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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Central American countries face a major challenge in the control of Triatoma dimidiata , a widespread vector of Chagas disease that cannot be eliminated . The key to maintaining the risk of transmission of Trypanosoma cruzi at lowest levels is to sustain surveillance throughout endemic areas . Guatemala , El Salvador ,...	Elimination of domiciliated vectors led to a decreased prevalence of Chagas disease in parts of Latin America . In Central America , where the domiciliated vector Rhodnius prolixus has been almost eliminated , Triatoma dimidiata , which cannot be eliminated , continues to threaten the population in vast areas . To main...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Determinants of Health Service Responsiveness in Community-Based Vector Surveillance for Chagas Disease in Guatemala, El Salvador, and Honduras
Malaria in sub-Saharan Africa has historically been almost exclusively attributed to Plasmodium falciparum ( Pf ) . Current diagnostic and surveillance systems in much of sub-Saharan Africa are not designed to identify or report non-Pf human malaria infections accurately , resulting in a dearth of routine epidemiologic...	Plasmodium vivax ( Pv ) is the most widely distributed malaria parasite globally , but conspicuously “absent” from Africa . The majority of African populations do not express the Duffy blood group antigen , which is the only known receptor for Pv infection . Since this discovery in the 1970s , the low clinical incidenc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Plasmodium vivax Transmission in Africa
Genome-scale metabolic models have become a fundamental tool for examining metabolic principles . However , metabolism is not solely characterized by the underlying biochemical reactions and catalyzing enzymes , but also affected by regulatory events . Since the pioneering work of Covert and co-workers as well as Shlom...	Networks—the compact representation of systems in terms of nodes and links—are an efficient data structure for biological information . They also allow us to establish relationships between network structure and dynamical function and thus hold the potential of implementing a systems-level view on biological processes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "metabolism", "gene", "regulation", "metabolic", "processes", "regulatory", "proteins", "metabolic", "networks", "enzymology", "dna-binding", "proteins", "network", "analysis", "enzyme", "metabolism", "transcription", "factors", "enzyme", "chemistry", "computer",...	2019	A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli
Progress in science depends on the effective exchange of ideas among scientists . New ideas can be assessed and criticized in a meaningful manner only if they are formulated precisely . This applies to simulation studies as well as to experiments and theories . But after more than 50 years of neuronal network simulatio...	Scientists make precise , testable statements about their observations and models of nature . Other scientists can then evaluate these statements and attempt to reproduce or extend them . Results that cannot be reproduced will be duly criticized to arrive at better interpretations of experimental results or better mode...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2009	Towards Reproducible Descriptions of Neuronal Network Models
Secondary bacterial infections from snakebites contribute to the high complication rates that can lead to permanent function loss and disabilities . Although common in endemic areas , routine empirical prophylactic use of antibiotics aiming to prevent secondary infection lacks a clearly defined policy . The aim of this...	Bothrops genus is responsible by 80–90% of the snakebites in the Brazilian Amazon , resulting in a subcutaneous and muscular lesion at the site of bite , which many times evolve to local complications , mostly secondary bacterial infections . In this region , late medical assistance is common and probably contributes t...	[ "Abstract", "Introduction", "Methods", "and", "materials", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "c-reactive", "proteins", "chemical", "compounds", "fibrinogen", "aliphatic", "amino", "acids", "pathology", "and", "laboratory", "medicine", "drugs", "tropical", "diseases", "microbiology", "creatine", "vertebrat...	2017	Poor efficacy of preemptive amoxicillin clavulanate for preventing secondary infection from Bothrops snakebites in the Brazilian Amazon: A randomized controlled clinical trial
When sequencing an ancient DNA sample from a hominin fossil , DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material . This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating...	When extracting and sequencing ancient DNA from human remains , a recurrent problem is the presence of DNA from the paleontologists , archaeologists or geneticists that may have handled the fossil . If a DNA library is highly contaminated , this will introduce biases in downstream analyses , so it is important to deter...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "sequencing", "techniques", "demography", "social", "sciences", "anthropology", "ancient", "dna", "contaminants", "neanderthals", "genome", "sequencing", "materials", "science", "genome", "analysis", "paleontology", "dna", "paleogenetics", "molecular", "biology", "technique...	2016	Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans
The [PSI+] prion may enhance evolvability by revealing previously cryptic genetic variation , but it is unclear whether such evolvability properties could be favored by natural selection . Sex inhibits the evolution of other putative evolvability mechanisms , such as mutator alleles . This paper explores whether sex al...	Can evolvability evolve ? One obvious way to evolve faster is via mutator alleles that increase the mutation rate . Unfortunately , recombination will rapidly separate a mutator allele from the advantageous alleles that it creates . Mutators , therefore , gain very little benefit from promoting adaptations and are thou...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/evolutionary", "modeling", "evolutionary", "biology/microbial", "evolution", "and", "genomics" ]	2009	Complex Adaptations Can Drive the Evolution of the Capacitor [PSI+], Even with Realistic Rates of Yeast Sex
Anthrax is a soil-borne disease caused by the bacterium Bacillus anthracis and is considered a neglected zoonosis . In the country of Georgia , recent reports have indicated an increase in the incidence of human anthrax . Identifying sub-national areas of increased risk may help direct appropriate public health control...	Anthrax is a zoonotic bacterial disease that occurs nearly worldwide . Despite a large number of countries reporting endemic anthrax , persistence of the disease appears to be associated with specific ecological factors related to soil composition and climatic conditions . Human cases are most often associated with han...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "anthrax", "geography", "veterinary", "diseases", "social", "and", "behavioral", "sciences", "environmental", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "zoonotic", "diseases", "spa...	2013	Evidence of Local Persistence of Human Anthrax in the Country of Georgia Associated with Environmental and Anthropogenic Factors
