-based Approach for Predicting Missing Pathway Interactions	journal.pcbi.1002640	null	[ [ "Networks of protein interactions can reveal how complex molecular processes are activated in the cell .", "However , even for model species , only a fraction of true physical interactions are known [1] , [2] and experimental verification of all remaining potential interactions is unlikely in the near fut...	[ "Embedded within large-scale protein interaction networks are signaling pathways that encode response cascades in the cell .", "Unfortunately , even for well-studied species like S . cerevisiae , only a fraction of all true protein interactions are known , which makes it difficult to reason about the exact flow o...	[ "Networks of protein interactions encode a variety of molecular processes occurring in the cell .", "Embedded within these networks are important subnetworks called signaling pathways .", "Pathways are initiated by upstream proteins ( called sources ) that receive signals from the environment and trigger a casc...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "vero cells", "medicine and health sciences", "rift valley fever virus", "pathology and laboratory medicine", "pathogens", "biological cultures", "microbiology", "viral structure", "viruses", "rna viruses", "bunyaviruses", "microbial genomics", "research and analysis methods", "viral genom...	Single-Molecule FISH Reveals Non-selective Packaging of Rift Valley Fever Virus Genome Segments	journal.ppat.1005800	null	[ [ "Rift Valley fever virus ( RVFV ) is a zoonotic bunyavirus of the genus Phlebovirus that causes recurrent outbreaks on the African continent , the Arabian Peninsula and several islands off the coast of Southern Africa .", "The virus predominantly affects ruminants , of which sheep are the most severely af...	[ "The bunyavirus genome comprises a small ( S ) , medium ( M ) , and large ( L ) RNA segment of negative polarity .", "Although genome segmentation confers evolutionary advantages by enabling genome reassortment events with related viruses , genome segmentation also complicates genome replication and packaging .",...	[ "The bunyavirus family is one of the largest virus families on Earth , of which several members cause severe disease in humans , animals or plants .", "Little is known about the mechanisms that facilitate the production of infectious bunyavirus virions , which should contain at least one copy of the small ( S ) ,...	2016
[ "Introduction", "Results and Discussion", "Materials and Methods" ]	[ "ecology", "biology" ]	Global Gradients in Vertebrate Diversity Predicted by Historical Area-Productivity Dynamics and Contemporary Environment	journal.pbio.1001292	A novel hierarchical framework integrates the effects of time, area, productivity, and temperature at their respective relevant scales and successfully predicts the latitudinal gradient in global vertebrate diversity.	[ [ "The uneven distribution of species diversity is a key feature of life on Earth and has myriad implications .", "While the scale-dependence of the determinants of the global variation in diversity is well acknowledged [1]–[6] , to date a quantitative accounting of the roles of history and environment in g...	[ "Broad-scale geographic gradients in species richness have now been extensively documented , but their historical underpinning is still not well understood .", "While the importance of productivity , temperature , and a scale dependence of the determinants of diversity is broadly acknowledged , we argue here that...	[ "Understanding what determines the distribution of biodiversity across the planet remains one of the critical challenges in biology and has gained particular urgency in the face of environmental change and accelerating species extinctions .", "Our study develops a novel analytical framework to jointly evaluate hi...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "cell biology", "biology and life sciences" ]	Integration of UPRER and Oxidative Stress Signaling in the Control of Intestinal Stem Cell Proliferation	journal.pgen.1004568	null	[ [ "Long-term homeostasis of high-turnover tissues relies on the precise regulation of stem cell ( SC ) activity that allows tailoring regenerative responses to the needs of the tissue .", "Regenerative processes in barrier epithelia , such as the intestinal epithelium , are particularly vulnerable to exogen...	[ "The Unfolded Protein Response of the endoplasmic reticulum ( UPRER ) controls proteostasis by adjusting the protein folding capacity of the ER to environmental and cell-intrinsic conditions .", "In metazoans , loss of proteostasis results in degenerative and proliferative diseases and cancers .", "The cellular...	[ "Loss of proper protein homeostasis ( proteostasis ) as well as increased production of reactive oxygen species ( ROS ) is a hallmark of aging .", "In complex metazoans , these processes can result in proliferative diseases and cancers .", "The protein folding capacity of the endoplasmic reticulum ( ER ) is mon...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "parasite groups", "plasmodium", "engineering and technology", "transportation", "tropical diseases", "geographical locations", "social sciences", "indirect costs", "parasitic diseases", "parasitology", "health care", "apicomplexa", "inpatients", "patients...	Patients’ costs, socio-economic and health system aspects associated with malaria in pregnancy in an endemic area of Colombia	journal.pntd.0006431	null	[ [ "Malaria is a harsh , undesirable and life-threatening disease and , if experienced during pregnancy , can cause adverse effects on birth outcomes and on the health of women and newborns [1] .", "Such effects encompass long term disabilities and , at the aggregate level , are likely to slow down considera...	[ "Malaria in pregnancy threatens birth outcomes and the health of women and their newborns .", "This is also the case in low transmission areas , such as Colombia , where Plasmodium vivax is the dominant parasite species .", "Within the Colombian health system , which underwent major reforms in the 90s , malaria...	[ "Malaria in pregnancy is a harsh and undesirable illness and is the cause of adverse effects on birth outcomes and on the health of women and newborns .", "Despite the low transmission , the predominance of Plasmodium vivax over Plasmodium falciparum and free treatment , estimated costs incurred by pregnant women...	2018