Insertions of parasitic DNA within coding sequences are usually deleterious and are generally counter-selected during evolution . Thanks to nuclear dimorphism , ciliates provide unique models to study the fate of such insertions . Their germline genome undergoes extensive rearrangements during development of a new soma...	Ciliates are unicellular eukaryotes that rearrange their genomes at every sexual generation when a new somatic macronucleus , responsible for gene expression , develops from a copy of the germline micronucleus . In Paramecium , assembly of a functional somatic genome requires precise excision of interstitial DNA segmen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "evolutionary", "biology", "genome", "sequencing", "dna", "recombination", "molecular", "genetics", "dna", "sequence", "analysis", "transposons", "comparative", "genomics", "biology", "molecular", "biology", "nucleic", "acids", "dna", "transposons",...	2012	The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences
CpG islands were originally identified by epigenetic and functional properties , namely , absence of DNA methylation and frequent promoter association . However , this concept was quickly replaced by simple DNA sequence criteria , which allowed for genome-wide annotation of CpG islands in the absence of large-scale epi...	A key challenge for bioinformatic research is the identification of regulatory regions in the human genome . Regulatory regions are DNA elements that control gene expression and thereby contribute to the organism's phenotype . An important class of regulatory regions consists of so-called CpG islands , which are charac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "mammals", "computational", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	CpG Island Mapping by Epigenome Prediction
As tourism is the mainstay of the Maldives’ economy , this country recognizes the importance of controlling mosquito-borne diseases in an environmentally responsible manner . This study sought to estimate the economic costs of dengue in this Small Island Developing State of 417 , 492 residents . The authors reviewed re...	As tourism is the mainstay of the Maldives’ economy , this country recognizes the importance of controlling mosquito-borne diseases in an environmentally responsible manner . This study sought to estimate the economic costs of dengue in this Small Island Developing State of 417 , 492 residents with an annual average of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine", "and", "health", "sciences", "landforms", "topography", "geographical", "locations", "social", "sciences", "biological", "locomotion", "health", "care", "infectious", "disease", "control", "islands", "infectious", "diseases", "health", "econom...	2018	Economic analysis of dengue prevention and case management in the Maldives
Integrative and Conjugative Elements ( ICEs ) of the SXT/R391 family disseminate multidrug resistance among pathogenic Gammaproteobacteria such as Vibrio cholerae . SXT/R391 ICEs are mobile genetic elements that reside in the chromosome of their host and eventually self-transfer to other bacteria by conjugation . Conju...	Integrative and conjugative elements ( ICEs ) constitute a class of mobile genetic elements defined by their ability to integrate into the chromosome of their host cell and to transfer by conjugation . Some of the most studied ICEs belong to the SXT/R391 family , which are major drivers of multidrug resistance dissemin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Replication and Active Partition of Integrative and Conjugative Elements (ICEs) of the SXT/R391 Family: The Line between ICEs and Conjugative Plasmids Is Getting Thinner
Certain cutaneous human papillomaviruses ( HPVs ) , which are ubiquitous and acquired early during childhood , can cause a variety of skin tumors and are likely involved in the development of non-melanoma skin cancer , especially in immunosuppressed patients . Hence , the burden of these clinical manifestations demands...	Organ transplant recipients ( OTR ) frequently suffer from fulminant warts that are induced by cutaneous human papillomaviruses ( HPV ) . Moreover , some skin HPV types may also be involved in the development of non-melanoma skin cancer . Mimicking the situation of immunosuppressed OTR who acquire cutaneous HPV infecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "vaccines", "oncology", "medicine", "vaccination", "dermatology", "viral", "vaccines", "skin", "neoplasms", "clinical", "immunology", "immunity", "virology", "benign", "skin", "neoplasms", "biology", "microbiology", "cancer", "prevention", "cancer", "vaccines", "malignant...	2014	Protective Vaccination against Papillomavirus-Induced Skin Tumors under Immunocompetent and Immunosuppressive Conditions: A Preclinical Study Using a Natural Outbred Animal Model
Human T-cell leukemia virus type 1 ( HTLV-1 ) infection is linked to the development of adult T-cell leukemia ( ATL ) and the neuroinflammatory disease HTLV-1 associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . The HTLV-1 Tax protein functions as a potent viral oncogene that constitutively activates the NF...	The retrovirus HTLV-1 is the causative agent of an aggressive lymphoproliferative disorder known as adult T-cell leukemia ( ATL ) . The HTLV-1 Tax regulatory protein constitutively activates the host NF-κB transcription factor to promote T-cell proliferation , survival and cell transformation . However , it remains unk...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "microbiology", "medicine", "and", "health", "sciences" ]	2014	A Critical Role for IL-17RB Signaling in HTLV-1 Tax-Induced NF-κB Activation and T-Cell Transformation
Protein kinases use ATP as a phosphoryl donor for the posttranslational modification of signaling targets . It is generally thought that the binding of this nucleotide induces conformational changes leading to closed , more compact forms of the kinase domain that ideally orient active-site residues for efficient cataly...	The Src protein kinases are integral members of numerous signaling pathways involved in cellular growth and differentiation . The master regulator of the Src family is the protein kinase Csk , which adds a phosphate to the C-terminal tail , inhibiting Src Kinase function . Proper regulation of these signaling pathways ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "enzyme", "structure", "protein", "chemistry", "cofactors", "biochemistry", "simulations", "proteins", "biophysic", "al", "simulations", "enzymes", "protein", "structure", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2012	Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function
Malarial infection is associated with complex immune and erythropoietic responses in the host . A quantitative understanding of these processes is essential to help inform malaria therapy and for the design of effective vaccines . In this study , we use a statistical model-fitting approach to investigate the immune and...	Malaria is a disease caused by a protozoan parasite of the genus Plasmodium . Every year there are around 250 million human cases of malaria , resulting in around a million deaths . Most of the severe cases and deaths are due to Plasmodium falciparum , which is endemic in much of sub-Saharan Africa and other tropical a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "public", "health", "and", "epidemiology/infectious", "diseases", "immunology/immune", "response", "computational", "biology" ]	2010	Quantitative Analysis of Immune Response and Erythropoiesis during Rodent Malarial Infection
Homeostasis of most adult tissues is maintained by balancing stem cell self-renewal and differentiation , but whether post-transcriptional mechanisms can regulate this process is unknown . Here , we identify that an RNA methyltransferase ( Misu/Nsun2 ) is required to balance stem cell self-renewal and differentiation i...	We demonstrate that the RNA methyltransferase activity of Misu/NSun2 is required for the proper maintenance of the epidermal differentiation program , and thus post-transcriptional mechanisms are involved in controlling the balance between stem cell self-renewal and differentiation .	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "stem", "cells", "biology", "adult", "stem", "cells" ]	2011	The RNA–Methyltransferase Misu (NSun2) Poises Epidermal Stem Cells to Differentiate
A 30-node signed and directed network responsible for self-renewal and pluripotency of mouse embryonic stem cells ( mESCs ) was extracted from several ChIP-Seq and knockdown followed by expression prior studies . The underlying regulatory logic among network components was then learned using the initial network topolog...	For this study we first constructed a directed and signed network consisting of 15 pluripotency regulators and 15 lineage commitment markers that extensively interact to regulate mouse embryonic stem cells fate decisions from data available in the public domain . Given the connectivity structure of this network , the u...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computer", "and", "information", "sciences", "systems", "science", "mathematics", "stem", "cells", "animal", "cells", "cell", "biology", "embryonic", "stem", "cells", "single", "cell", "primary", "cell", "culture", "cell", "culturing", "techniques", "biology", "and...	2014	Construction and Validation of a Regulatory Network for Pluripotency and Self-Renewal of Mouse Embryonic Stem Cells
Genome-wide association studies have identified hundreds of risk loci for autoimmune disease , yet only a minority ( ~25% ) share genetic effects with changes to gene expression ( eQTLs ) in immune cells . RNA-Seq based quantification at whole-gene resolution , where abundance is estimated by culminating expression of ...	It is well acknowledged that non-coding genetic variants contribute to disease susceptibility through alteration of gene expression levels ( known as eQTLs ) . Identifying the variants that are causal to both disease risk and changes to expression levels has not been easy and we believe this is in part due to how expre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "rheumatology", "medicine", "and", "health", "sciences", "immunology", "clinical", "medicine", "genome", "analysis", "molecular", "genetics", "epigenetics", "chromatin", "systemic", "lupus", "erythematosus", "genome", "complexity", ...	2017	Profiling RNA-Seq at multiple resolutions markedly increases the number of causal eQTLs in autoimmune disease
LINC complexes are evolutionarily conserved nuclear envelope bridges , composed of SUN ( Sad-1/UNC-84 ) and KASH ( Klarsicht/ANC-1/Syne/homology ) domain proteins . They are crucial for nuclear positioning and nuclear shape determination , and also mediate nuclear envelope ( NE ) attachment of meiotic telomeres , essen...	Correct genome haploidization during meiosis requires tightly regulated chromosome movements that follow a highly conserved choreography during prophase I . Errors in these movements cause subsequent meiotic defects , which typically lead to infertility . At the beginning of meiotic prophase , chromosome ends are tethe...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "meiosis", "telomeres", "cell", "division", "transmembrane", "proteins", "chromosome", "biology", "proteins", "biology", "molecular", "cell", "biology" ]	2014	Analysis of Meiosis in SUN1 Deficient Mice Reveals a Distinct Role of SUN2 in Mammalian Meiotic LINC Complex Formation and Function
Wolbachia pipientis is an intracellular endosymbiont known to confer host resistance against RNA viruses in insects . However , the causal mechanism underlying this antiviral defense remains poorly understood . To this end , we have established a robust arthropod model system to study the tripartite interaction involvi...	Effective vector control is critically important to reduce the incidence of diseases caused by arthropod transmitted viruses . One proposed strategy involves the use of endosymbiotic bacteria Wolbachia pipientis as a novel biocontrol agent to prevent RNA virus transmission in mosquitoes . Previous work in the field sug...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "rna", "extraction", "microbiology", "animals", "wolbachia", "animal", "models", "viruses", "virus", "effects", "on", "host", "gene", "expression", "drosophila", "melanogaster", ...	2017	Wolbachia elevates host methyltransferase expression to block an RNA virus early during infection
Identifying the genomic regions bound by sequence-specific regulatory factors is central both to deciphering the complex DNA cis-regulatory code that controls transcription in metazoans and to determining the range of genes that shape animal morphogenesis . We used whole-genome tiling arrays to map sequences bound in D...	One of the largest classes of regulatory proteins in animals , sequence-specific DNA binding transcription factors determine in which cells genes will be expressed and so control the development of an animal from a single cell to a morphologically complex adult . Understanding how this process is coordinated depends on...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "genetics", "and", "genomics" ]	2008	Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
In Borrelia burgdorferi ( Bb ) , the Lyme disease spirochete , the alternative σ factor σ54 ( RpoN ) directly activates transcription of another alternative σ factor , σS ( RpoS ) which , in turn , controls the expression of virulence-associated membrane lipoproteins . As is customary in σ54-dependent gene control , a ...	Lyme disease , caused by the bacterium Borrelia burgdorferi ( Bb ) , remains the most common arthropod-borne illness in the United States . A critical strategy for Bb to maintain its presence in nature is adaptation to its diverse tick and mammalian ( mouse ) hosts . To accomplish this , Bb encodes a potential gene reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/medical", "microbiology" ]	2011	BosR (BB0647) Controls the RpoN-RpoS Regulatory Pathway and Virulence Expression in Borrelia burgdorferi by a Novel DNA-Binding Mechanism
Ascariasis remains the most common helminth infection in humans . As an alternative or complementary approach to global deworming , a pan-anthelminthic vaccine is under development targeting Ascaris , hookworm , and Trichuris infections . As16 and As14 have previously been described as two genetically related proteins ...	Roundworms ( Ascaris ) infect more than 700 million people living in poverty worldwide and cause malnutrition and physical and mental developmental delays in children . As an alternative or complementary approach to global deworming , a pan-anthelminthic vaccine is under development that targets ascariasis in addition ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "immunology", "parasitic", "diseases", "vaccines", "preventive", "medicine", "developmental", "biology", "immunologic", "adjuvants", "molecular", "development", "in...	2017	Yeast-expressed recombinant As16 protects mice against Ascaris suum infection through induction of a Th2-skewed immune response
To improve schistosomiasis control programs in Uganda , where intestinal schistosomiasis is a widespread public health problem , a country-wide assessment of the disease prevalence among all age ranges is needed . Few studies have aimed to quantify the relationships between disease prevalence and water and sanitation c...	Schistosomiasis is a neglected tropical disease in sub-Saharan Africa that has remained intractable despite efforts to eliminate it through mass drug administration . The transmission cycle is perpetuated when sanitation infrastructure does not adequately capture infected urine or feces and local water bodies , with sn...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "surface", "water", "helminths", "tropical", "diseases", "geographical", "locations", "uganda", "parasitic", "diseases", "animals", "health", "care", "age", "groups", "pha...	2019	The prevalence of schistosomiasis in Uganda: A nationally representative population estimate to inform control programs and water and sanitation interventions