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics", "molecular genetics", "biology", "genetics and genomics", "gene function" ]	Heteroduplex DNA Position Defines the Roles of the Sgs1, Srs2, and Mph1 Helicases in Promoting Distinct Recombination Outcomes	journal.pgen.1003340	null	[ [ "Faithful transmission of genetic information in mitotically dividing cells requires the repair of DNA damage that occurs from exogenous and endogenous sources .", "Damage to both strands of DNA can cause a double-strand break ( DSB ) , as can replication of a damaged DNA template containing a nick .", ...	[ "The contributions of the Sgs1 , Mph1 , and Srs2 DNA helicases during mitotic double-strand break ( DSB ) repair in yeast were investigated using a gap-repair assay .", "A diverged chromosomal substrate was used as a repair template for the gapped plasmid , allowing mismatch-containing heteroduplex DNA ( hDNA ) f...	[ "Chromosomal damage that occurs during normal cell division can be repaired using an intact sequence elsewhere in the genome as a template .", "This process , termed homologous recombination , is crucial for the repair of a particularly deleterious lesion , the DNA double-strand break .", "Although recombinatio...	2013
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "blood cells", "medicine and health sciences", "body fluids", "pathology and laboratory medicine", "fibrinogen", "platelet aggregation", "tropical diseases", "platelet activation", "bacterial diseases", "signs and symptoms", "platelets", "neglected tropical diseases", "glycoproteins", "inf...	Platelet dysfunction contributes to bleeding complications in patients with probable leptospirosis	journal.pntd.0005915	null	[ [ "Leptospirosis is a zoonotic disease of global importance caused by the pathogenic spirochaetes of the genus Leptospira [1 , 2] .", "A modeling exercise by the World Health Organization's ( WHO's ) Leptospirosis Burden Epidemiology Group , estimated that 873 , 000 cases and 48 , 600 deaths occur worldwide...	[ "Severe leptospirosis is frequently complicated by a hemorrhagic diathesis , of which the pathogenesis is still largely unknown .", "Thrombocytopenia is common , but often not to the degree that spontaneous bleeding is expected .", "We hypothesized that the hemorrhagic complications are not only related to thro...	[ "Bleeding is a frequent complication of leptospirosis , a disease caused by the pathogenic spirochaete Leptospira .", "Although thrombocytopenia is common , studies have shown that it does not fully explain the bleeding events seen in these patients .", "We hypothesized that platelet dysfunction plays a role in...	2017
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "dna damage", "biochemistry", "nucleotide excision repair", "genetic disorders", "dna replication", "genetics", "biology and life sciences", "dna repair", "dna", "genetics of disease", "molecular biology" ]	The rem Mutations in the ATP-Binding Groove of the Rad3/XPD Helicase Lead to Xeroderma pigmentosum-Cockayne Syndrome-Like Phenotypes	journal.pgen.1004859	null	[ [ "Accuracy of DNA enzymatic processes , such as transcription , replication and repair , is essential to guarantee genome integrity and , at a higher scale , cell and organism fitness .", "Such processes are functionally connected to checkpoint mechanisms that respond to DNA damage and stresses compromisin...	[ "The eukaryotic TFIIH complex is involved in Nucleotide Excision Repair and transcription initiation .", "We analyzed three yeast mutations of the Rad3/XPD helicase of TFIIH known as rem ( recombination and mutation phenotypes ) .", "We found that , in these mutants , incomplete NER reactions lead to replicatio...	[ "TFIIH is a protein complex that functions in the repair of bulky adducts distorting the DNA via the pathway of Nucleotide Excision Repair , and in transcription initiation and transactivation , the latter being a specific transcription activation process occurring in response to hormones .", "We have taken advan...	2014
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "socioeconomic aspects of health", "environmental health", "science policy and economics", "non-clinical medicine", "health economics", "cost-benefit analysis", "science policy", "dengue fever", "neglected tropical diseases", "cost effectiveness" ]	Economic Impact of Dengue Illness and the Cost-Effectiveness of Future Vaccination Programs in Singapore	journal.pntd.0001426	null	[ [ "Dengue and dengue hemorrhagic fever ( DF and DHF , respectively ) are substantial public health threats throughout the tropical and subtropical regions [1] , [2] .", "The distribution of dengue and its vectors has expanded dramatically over the last 30 years , among other reasons because of insufficient ...	[ "Dengue illness causes 50–100 million infections worldwide and threatens 2 . 5 billion people in the tropical and subtropical regions .", "Little is known about the disease burden and economic impact of dengue in higher resourced countries or the cost-effectiveness of potential dengue vaccines in such settings ."...	[ "Dengue illness is a tropical disease transmitted by mosquitoes that threatens more than one third of the worldwide population .", "Dengue has important economic consequences because of the burden to hospitals , work absenteeism and risk of death of symptomatic cases .", "Governments attempt to reduce the disea...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "evolutionary biology/microbial evolution and genomics", "infectious diseases", "virology/virulence factors and mechanisms", "evolutionary biology/human evolution", "virology/virion structure, assembly, and egress", "virology/immunodeficiency viruses", "virology/animal models of infection", "evolution...	Mutation of a Single Residue Renders Human Tetherin Resistant to HIV-1 Vpu-Mediated Depletion	journal.ppat.1000443	null	[ [ "Retroviruses are obligate cellular parasites and as such rely on a wide variety of host proteins and pathways to complete their lifecycle .", "Moreover , they are subject to a variety of cellular antiviral activities that they must either overcome or avoid in order to successfully infect a cell .", "...	[ "The recently identified restriction factor tetherin/BST-2/CD317 is an interferon-inducible trans-membrane protein that restricts HIV-1 particle release in the absence of the HIV-1 countermeasure viral protein U ( Vpu ) .", "It is known that Tantalus monkey CV1 cells can be rendered non-permissive to HIV-1 releas...	[ "Pathogenic viruses have been infecting mammals throughout their evolution , exerting selective pressure to evolve systems to limit or eliminate these parasites .", "For example , intracellular proteins called restriction factors specifically restrict viral infection by targeting important viral processes .", "...	2009