Soil-transmitted helminths ( STH ) infect more than 2 billion humans worldwide , causing significant morbidity in children . There are few data on the epidemiology and risk factors for infection in pre-school children . To investigate risk factors for infection in early childhood , we analysed data prospectively collec...	Soil-transmitted helminths ( STH ) are intestinal worms that cause significant morbidity in school age and pre-school children in developing countries . Infections are associated with poverty , particularly through lack of access to sanitation and clean drinking water . Current control strategies rely on periodic anthe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "soil-transmitted", "helminths", "parasitic", "intestinal", "diseases", "trichuriasis", "infectious", "disease", "epidemiology", "epidemiology", "neglected", "tropical", "diseases", "infectious", "disease", "control", "ascariasis", "paras...	2014	Risk Factors for Soil-Transmitted Helminth Infections during the First 3 Years of Life in the Tropics; Findings from a Birth Cohort
In bacteria , one paradigm for signal transduction is the two-component regulatory system , consisting of a sensor kinase ( usually a membrane protein ) and a response regulator ( usually a DNA binding protein ) . The EnvZ/OmpR two-component system responds to osmotic stress and regulates expression of outer membrane p...	The human pathogenic bacteria Salmonella encounters extreme and diverse conditions during the course of host infection . Survival and adaptation inside the host requires highly regulated virulence factors . When Salmonella is engulfed by a macrophage , it forms a vacuole-type structure that is actively acidified by the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A FRET-Based DNA Biosensor Tracks OmpR-Dependent Acidification of Salmonella during Macrophage Infection
Polycomb group ( PcG ) proteins act as evolutionary conserved epigenetic mediators of cell identity because they repress transcriptional programs that are not required at particular developmental stages . Each tissue is likely to have a specific epigenetic profile , which acts as a blueprint for its developmental fate ...	Cell identity is established by the evolutionary conserved Polycomb group ( PcG ) proteins that repress transcriptional programs which are not required at particular developmental stages . The plant FERTILIZATION INDEPENDENT SEED ( FIS ) PcG complex is specifically expressed in the endosperm where it is essential for n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/histone", "modification", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "developmental", "biology/plant", "growth", "and", "development", "molecular", "biology/dna", "methylation", ...	2010	H3K27me3 Profiling of the Endosperm Implies Exclusion of Polycomb Group Protein Targeting by DNA Methylation
All skeletal muscle progenitor cells in the body derive from the dermomyotome , the dorsal epithelial domain of developing somites . These multipotent stem cells express Pax3 , and this expression is maintained in the myogenic lineage where Pax3 plays an important role . Identification of Pax3 targets is therefore impo...	It is well established that skeletal muscle derives from segmented structures called somites that form on either side of the axis of the embryo . The part of the somite that contains muscle stem cells is called the dermomyotome . These cells express the transcription factor Pax3 , which regulates muscle stem cell behav...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "developmental", "biology/developmental", "molecular", "mechanisms", "genetics", "and", "genomics/gene", "expression" ]	2010	A Pax3/Dmrt2/Myf5 Regulatory Cascade Functions at the Onset of Myogenesis
Non-typhoidal Salmonella ( NTS ) is a leading cause of bloodstream infections in Africa , but the various contributions of host susceptibility versus unique pathogen virulence factors are unclear . We used data from a population-based surveillance platform ( population ~25 , 000 ) between 2007–2014 and NTS genome-seque...	Though NTS is normally associated with self-limiting gastroenteritis in humans , it is a leading cause of bloodstream infection in Africa . The biological mechanisms that contribute to invasiveness in NTS in Africa are unclear . In this paper we address which specific host and pathogen risk factors are associated with ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "parasitic", "diseases", "salmonellosis", "retroviruses", "viruses", "diarrhea", "bacterial", "diseases", "immunod...	2018	Multi-drug resistant non-typhoidal Salmonella associated with invasive disease in western Kenya
The aim of this study was to investigate the relationship between prior Anisakis infections and upper gastrointestinal bleeding ( UGIB ) , and its interaction with non-steroidal anti-inflammatory drug ( NSAID ) intake . We conducted a hospital-based case-control study covering 215 UGIB cases and 650 controls . Odds rat...	Anisakiasis is a worldwide re-emerging disease produced by the consumption of raw , lightly cooked , smoked or marinated fish containing live Anisakis larvae . In acute anisakiasis , mucosal lesions generated by the larvae may provoke upper gastrointestinal bleeding ( UGIB ) . However , the effect of past unnoticed Ani...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "parasitic", "intestinal", "diseases", "clinical", "epidemiology", "epidemiology", "gastroenterology", "and", "hepatology", "parasitic", "diseases", "helminth", "infection" ]	2011	Synergism between Prior Anisakis simplex Infections and Intake of NSAIDs, on the Risk of Upper Digestive Bleeding: A Case-Control Study
Patients with chronic granulomatous disease ( CGD ) lack generation of reactive oxygen species ( ROS ) through the phagocyte NADPH oxidase NOX2 . CGD is an immune deficiency that leads to frequent infections with certain pathogens; this is well documented for S . aureus and A . fumigatus , but less clear for mycobacter...	The vaccine Mycobacterium bovis BCG is administrated to prevent early age tuberculosis in endemic areas . BCG is a live vaccine with a low incidence of complications . However , local or disseminated BCG infection may occur , in particular in immunodeficient individuals . Chronic granulomatous disease ( CGD ) , a defic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "infectious", "diseases", "mycobacteria", "medicine", "and", "health", "sciences", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "immunology", "microbiology", "bacterial", "pathogens", "...	2014	Bacillus Calmette-Guerin Infection in NADPH Oxidase Deficiency: Defective Mycobacterial Sequestration and Granuloma Formation
The biogenesis of bacterial cell-envelope polysaccharides requires the translocation , across the plasma membrane , of sugar sub-units that are produced inside the cytoplasm . To this end , the hydrophilic sugars are anchored to a lipid phosphate carrier ( undecaprenyl phosphate ( C55-P ) ) , yielding membrane intermed...	Helicobacter pylori colonizes the human’s gastric mucosa and infects around 50% of the world’s population . This pathogen is responsible for chronic gastritis , peptic ulcers and in worst cases leads to gastric cancer . It has been classified as a class I carcinogen by the World Health Organization in 1994 . Here , we ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2019	HupA, the main undecaprenyl pyrophosphate and phosphatidylglycerol phosphate phosphatase in Helicobacter pylori is essential for colonization of the stomach
Considerable evidence has accumulated in recent years suggesting that G protein-coupled receptors ( GPCRs ) associate in the plasma membrane to form homo- and/or heteromers . Nevertheless , the stoichiometry , fraction and lifetime of such receptor complexes in living cells remain topics of intense debate . Motivated b...	G Protein-Coupled Receptors ( GPCRs ) are the largest family of membrane proteins targeted by drugs in clinical practice . Despite being at the forefront of biomedical research for many years , there is still considerable uncertainty about how GPCRs function at a molecular level . Although substantial evidence exists i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2012	Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors
Host responses to infection encompass many processes in addition to activation of the immune system , including metabolic adaptations , stress responses , tissue repair , and other reactions . The response to bacterial infection in Drosophila melanogaster has been classically described in studies that focused on the im...	How does an organism survive infection ? How generic or specific is the host response to diverse pathogens ? To address these questions , we infected fruit flies with 10 different bacteria that vary in their ability to kill flies and measured changes in global gene expression . In general , we found that the host respo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "gene", "regulation", "regulatory", "proteins", "immunology", "dna-binding", "proteins", "animals", "animal", "models", "bacterial", "diseases", "drosophila", "melanogaster", "model", "organi...	2018	Comparative transcriptomics reveals CrebA as a novel regulator of infection tolerance in D. melanogaster
The interaction with brain endothelial cells is central to the pathogenicity of Neisseria meningitidis infections . Here , we show that N . meningitidis causes transient activation of acid sphingomyelinase ( ASM ) followed by ceramide release in brain endothelial cells . In response to N . meningitidis infection , ASM ...	Neisseria meningitidis , an obligate human pathogen , is a causative agent of septicemia and meningitis worldwide . Meningococcal infection manifests in a variety of forms , including meningitis , meningococcemia with meningitis or meningococcemia without obvious meningitis . The interaction of N . meningitidis with hu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "bacterial", "diseases", "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "medicine", "and", "health", "sciences", "cell", "biology", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions"...	2014	Differential Activation of Acid Sphingomyelinase and Ceramide Release Determines Invasiveness of Neisseria meningitidis into Brain Endothelial Cells
In forebrain neurons , Ca2+ triggers exocytosis of readily releasable vesicles by binding to synaptotagmin-1 and -7 , thereby inducing fast and slow vesicle exocytosis , respectively . Loss-of-function of synaptotagmin-1 or -7 selectively impairs the fast and slow phase of release , respectively , but does not change t...	Neurons communicate with each other at specialized contact points called synapses . Presynaptic neurons store chemical neurotransmitters within presynaptic vesicles at the nerve terminal . During synaptic transmission , the presynaptic vesicles fuse with the plasma membrane , releasing their neurotransmitter content in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Synaptotagmin-1 and -7 Are Redundantly Essential for Maintaining the Capacity of the Readily-Releasable Pool of Synaptic Vesicles
There is limited published information on the prevalence of human cysticercosis in West Africa . The aim of this pilot study was to estimate the prevalence of Taenia solium cysticercosis antigens in residents of three villages in Burkina Faso . Three villages were selected: The village of Batondo , selected to represen...	Taenia solium cysticercosis is a neglected tropical zoonosis transmitted between humans and pigs . This infection is particularly prevalent in areas where sanitation , hygiene and pig management practices are poor . There is very little information about the importance of this infection in West Africa , even though por...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology/social...	2009	Seroprevalence to the Antigens of Taenia solium Cysticercosis among Residents of Three Villages in Burkina Faso: A Cross-Sectional Study
Entomological indicators are considered key metrics to document the interruption of transmission of Onchocerca volvulus , the etiological agent of human onchocerciasis . Human landing collection is the standard employed for collection of the vectors for this parasite . Recent studies reported the development of traps t...	Human landing collections , which are the current standard for collecting the black fly vectors of Onchocerca volvulus , the causative agent of river blindness , are inefficient and pose certain ethical issues . As entomological methods are among the primary techniques recommended by the international community for ver...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "epidemiology", "arthropod", "vectors", "parasitic", "diseases", "disease", "vectors", "nematode", "infections" ]	2015	Identification of Human Semiochemicals Attractive to the Major Vectors of Onchocerciasis
Metagenomic sequencing is becoming widespread in biomedical and environmental research , and the pace is increasing even more thanks to nanopore sequencing . With a rising number of samples and data per sample , the challenge of efficiently comparing results within a specimen and between specimens arises . Reagents , l...	Whether in a clinical or environmental sample , metagenomics can reveal what microorganisms exist and what they do . It is indeed a powerful tool for the study of microbial communities which requires equally powerful methods of analysis . Current challenges in the analysis of metagenomic data include the comparative st...	[ "Abstract", "Introduction", "Design", "and", "implementation", "Results", "and", "discussion", "Availability", "and", "future", "directions" ]	[]	2019	Recentrifuge: Robust comparative analysis and contamination removal for metagenomics
A description of many biological processes requires knowledge of the 3-D structure of proteins and , in particular , the defined active site responsible for biological function . Many proteins , the genes of which have been identified as the result of human genome sequencing , and which were synthesized experimentally ...	We present here a method of defining functional site recognition in proteins . The active site ( enzymatic cavity or ligand-binding site ) is localized on the basis of hydrophobicity deficiency , which is understood as the difference between empirical ( dependent on amino acid positions ) and idealized ( 3-D Gauss func...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "chicken", "eubacteria", "computational", "biology" ]	2007	Prediction of Functional Sites Based on the Fuzzy Oil Drop Model
During the past twenty years , a number of molecular analyses have been performed to determine the evolutionary relationships of Onchocercidae , a family of filarial nematodes encompassing several species of medical or veterinary importance . However , opportunities for broad taxonomic sampling have been scarce , and a...	Filariae are predominantly tissue-dwelling nematodes of the Onchocercidae ( Spirurida ) . They are parasites of terrestrial vertebrates and some of them are particularly well known as agents of human diseases in tropical environments ( e . g . onchocercosis , lymphatic filariosis , loaosis ) . Because of their predilec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[]	2015	Shaking the Tree: Multi-locus Sequence Typing Usurps Current Onchocercid (Filarial Nematode) Phylogeny