[ "Introduction", "Results", "Discussion", "Methods" ]	[ "blood cells", "sequencing techniques", "medicine and health sciences", "immune cells", "immune physiology", "applied mathematics", "immunology", "cloning", "simulation and modeling", "algorithms", "mathematics", "molecular biology techniques", "cytotoxic t cells", "research and analysis m...	Identifying T Cell Receptors from High-Throughput Sequencing: Dealing with Promiscuity in TCRα and TCRβ Pairing	journal.pcbi.1005313	null	[ [ "The ability of T cells to recognise antigens is conferred by a process of gene rearrangement that generates a diverse repertoire of T cell receptors ( TCR ) , or clonotypes .", "Identifying the clonotypes involved in responses against pathogens and tumours or those involved in autoimmune disease can guid...	[ "Characterisation of the T cell receptors ( TCR ) involved in immune responses is important for the design of vaccines and immunotherapies for cancer and autoimmune disease .", "The specificity of the interaction between the TCR heterodimer and its peptide-MHC ligand derives largely from the juxtaposed hypervaria...	[ "Our repertoires of T cell receptors ( TCR ) give our immune system the ability to recognise a huge diversity of foreign and self antigens , and identifying the TCRs involved in infectious disease , cancer , and autoimmune disease is important for designing vaccines and immunotherapies .", "The majority of T cell...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "forestry", "plant science", "plant evolution", "plant biology", "crops", "genetics", "plant genetics", "population genetics", "biology", "evolutionary biology", "molecular genetics", "evolutionary genetics", "genetics and genomics", "agriculture" ]	New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties	journal.pgen.1002703	null	[ [ "Domestication is a process of increasing codependence between plants and animals on the one hand , and human societies on the other [1] , [2] .", "The key questions relating to the evolutionary processes underlying domestication concern the identity and geographic origin of the wild progenitors of domest...	[ "The apple is the most common and culturally important fruit crop of temperate areas .", "The elucidation of its origin and domestication history is therefore of great interest .", "The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultiva...	[ "The apple , one of the most ubiquitous and culturally important temperate fruit crops , provides us with a unique opportunity to study the process of domestication in trees .", "The number and identity of the progenitors of the domesticated apple and the erosion of genetic diversity associated with the domestica...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "protein transport", "cell processes", "neuroscience", "developmental biology", "protein expression", "chaperone proteins", "nerve fibers", "molecular biology techniques", "embryos", "neuronal dendrites", "research and analysis methods", "embryology", "animal cells", "axons", "proteins",...	A Bystander Mechanism Explains the Specific Phenotype of a Broadly Expressed Misfolded Protein	journal.pgen.1006450	null	[ [ "Cellular and organismal functions depend critically on the correct folding and intracellular targeting of proteins , and folding mutations are associated with many human pathologies , including neurodegenerative diseases and some forms of diabetes and cancer [1] .", "In addition to directly impairing the...	[ "Misfolded proteins in transgenic models of conformational diseases interfere with proteostasis machinery and compromise the function of many structurally and functionally unrelated metastable proteins .", "This collateral damage to cellular proteins has been termed 'bystander' mechanism .", "How a single misfo...	[ "Correct protein folding and localization ensures cellular health .", "Dedicated proteostasis machinery assists in protein folding and protects against misfolding .", "Yet , folding mutations cause many conformational diseases , including neurodegenerative diseases and certain types of diabetes and cancer .", ...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[]	Whisker Movements Reveal Spatial Attention: A Unified Computational Model of Active Sensing Control in the Rat	journal.pcbi.1003236	null	[ [ "A succinct summary of contemporary models of primate visual spatial attention is that exogenous signals ( those arising from external stimuli ) from multiple sensory modalities and endogenous signals ( those arising from internal processes ) compete and combine to produce a spatial map of salience from which...	[ "Spatial attention is most often investigated in the visual modality through measurement of eye movements , with primates , including humans , a widely-studied model .", "Its study in laboratory rodents , such as mice and rats , requires different techniques , owing to the lack of a visual fovea and the particula...	[ "The management of attention is central to animal behaviour and a central theme of study in both neuroscience and psychology .", "Attention is usually studied in the visual system ( most often using cats or primates ) owing to the ease of generating controlled visual stimuli and of measuring its expression throug...	2013