The mechanisms of stress tolerance in sessile animals , such as molluscs , can offer fundamental insights into the adaptation of organisms for a wide range of environmental challenges . One of the best studied processes at the molecular level relevant to stress tolerance is the heat shock response in the genus Mytilus ...	Adaptation of sessile animals , such as molluscs , to stress is achieved by a number of molecular mechanisms , few of which are clearly understood . Insights from this research can provide clues about stress tolerance both for sessile and mobile organisms . The Mediterranean mussel , of the genus Mytilus , is a model o...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/sequence", "motif", "analysis", "computational", "biology/transcriptional", "regulation", "genetics", "and", "genomics/gene", "expression", "physiology/genomics", "computational", "biology/comparative"...	2010	Promoter Complexity and Tissue-Specific Expression of Stress Response Components in Mytilus galloprovincialis, a Sessile Marine Invertebrate Species
Retrotransposition of endogenous retroviruses ( ERVs ) poses a substantial threat to genome stability . Transcriptional silencing of a subset of these parasitic elements in early mouse embryonic and germ cell development is dependent upon the lysine methyltransferase SETDB1 , which deposits H3K9 trimethylation ( H3K9me...	Retroelements , including endogenous retroviruses ( ERVs ) , pose a significant threat to genome stability . In mouse embryonic stem ( ES ) cells , the enzyme SETDB1 safeguards the genome against transcription of specific ERVs by depositing a repressive mark H3K9 trimethylation ( H3K9me3 ) . Although SETDB1 is recruite...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	hnRNP K Coordinates Transcriptional Silencing by SETDB1 in Embryonic Stem Cells
The opa genes of the Gram negative bacterium Neisseria meningitidis encode Opacity-associated outer membrane proteins whose role is to promote adhesion to the human host tissue during colonisation and invasion . Each meningococcus contains 3–4 opa loci , each of which may be occupied by one of a large number of alleles...	Neisseria meningitidis is a globally important pathogen that causes 2 , 000–3 , 000 cases of invasive meningococcal disease annually in the United Kingdom . The meningococcal Opa proteins are important in mediating adhesion to and invasion of human tissues , and are important for evasion of the host immune response . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "microbiology/immunity", "to", "infections", "computational", "biology/molecular", "g...	2008	The Effect of Immune Selection on the Structure of the Meningococcal Opa Protein Repertoire
The macromolecular assembly required to initiate transcription of protein-coding genes , known as the Pre-Initiation Complex ( PIC ) , consists of multiple protein complexes and is approximately 3 . 5 MDa in size . At the heart of this assembly is the Mediator complex , which helps regulate PIC activity and interacts w...	Transcription initiation in humans is regulated by a macromolecular complex formed by the RNA polymerase II enzyme ( pol II ) , Mediator , and the general transcription factors TFIIA , TFIIB , TFIID , TFIIE , TFIIF , and TFIIH . Collectively , these factors are known as the Pre-Initiation Complex ( PIC ) . Although the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "molecular", "biology/transcription", "initiation", "and", "activation", "biochemistry/macromolecular", "assemblies", "and", "machines", "biochemistry/transcription", "and", "translation", "biophysics/transcription", "an...	2011	Molecular Architecture of the Human Mediator–RNA Polymerase II–TFIIF Assembly
Invasive fungal infections by Candida albicans ( Ca ) are a frequent cause of lethal sepsis in intensive care unit patients . While a contribution of type I interferons ( IFNs-I ) in fungal sepsis remains unknown , these immunostimulatory cytokines mediate the lethal effects of endotoxemia and bacterial sepsis . Using ...	Inflammation constitutes a major host response in many microbial infections . Innate immune cells orchestrate the inflammatory response to kill pathogens and clear infections . However , invasive infections by pathogenic microbes including the fungus Candida albicans , can result in an uncontrolled hyper-inflammatory r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "inflammation", "clinical", "immunology", "immunity", "immunology", "biology", "fungal", "diseases" ]	2012	Type I Interferons Promote Fatal Immunopathology by Regulating Inflammatory Monocytes and Neutrophils during Candida Infections
DNA double-strand breaks are repaired by multiple mechanisms that are roughly grouped into the categories of homology-directed repair and non-homologous end joining . End-joining repair can be further classified as either classical non-homologous end joining , which requires DNA ligase 4 , or “alternative” end joining ...	DNA double-strand breaks , in which both strands of the DNA double helix are cut , must be recognized and accurately repaired in order to promote cell survival and prevent the accumulation of mutations . However , error-prone repair occasionally occurs , even when accurate repair is possible . We have investigated the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/chromosome", "biology", "molecular", "biology/dna", "repair" ]	2010	Dual Roles for DNA Polymerase Theta in Alternative End-Joining Repair of Double-Strand Breaks in Drosophila
Adenosine-to-inosine ( A-to-I ) editing is hypothesized to facilitate adaptive evolution by expanding proteomic diversity through an epigenetic approach . However , it is challenging to provide evidences to support this hypothesis at the whole editome level . In this study , we systematically characterized 2 , 114 A-to...	Adenosine-to-inosine ( A-to-I ) RNA editing is an evolutionarily conserved mechanism that alters RNA sequences at the co-transcriptional or post-transcriptional level . RNA editing is hypothesized to facilitate adaptation in that it expands the transcriptomic and proteomic diversity . However , evidence for adaptation ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "glycosylamines", "computational", "biology", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "genome", "analysis", "drosophila", "adenosine", "research", ...	2017	Adaptation of A-to-I RNA editing in Drosophila
Rift Valley fever ( RVF ) is a re-emerging zoonotic disease responsible for major losses in livestock production , with negative impact on the livelihoods of both commercial and resource-poor farmers in sub-Sahara African countries . The disease remains a threat in countries where its mosquito vector thrives . Outbreak...	A single RVF virus serotype exists , yet differences in virulence and pathogenicity of the virus have been observed . This necessitates the need for detailed genetic characterization of various isolates of the virus . Some of the RVF virus isolates that caused the 2008–2010 disease outbreaks in South Africa were most p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "viruses", "rift", "valley", "fever", "south", "africa", "rna",...	2019	A comparative genome analysis of Rift Valley Fever virus isolates from foci of the disease outbreak in South Africa in 2008-2010
Microbial tropism , the infection of specific cells and tissues by a microorganism , is a fundamental aspect of host-microbe interactions . The intracellular bacteria Wolbachia have a peculiar tropism for the stem cell niches in the Drosophila ovary , the microenvironments that support the cells producing the eggs . Th...	Microbes evolve to infect structures favoring their transmission in host populations . A large fraction of insects are infected with Wolbachia bacteria . Usually Wolbachia are transmitted the same way we inherit our mitochondria , via the eggs from the mother . In fruit flies , to favor maternal transmission , Wolbachi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "symbiosis", "animals", "wolbachia", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "stem", "cells", "bacteria", "drosophila", "research", "and", "analysis", "methods", "animal", "cells", "stem", "cell", "niche", "insects", "a...	2014	Extreme Divergence of Wolbachia Tropism for the Stem-Cell-Niche in the Drosophila Testis
According to the Red Queen hypothesis or arms race dynamics , coevolution drives continuous adaptation and counter-adaptation . Experimental models under simplified environments consisting of bacteria and bacteriophages have been used to analyze the ongoing process of coevolution , but the analysis of both parasites an...	To examine the ongoing changes driven by host–parasite interactions , we have constructed a coevolution model consisting of Escherichia coli and the lytic RNA bacteriophage Qβ ( Qβ ) in a spatially unstructured environment . In coevolution through 54 daily copropagations of the parasite and its host , E . coli first ev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "organismal", "evolution", "evolutionary", "ecology", "population", "genetics", "microbiology", "escherichia", "coli", "mutation", "prokaryotic", "models", "model", "organisms", "coevolution", "microbial", "evolution", "forms", "of",...	2011	Ongoing Phenotypic and Genomic Changes in Experimental Coevolution of RNA Bacteriophage Qβ and Escherichia coli
Abnormalities in glycan biosynthesis have been conclusively linked to many diseases but the complexity of glycosylation has hindered the analysis of glycan data in order to identify glycoforms contributing to disease . To overcome this limitation , we developed a quantitative N-glycosylation model that interprets and i...	Glycans are the sugar attachments that are found on proteins and lipids . These highly variable and structurally diverse sugar chains confer distinctive characteristics to the cell surface . Recent research has revealed that these glycan profiles can represent important signatures of disease states and thus understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "genetics", "and", "genomics" ]	2013	Integration of the Transcriptome and Glycome for Identification of Glycan Cell Signatures
Visceral leishmaniasis ( VL ) has become an important opportunistic infection in persons with HIV-infection in VL-endemic areas . The co-infection leads to profound immunosuppression and high rate of annual VL recurrence . This study assessed the effectiveness , safety and feasibility of monthly pentamidine infusions t...	Relapse of visceral leishmaniasis ( VL ) among HIV co-infected patients occurs universally . Evidence on the use of secondary prophylaxis especially in anthroponotic transmission regions was lacking . It was found out now that secondary prophylaxis in addition to antiretroviral therapy for VL in people with HIV infecti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Use of Pentamidine As Secondary Prophylaxis to Prevent Visceral Leishmaniasis Relapse in HIV Infected Patients, the First Twelve Months of a Prospective Cohort Study
Trachoma , the worldwide leading infectious cause of blindness , is due to repeated conjunctival infection with Chlamydia trachomatis . The effects of control interventions on population levels of infection and active disease can be promptly measured , but the effects on severe ocular sequelae require long-term monitor...	Trachoma is the worldwide leading infectious cause of blindness and is due to repeated conjunctival infection with Chlamydia trachomatis bacteria . The effects of control interventions on population levels of infection and active disease can be promptly measured , but the effects on severe ocular disease outcomes requi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	The Development of an Age-Structured Model for Trachoma Transmission Dynamics, Pathogenesis and Control
Deleterious mutations inevitably emerge in any evolutionary process and are speculated to decisively influence the structure of the genome . Meiosis , which is thought to play a major role in handling mutations on the population level , recombines chromosomes via non-randomly distributed hot spots for meiotic recombina...	Sexual life cycles constitute a costly alternative to vegetative modes of reproduction . Two categories of hypotheses seek to explain why sexual life cycles exist: those investigating the selective advantages that have driven the evolution of individual parts of this life cycle and those rationalizing the advantages se...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/population", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/chromosome", "biology", "computational", "biology/evolutionary", "mo...	2009	Evolution of Mutational Robustness in the Yeast Genome: A Link to Essential Genes and Meiotic Recombination Hotspots
In summer 2014 , an autochthonous outbreak of dengue occurred in Tokyo , Japan , in which Yoyogi Park acted as the focal area of transmission . Recognizing the outbreak , concerted efforts were made to control viral spread , which included mosquito control , public announcement of the outbreak , and a total ban on ente...	Evaluating the interventions implemented during an outbreak of mosquito-borne disease is of utmost importance , offering lessons for future control strategies . By retrospectively analyzing data of the first autochthonous dengue epidemic of the 21st century in Tokyo , Japan , we assessed the effectiveness of the interv...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "japan", "pathogens", "geographical", "locations", "microbiology", "mathematical", "models", "animals", "viruses", "probability", "distribution", "ma...	2019	Assessing dengue control in Tokyo, 2014
Processing of the Gag precursor protein by the viral protease during particle release triggers virion maturation , an essential step in the virus replication cycle . The first-in-class HIV-1 maturation inhibitor dimethylsuccinyl betulinic acid [PA-457 or bevirimat ( BVM ) ] blocks HIV-1 maturation by inhibiting the cle...	Maturation of HIV-1 particles , which occurs as they bud off from the infected cell , is triggered by the step-wise cleavage of the major viral structural polyprotein , Pr55Gag , to individual , mature Gag proteins . The viral protease is the enzyme responsible for Gag polyprotein cleavage . Maturation inhibitors preve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "chemistry", "biology" ]	2012	Structural and Functional Insights into the HIV-1 Maturation Inhibitor Binding Pocket
Chromosome 9 of Trypanosoma brucei contains two closely spaced , very similar open reading frames for cyclic nucleotide specific phosphodiesterases TbrPDEB1 and TbrPDEB2 . They are separated by 2379 bp , and both code for phosphodiesterases with two GAF domains in their N-terminal moieties and a catalytic domain at the...	Cyclic nucleotide specific phosphodiesterases are important regulators of cyclic nucleotide signalling in eukaryotes . In many organisms , including humans and trypanosomes , some of these enzymes contain specific domains ( GAF domains ) that bind cyclic nucleotides , and that are involved in the regulation of the cata...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "genetics", "and", "genomics/gene", "function", "cell", "biology/cell", "signaling" ]	2009	Gene Conversion Transfers the GAF-A Domain of Phosphodiesterase TbrPDEB1 to One Allele of TbrPDEB2 of Trypanosoma brucei
Several proteins involved in the response to DNA double strand breaks ( DSB ) form microscopically visible nuclear domains , or foci , after exposure to ionizing radiation . Radiation-induced foci ( RIF ) are believed to be located where DNA damage occurs . To test this assumption , we analyzed the spatial distribution...	DNA damages are daily cellular events . If such events are left unchecked in an organism , they can lead to DNA mutations and possibly cancer over a long period of time . Consequently , cells have very efficient DNA repair machinery . Many studies have focused on the different molecular factors involved in the repair m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "homo", "(human)" ]	2007	Image-Based Modeling Reveals Dynamic Redistribution of DNA Damage into Nuclear Sub-Domains