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "dimers (chemical physics)", "chemical characterization", "crystal structure", "chemical compounds", "salicylic acid", "nmr spectroscopy", "condensed matter physics", "dna-binding proteins", "crystallography", "research and analysis methods", "solid state physics", "proteins", "acids", "ch...	Molecular Basis of Ligand-Dependent Regulation of NadR, the Transcriptional Repressor of Meningococcal Virulence Factor NadA	journal.ppat.1005557	null	[ [ "The ‘Reverse Vaccinology’ approach was pioneered to identify antigens for a protein-based vaccine against serogroup B Neisseria meningitidis ( MenB ) , a human pathogen causing potentially-fatal sepsis and invasive meningococcal disease [1] .", "Indeed , Reverse Vaccinology identified Neisseria adhesin A...	[ "Neisseria adhesin A ( NadA ) is present on the meningococcal surface and contributes to adhesion to and invasion of human cells .", "NadA is also one of three recombinant antigens in the recently-approved Bexsero vaccine , which protects against serogroup B meningococcus .", "The amount of NadA on the bacteria...	[ "Serogroup B meningococcus ( MenB ) causes fatal sepsis and invasive meningococcal disease , particularly in young children and adolescents , as highlighted by recent MenB outbreaks in universities of the United States and Canada .", "The Bexsero vaccine protects against MenB and has recently been approved in > 3...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	An siRNA Screen Identifies the U2 snRNP Spliceosome as a Host Restriction Factor for Recombinant Adeno-associated Viruses	journal.ppat.1005082	null	[ [ "Viral pathogens are known to reorganize different components of the host cell machinery during the course of infection .", "For instance , adenoviruses have been shown to induce nuclear reorganization of host splicing factors and mislocalization of the DNA damage response machinery [1] .", "Similarly...	[ "Adeno-associated viruses ( AAV ) have evolved to exploit the dynamic reorganization of host cell machinery during co-infection by adenoviruses and other helper viruses .", "In the absence of helper viruses , host factors such as the proteasome and DNA damage response machinery have been shown to effectively inhi...	[ "Mammalian cells have developed diverse innate/intrinsic immune strategies to counteract viral infections .", "Post-entry infection steps of a single-strand DNA virus , adeno-associated virus ( AAV ) , are subject to such restrictions .", "Here , we screened an siRNA library to identify a novel cellular factor ...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "molecular dynamics", "plant biology", "macromolecular assemblies", "plant science", "plant pathology", "biophysics simulations", "chemistry", "biology", "biophysics", "macromolecular complex analysis", "plant pathogens", "computational chemistry", "computational biology", "macromolecular ...	Virus Capsid Dissolution Studied by Microsecond Molecular Dynamics Simulations	journal.pcbi.1002502	null	[ [ "Non-enveloped icosahedral viruses often contain binding sites for divalent cations , usually .", "The ions are typically bound between coat proteins or on the icosahedral symmetry axes .", "This is broadly observed in three plant virus taxa: the family Tombusviridae ( and an associate satellite virus...	[ "Dissolution of many plant viruses is thought to start with swelling of the capsid caused by calcium removal following infection , but no high-resolution structures of swollen capsids exist .", "Here we have used microsecond all-atom molecular simulations to describe the dynamics of the capsid of satellite tobacc...	[ "We have studied the capsid of satellite tobacco necrosis virus using large scale molecular dynamics simulations , where the atomic motions of 1 , 2 million particles were tracked over one microsecond .", "We find that the capsid swells in the simulations , and that the permeability for water increases 10-fold up...	2012
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "medicine and health sciences", "reproductive system", "gonads", "developmental biology", "molecular biology techniques", "embryos", "immunologic techniques", "morphogenesis", "research and analysis methods", "embryology", "artificial gene amplification and extension", "gene expression", "im...	Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone	journal.pgen.1006520	null	[ [ "Cell fate choices during development often depend on the expression of key genes that must themselves be regulated in a controlled manner by the action of transcription factors at critical cis-regulatory regions or enhancers .", "Some of these genes play major roles in multiple cell types and stages , as...	[ "During mouse sex determination , transient expression of the Y-linked gene Sry up-regulates its direct target gene Sox9 , via a 3 . 2 kb testis specific enhancer of Sox9 ( TES ) , which includes a core 1 . 4 kb element , TESCO .", "SOX9 activity leads to differentiation of Sertoli cells , rather than granulosa c...	[ "SOX9 , a member of the SOX family of developmental transcription factors related to the Y-chromosomal sex-determining factor SRY , plays pivotal roles in cell differentiation in a variety of developmental contexts including formation of the testes , skeleton , brain , skin , pancreas , gut and kidneys .", "Durin...	2017
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[]	The RhoGAP SPIN6 Associates with SPL11 and OsRac1 and Negatively Regulates Programmed Cell Death and Innate Immunity in Rice	journal.ppat.1004629	null	[ [ "To resist pathogen invasion , plants have evolved two layers of innate immunity: pathogen-associated molecular pattern ( PAMP ) -triggered immunity ( PTI ) and effector-triggered immunity ( ETI ) [1] .", "The first layer is PTI , which employs pattern-recognition receptors ( PRRs ) to perceive a broad ra...	[ "The ubiquitin proteasome system in plants plays important roles in plant-microbe interactions and in immune responses to pathogens .", "We previously demonstrated that the rice U-box E3 ligase SPL11 and its Arabidopsis ortholog PUB13 negatively regulate programmed cell death ( PCD ) and defense response .", "H...	[ "Rice diseases are the major threat for stable rice production and food security worldwide .", "Deep understanding of the disease resistance pathway in rice is essential for effective control of the diseases .", "Although rice contains many E3 ubiquitin ligases , the function of their substrates in immune respo...	2015
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "cancer detection and diagnosis", "medicine and health sciences", "genetic diseases", "cancer risk factors", "cancers and neoplasms", "oncology", "mutation", "hereditary nonpolyposis colorectal cancer", "mismatch repair", "dna", "autosomal dominant diseases", "clinical genetics", "genetic ca...	Genetic anticipation in Swedish Lynch syndrome families	journal.pgen.1007012	null	[ [ "Lynch syndrome ( LS ) is an autosomal dominant inherited syndrome that increases the risk of cancer , primarily in the colon , the rectum and the endometrial lining of the uterus , and to a lesser degree also in the stomach , the ovary , the hepatobiliary tract , the urinary tract , the small bowel and the b...	[ "Among hereditary colorectal cancer predisposing syndromes , Lynch syndrome ( LS ) caused by mutations in DNA mismatch repair genes MLH1 , MSH2 , MSH6 or PMS2 is the most common .", "Patients with LS have an increased risk of early onset colon and endometrial cancer , but also other tumors that generally have an ...	[ "Genetic anticipation is a phenomenon where symptoms of a hereditary disease appear at an earlier age and/or are more severe in successive generations .", "In genetic disorders such as Fragile X syndrome , Myotonic dystrophy type 1 and Huntington disease , anticipation is caused by the expansion of unstable trinu...	2017
[ "Introduction", "Materials and methods", "Results", "Discussion" ]	[ "invertebrates", "medicine and health sciences", "ecology and environmental sciences", "compasses", "engineering and technology", "locusts", "social sciences", "neuroscience", "animals", "insect pests", "animal behavior", "deserts", "eyes", "pests", "zoology", "hymenoptera", "animal ...	From skylight input to behavioural output: A computational model of the insect polarised light compass	journal.pcbi.1007123	null	[ [ "Orientation cues are required for spatial behaviours from following a straight line [1] to migrating across continents [2] ( for a theoretical proof see [3] ) .", "Idiothetic cues such as those generated in the mammalian vestibular system are useful for short time periods but are inherently problematic b...	[ "Many insects navigate by integrating the distances and directions travelled on an outward path , allowing direct return to the starting point .", "Fundamental to the reliability of this process is the use of a neural compass based on external celestial cues .", "Here we examine how such compass information cou...	[ "We propose a new hypothesis for how insects process polarised skylight to extract global orientation information that can be used for accurate path integration .", "Our model solves the problem of solar-antisolar meridian ambiguity by using a biologically constrained sensor array , and includes methods to deal w...	2019
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "invertebrates", "plant anatomy", "plant growth and development", "plant embryo anatomy", "animals", "hormones", "animal signaling and communication", "organisms", "animal models", "developmental biology", "plant science", "model organisms", "drosophila melanogaster", "animal behavior", ...	NCP1/AtMOB1A Plays Key Roles in Auxin-Mediated Arabidopsis Development	journal.pgen.1005923	null	[ [ "In recent years , the Hippo signaling pathway has emerged as a very important pathway for animal development [1] .", "This highly conserved pathway was initially identified in Drosophila as a key pathway controlling organ size , and later was shown to play a role in controlling cell fate and pattern form...	[ "MOB1 protein is a core component of the Hippo signaling pathway in animals where it is involved in controlling tissue growth and tumor suppression .", "Plant MOB1 proteins display high sequence homology to animal MOB1 proteins , but little is known regarding their role in plant growth and development .", "Here...	[ "MOB1 protein is a key component of the Hippo signaling pathway in animals , and it plays critical roles in organ size control .", "The plant hormone auxin regulates many aspects of plant growth and development including organogenesis .", "In this work , we showed that AtMOB1A , which is highly homologous to an...	2016
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "genetics and genomics/genome projects", "genetics and genomics/microbial evolution and genomics", "genetics and genomics/cancer genetics", "genetics and genomics/chromosome biology" ]	A Fine-Structure Map of Spontaneous Mitotic Crossovers in the Yeast Saccharomyces cerevisiae	journal.pgen.1000410	null	[ [ "Although mitotic recombination between homologous chromosomes was first described in 1936 [1] , our understanding of the mechanism of spontaneous mitotic recombination is still limited for two related reasons .", "First , spontaneous mitotic recombination events are very infrequent compared to meiotic ex...	[ "Homologous recombination is an important mechanism for the repair of DNA damage in mitotically dividing cells .", "Mitotic crossovers between homologues with heterozygous alleles can produce two homozygous daughter cells ( loss of heterozygosity ) , whereas crossovers between repeated genes on non-homologous chr...	[ "Most higher organisms have two copies of several different types of chromosomes .", "For example , the human female has 23 pairs of chromosomes .", "Although the chromosome pairs have very similar sequences , they are not identical .", "Members of a chromosome pair can swap segments from one chromosome to th...	2009
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "evolutionary biology", "drosophila", "genetics and genomics" ]	Adaptive Gene Expression Divergence Inferred from Population Genomics	journal.pgen.0030187	null	[ [ "Changes in gene expression are governed primarily by the evolution of cis-acting elements and trans-acting factors .", "Several single-gene studies have combined data on expression , protein abundance , function , and sequence evolution to make powerful statements about the role of adaptive evolution in ...	[ "Detailed studies of individual genes have shown that gene expression divergence often results from adaptive evolution of regulatory sequence .", "Genome-wide analyses , however , have yet to unite patterns of gene expression with polymorphism and divergence to infer population genetic mechanisms underlying expre...	[ "Changes in patterns of gene expression likely contribute greatly to phenotypic differences among closely related organisms .", "However , the evolutionary mechanisms , such as Darwinian selection and random genetic drift , which are underlying differences in patterns of expression , are only now being understood...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine and health sciences", "biopsy", "carcinomas", "cancers and neoplasms", "surgical and invasive medical procedures", "health care", "oncology", "systems science", "mathematics", "endoscopy", "probability distribution", "gastroenterology and hepatology", "adenocarcinomas", "epigenet...	A Molecular Clock Infers Heterogeneous Tissue Age Among Patients with Barrett’s Esophagus	journal.pcbi.1004919	null	[ [ "There is great interest in the molecular characterization of precancerous fields and lesions ( e . g . , colorectal adenomas or ductal carcinoma in situ ( DCIS ) in the breast ) to quantify their neoplastic potential , although it is generally not known how long such lesions ( or fields ) have sojourned in a...	[ "Biomarkers that drift differentially with age between normal and premalignant tissues , such as Barrett’s esophagus ( BE ) , have the potential to improve the assessment of a patient’s cancer risk by providing quantitative information about how long a patient has lived with the precursor ( i . e . , dwell time ) ....	[ "Barrett’s Esophagus ( BE ) is a metaplastic precursor to esophageal adenocarcinoma ( EAC ) .", "When a patient is diagnosed with BE , it is generally not known how long he/she has had this condition because BE is asymptomatic .", "While the question of how long a premalignant tissue or lesion has been resident...	2016
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary biology", "homo (human)", "genetics and genomics", "computational biology" ]	A Survey of Genomic Properties for the Detection of Regulatory Polymorphisms	journal.pcbi.0030106	null	[ [ "Our ability to identify the molecular mechanisms responsible for specific genetic traits within our population will be enhanced by our imminent ability to decipher each individual's genome .", "This is evident from recent advances in sequencing and genotyping technologies , which allow an increasing numb...	[ "Advances in the computational identification of functional noncoding polymorphisms will aid in cataloging novel determinants of health and identifying genetic variants that explain human evolution .", "To date , however , the development and evaluation of such techniques has been limited by the availability of k...	[ "Computational techniques are used in biology to prioritize DNA sequence variants ( or polymorphisms ) that may be responsible for population diversity and the manifestation of species-specific traits .", "Predominantly , they have been used to predict the class of polymorphisms that alter protein function throug...	2007
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "plant science", "plant biology", "biology", "microbiology" ]	The TPR Domain in the Host Cyp40-like Cyclophilin Binds to the Viral Replication Protein and Inhibits the Assembly of the Tombusviral Replicase	journal.ppat.1002491	null	[ [ "Replication of plus-stranded ( + ) RNA viruses takes place in membrane-bound viral replicase complexes ( VRCs ) in the cytoplasm of infected cells .", "( + ) RNA viruses usurp a number of host-coded proteins to aid the replication process [1]–[8] .", "Many host proteins , however , have antiviral act...	[ "Replication of plus-stranded RNA viruses is greatly affected by numerous host-coded proteins acting either as susceptibility or resistance factors .", "Previous genome-wide screens and global proteomics approaches with Tomato bushy stunt tombusvirus ( TBSV ) in a yeast model host revealed the involvement of cycl...	[ "Replication of plus-stranded RNA viruses , which are important pathogens of humans , animals and plants , can be inhibited by host-coded proteins .", "In this paper , the authors show that the Cyp40-like Cpr7p prolyl isomerase of yeast can effectively inhibit tombusvirus replication .", "This inhibition is due...	2012
[ "Introduction", "Results/Discussion", "Materials and Methods" ]	[ "genetics and genomics/epigenetics", "genetics and genomics/cancer genetics", "genetics and genomics/functional genomics" ]	Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus	journal.pgen.1000597	null	[ [ "Chromosome 8q24 is an established risk locus for many common epithelial cancers .", "The region was originally discovered by fine-mapping of a prostate cancer linkage peak from a family-based study by deCODE genetics [1] and common alleles in the region have subsequently been found in genome-wide scans o...	[ "Multiple discrete regions at 8q24 were recently shown to contain alleles that predispose to many cancers including prostate , breast , and colon .", "These regions are far from any annotated gene and their biological activities have been unknown .", "Here we profiled a 5-megabase chromatin segment encompassing...	[ "Genome-wide scans of inherited genetic variation in the normal population have recently identified many sites ( loci ) associated with the predisposition to complex diseases such as cancer .", "Some of these cancer-associated loci , however , are devoid of genes ( situated in so-called “gene deserts” ) and the m...	2009
[ "Introduction", "Results and Discussion", "Methods" ]	[ "blood cells", "cell death", "medicine and health sciences", "immune cells", "pathology and laboratory medicine", "viral transmission and infection", "pathogens", "immunology", "cell processes", "microbiology", "staphylococcus aureus", "toxicology", "epithelial cells", "genetic elements", ...	Staphylococcus aureus Exploits a Non-ribosomal Cyclic Dipeptide to Modulate Survival within Epithelial Cells and Phagocytes	journal.ppat.1005857	null	[ [ "Staphylococcus aureus is a notorious human pathogen that can cause a variety of diseases and thus causes a dramatic disease burden and death toll especially in the hospital setting [1 , 2] .", "The advent of methicillin resistant S . aureus ( MRSA ) led to a loss of therapeutic options and in recent year...	[ "Community-acquired ( CA ) Staphylococcus aureus cause various diseases even in healthy individuals .", "Enhanced virulence of CA-strains is partly attributed to increased production of toxins such as phenol-soluble modulins ( PSM ) .", "The pathogen is internalized efficiently by mammalian host cells and intra...	[ "Staphylococcus aureus is a notorious microbe that causes a variety of diseases in man ranging from skin abscesses to blood poisoning .", "S . aureus can be internalized by cells of its human host , break out of membrane enclosures , and subsequently kill the cells from within .", "For these processes the bacte...	2016
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "invertebrates", "animals", "invertebrate genomics", "animal models", "fungi", "drosophila melanogaster", "model organisms", "experimental organism systems", "sequence motif analysis", "cellular structures and organelles", "drosophila", "research and analysis methods", "saccharomyces", "se...	Stop-codon read-through arises largely from molecular errors and is generally nonadaptive	journal.pgen.1008141	null	[ [ "In the standard genetic code , three ( TAA , TAG , and TGA ) of the 64 codons are stop codons , which , unlike sense codons , do not have corresponding tRNAs .", "These stop codons are instead recognized by release factors , causing the translating ribosome to terminate peptide synthesis and be released ...	[ "Stop-codon read-through refers to the phenomenon that a ribosome goes past the stop codon and continues translating into the otherwise untranslated region ( UTR ) of a transcript .", "Recent ribosome-profiling experiments in eukaryotes uncovered widespread stop-codon read-through that also varies among tissues ,...	[ "The stop codon gives the translating ribosome the signal for the termination of peptide synthesis , but occasionally the ribosome goes past the stop codon and continues translating into the otherwise untranslated region of a transcript .", "Stop-codon read-through generates an elongated peptide , which could be ...	2019
[ "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "biophysics/theory and simulation", "computational biology", "mathematics/statistics", "biophysics" ]	Theoretical Analysis of the Stress Induced B-Z Transition in Superhelical DNA	journal.pcbi.1001051	null	[ [ "DNA often occurs in an underwound , negatively superhelical topological state in vivo .", "In bacteria , gyrase enzymes act to generate negative supercoils , while topoisomerases dissipate them .", "The dynamic balance between these two processes determines a basal level of superhelicity that can cha...	[ "We present a method to calculate the propensities of regions within a DNA molecule to transition from B-form to Z-form under negative superhelical stresses .", "We use statistical mechanics to analyze the competition that occurs among all susceptible Z-forming regions at thermodynamic equilibrium in a superhelic...	[ "We present the SIBZ algorithm that calculates the equilibrium properties of the transition from right-handed B-form to left-handed Z-form in a DNA sequence that is subjected to imposed stresses .", "SIBZ calculates the probability of transition of each base pair in a user-defined sequence .", "By examining ill...	2011
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "infectious diseases/protozoal infections", "genetics and genomics/gene function", "microbiology/cellular microbiology and pathogenesis", "microbiology/parasitology" ]	Degradation of Host Sphingomyelin Is Essential for Leishmania Virulence	journal.ppat.1000692	null	[ [ "Leishmania parasites infect 10–12 million people worldwide , causing a spectrum of diseases known as leishmaniasis [1] .", "Transmitted by sandflies , these protozoan pathogens have tremendous negative impacts on public health worldwide , especially in developing countries [1] .", "During their life ...	[ "In eukaryotes , sphingolipids ( SLs ) are important membrane components and powerful signaling molecules .", "In Leishmania , the major group of SLs is inositol phosphorylceramide ( IPC ) , which is common in yeast and Trypanosomatids but absent in mammals .", "In contrast , sphingomyelin is not synthesized by...	[ "Leishmania are obligate intracellular parasites responsible for a spectrum of diseases in humans ranging from self-healing skin lesions to deadly visceral infections .", "To survive , they must downregulate the microbicidal activity and scavenge nutrients from the host .", "Although Leishmania parasites do not...	2009
[ "Introduction", "Results", "Discussion", "Materials and Methods", "Supporting Information" ]	[ "primates", "viruses", "public health and epidemiology", "infectious diseases", "ecology", "homo (human)", "virology", "vertebrates", "animals", "genetics and genomics" ]	Co-Circulation and Evolution of Polioviruses and Species C Enteroviruses in a District of Madagascar	journal.ppat.0030191	null	[ [ "Polioviruses ( PVs ) , members of the Enterovirus genus in the Picornaviridae family , are major human pathogens causing the acute paralytic disease poliomyelitis .", "The human enteroviruses ( HEV ) are classified into five species , HEV-A to -D , and the PV species ( PV-1 to −3 ) .", "The species H...	[ "Between October 2001 and April 2002 , five cases of acute flaccid paralysis ( AFP ) associated with type 2 vaccine-derived polioviruses ( VDPVs ) were reported in the southern province of the Republic of Madagascar .", "To determine viral factors that favor the emergence of these pathogenic VDPVs , we analyzed i...	[ "Following extensive vaccination campaigns using the attenuated oral polio vaccine , wild polioviruses remain endemic in only a few countries .", "Nevertheless , several poliomyelitis outbreaks associated with vaccine-derived polioviruses ( VDPVs ) were reported in different parts of the world in recent years , p...	2007
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Head and Neck Mycetoma: The Mycetoma Research Centre Experience	journal.pntd.0003587	null	[ [ "Mycetoma is one of the neglected tropical diseases , characterised by massive deformity , disability and can be fatal if not managed properly and timely [1–3] .", "It is a chronic , specific , granulomatous , progressive subcutaneous inflammatory disease that spreads to involve the skin , deep structures...	[ "Mycetoma is a unique neglected tropical disease which is endemic in what is known as the “mycetoma belt” .", "The disease has many devastating impacts on patients and communities in endemic area and is characterised by massive deformity , destruction and disability .", "Mycetoma is commonly seen in the foot an...	[ "Although head and neck mycetoma is a rare disease entity yet it is a dreadful disease for the patient , the family and the treating physician .", "It is potentially fatal and the most challenging to treat .", "The current study highlighted that , most patients were young adult males , from rural areas of the S...	2015
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[ "medicine", "infectious diseases", "nephrology", "neglected tropical diseases", "acute renal failure", "critical care and emergency medicine", "toxicology" ]	Loxosceles gaucho Venom-Induced Acute Kidney Injury – In Vivo and In Vitro Studies	journal.pntd.0001182	null	[ [ "Loxosceles spiders can be found worldwide in temperate and tropical regions but their distribution is heavily concentrated in the Western Hemisphere [1] , [2] .", "In fact , in South America , loxoscelism is considered the most important form of araneism due to its high incidence and morbidity [1]–[3] ."...	[ "Accidents caused by Loxosceles spider may cause severe systemic reactions , including acute kidney injury ( AKI ) .", "There are few experimental studies assessing Loxosceles venom effects on kidney function in vivo .", "In order to test Loxosceles gaucho venom ( LV ) nephrotoxicity and to assess some of the p...	[ "Loxosceles ( recluse or brown spider ) is the most important spider genus causing human envenomation .", "In Brazil Loxosceles spiders were responsible for approximately 7 , 000 cases of spider envenomation per year .", "The brown spider accidents may cause late cutaneous necrosis at the bite site , intravascu...	2011
[ "Introduction", "Materials and Methods", "Results", "Discussion" ]	[]	Mansonella, including a Potential New Species, as Common Parasites in Children in Gabon	journal.pntd.0004155	null	[ [ "Tropical African countries are afflicted by many febrile diseases including HIV , tuberculosis , malaria , and bacteremia; it has been suggested that their emergence can be influenced by infectious factors such as filarial parasites , including Mansonella perstans [1 , 2] .", "In 2012 , Dolo et al . , du...	[ "Like other tropical African countries , Gabon is afflicted by many parasitic diseases , including filariases such as loiasis and mansonellosis .", "This study aimed to assess the prevalence of these two filarial diseases in febrile and afebrile children using quantitative real-time PCR and standard PCR assays co...	[ "Approximately 114 million people in Africa , mostly located in 33 Sub-Saharan African countries , are infected with Mansonella perstans , a filarial nematode .", "The ability of M . perstans to induce severe clinical features has only recently been considered .", "Unfortunately , no study has evaluated its bur...	2015
[ "Introduction", "Results", "Discussion", "Materials and Methods" ]	[ "telomeres", "cell biology", "chromosome biology", "biology", "molecular cell biology" ]	The Chromosomal Proteins JIL-1 and Z4/Putzig Regulate the Telomeric Chromatin in Drosophila melanogaster	journal.pgen.1003153	null	[ [ "Telomere elongation is needed in all eukaryotes with linear chromosomes due to the incapacity of cellular polymerases to proceed in 3′ to 5′ direction .", "Telomere length homeostasis is important for protecting the chromosomes from terminal erosion and the loss of important genetic information .", "...	[ "Drosophila telomere maintenance depends on the transposition of the specialized retrotransposons HeT-A , TART , and TAHRE .", "Controlling the activation and silencing of these elements is crucial for a precise telomere function without compromising genomic integrity .", "Here we describe two chromosomal prote...	[ "Drosophila telomeres constitute a remarkable exception to the general telomerase mechanism of telomere maintenance in eukaryotes .", "The essential role of the telomeric transposons HeT-A , TART , and TAHRE ( HTT ) in this organism contrasts with the strong conservation of their retrotransposon personalities .",...	2012
[ "Introduction", "Methods", "Results and Discussion" ]	[]	Differential Chromosome Conformations as Hallmarks of Cellular Identity Revealed by Mathematical Polymer Modeling	journal.pcbi.1004306	null	[ [ "The three-dimensional organization of the genome was shown to dynamically adapt to nuclear function and complexity [1–3] .", "Chromatin fibers can be represented by a polymer random coil adopting a considerable , largely unappreciated number of states in response to DNA metabolism [4–7] .", "How the ...	[ "Inherently dynamic , chromosomes adopt many different conformations in response to DNA metabolism .", "Models of chromosome organization in the yeast nucleus obtained from genome-wide chromosome conformation data or biophysical simulations provide important insights into the average behavior but fail to reveal f...	[ "The spatial organization of the genome inside eukaryotic cell nuclei has been shown to play a role in transcription , replication , recombination and DNA repair .", "Probabilistic models have correlated structural fluctuations with these processes , but methods to detect transient features describing chromosome ...	2015
[ "Introduction", "Results", "Discussion", "Materials and methods" ]	[ "blood cells", "cell death", "uterus", "medicine and health sciences", "reproductive system", "immune cells", "cell processes", "immunology", "epithelial cells", "animal models", "model organisms", "experimental organism systems", "research and analysis methods", "white blood cells", "an...	The uterine epithelial loss of Pten is inefficient to induce endometrial cancer with intact stromal Pten	journal.pgen.1007630	null	[ [ "Endometrial carcinoma ( EMC ) is the most common cancer of the female reproductive organs in the United States .", "In 2017 , about 60 , 000 new cases were diagnosed and about 11 , 000 deaths occurred related to EMC in the US [1 , 2] .", "EMC has been categorized into two major types: type I endometr...	[ "Mutation of the tumor suppressor Pten often leads to tumorigenesis in various organs including the uterus .", "We previously showed that Pten deletion in the mouse uterus using a Pgr-Cre driver ( Ptenf/fPgrCre/+ ) results in rapid development of endometrial carcinoma ( EMC ) with full penetration .", "We also ...	[ "Endometrial cancer is highly prevalent gynecological cancer in the United States .", "Pten is the most commonly mutated gene in endometrial carcinoma originating in the epithelium .", "Previous studies focused on PTEN’s role in epithelial growth regulation .", "Here we show that in addition to Pten mutation ...	2018

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