Animals acquire predictive values of sensory stimuli through reinforcement . In the brain of Drosophila melanogaster , activation of two types of dopamine neurons in the PAM and PPL1 clusters has been shown to induce aversive odor memory . Here , we identified the third cell type and characterized aversive memories ind...	Punishment not only repels animals but also drives the formation of aversive memory of contiguous stimuli . Guided by the memory , animals can later avoid the cues that predict negative outcome . How is a punishing event represented in the brain ? We have found that at least three types of dopamine neurons in the Droso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "behavioral", "neuroscience", "animal", "genetics", "physiology", "genetics", "integrative", "physiology", "biology", "anatomy", "and", "physiology", "neuroscience", "learning", "and", "memory", "genetics", "and", "genomics" ]	2012	Three Dopamine Pathways Induce Aversive Odor Memories with Different Stability
Schistosomiasis is a neglected infection affecting millions of people , mostly living in sub-Saharan Africa . Morbidity and mortality due to chronic infection are relevant , although schistosomiasis is often clinically silent . Different diagnostic tests have been implemented in order to improve screening and diagnosis...	Schistosomiasis is probably the most important of the neglected tropical diseases ( NTD ) caused by helminthes ( worms ) . It is acquired bathing in freshwater in endemic areas . The life cycle is complex and involves freshwater snails . Schistosomiasis , caused by Schistosoma mansoni , S . haematobium and less frequen...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "helminths", "tropical", "diseases", "parasitic", "diseases", "animals", "ur...	2017	Accuracy of parasitological and immunological tests for the screening of human schistosomiasis in immigrants and refugees from African countries: An approach with Latent Class Analysis
The World Health Organization ( WHO ) recommends oral cholera vaccines ( OCVs ) as a supplementary tool to conventional prevention of cholera . Dukoral , a killed whole-cell two-dose OCV , was used in a mass vaccination campaign in 2009 in Zanzibar . Public and private costs of illness ( COI ) due to endemic cholera an...	Despite efforts to improve water supply and sanitation , cholera still represents a serious burden in developing countries . Use of oral cholera vaccines ( OCVs ) in endemic and epidemic situations has recently shown a promising potential to mitigate this burden . To provide local decision-makers with specific informat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "social", "and", "behavioral", "sciences", "cost-effectiveness", "analysis", "non-clinical", "medicine", "neglected", "tropical", "diseases", "cost", "effectiveness", "immunizations", "infectious", "diseases", "cholera"...	2012	Costs of Illness Due to Cholera, Costs of Immunization and Cost-Effectiveness of an Oral Cholera Mass Vaccination Campaign in Zanzibar
The mitochondrial genome of Trypanosoma brucei contains many cryptogenes that must be extensively edited following transcription . The RNA editing process is directed by guide RNAs ( gRNAs ) that encode the information for the specific insertion and deletion of uridylates required to generate translatable mRNAs . We ha...	Trypanosoma brucei is the causative agent of African sleeping sickness , a disease that threatens millions of people in sub-Saharan Africa . During its life cycle , Trypanosoma brucei lives in either its mammalian host or its insect vector . These environments are very different , and the transition between these envir...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "messenger", "rna", "parasitic", "protozoans", "parasitology", "developmental", "biology", "trypanosoma", "brucei", "gambiense", "protozoans", "genome", "analysis", "energy-producing", "organelles", "mitochondria", "bioenergetics", "molecular", "bi...	2016	Analysis of the Trypanosoma brucei EATRO 164 Bloodstream Guide RNA Transcriptome
Due to their error-prone replication , RNA viruses typically exist as a diverse population of closely related genomes , which is considered critical for their fitness and adaptive potential . Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to mainta...	During infection of their arthropod vectors , arthropod-borne viruses ( arboviruses ) such as dengue viruses traverse several anatomical barriers that are believed to cause dramatic reductions in population size . Such population bottlenecks challenge the maintenance of viral genetic diversity , which is considered cri...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "viral", "transmission", "and", "infection", "population", "genetics", "conservation", "genetics", "microbiology", "animals", "viral", "vectors", "population", "biolog...	2016	Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes
The Caenorhabditis elegans dauer larva is a facultative state of diapause . Mutations affecting dauer signal transduction and morphogenesis have been reported . Of these , most that result in constitutive formation of dauer larvae are temperature-sensitive ( ts ) . The daf-31 mutant was isolated in genetic screens look...	The development of a living organism is influenced by the environmental conditions such as nutrient availability . Under starvation conditions , the C . elegans larvae will enter a special developmental stage called dauer larva . An insulin-like signaling pathway controls dauer formation as well as adult lifespan by in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	daf-31 Encodes the Catalytic Subunit of N Alpha-Acetyltransferase that Regulates Caenorhabditis elegans Development, Metabolism and Adult Lifespan
Trachoma , caused by Chlamydia trachomatis ( Ct ) , is the leading infectious cause of blindness worldwide . Yearly azithromycin mass drug administration ( MDA ) plays a central role in efforts to eliminate blinding trachoma as a public health problem . Programmatic decision-making is currently based on the prevalence ...	Trachoma is the leading infectious cause of blindness . The infectious agent , Chlamydia trachomatis , can be treated with a single oral dose of azithromycin . Donated drug is a cornerstone of programs dedicated to the elimination of trachoma as a public health problem . Azithromycin is given to the entire district for...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Serology for Trachoma Surveillance after Cessation of Mass Drug Administration
Apicomplexan parasites are responsible for a myriad of diseases in humans and livestock; yet despite intensive effort , development of effective sub-unit vaccines remains a long-term goal . Antigenic complexity and our inability to identify protective antigens from the pool that induce response are serious challenges i...	Protozoan parasites are responsible for serious diseases in humans and livestock species . Vaccination is a declared intervention of choice with these infections , but even after many years of effort few effective vaccines are available . Identification of the right antigens for inclusion in sub-unit vaccines is a part...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "microbiology/immunity", "to", "infections", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "disease", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections",...	2011	Genetic Mapping Identifies Novel Highly Protective Antigens for an Apicomplexan Parasite
Yeast prions are heritable amyloid aggregates of functional yeast proteins; their propagation to subsequent cell generations is dependent upon fragmentation of prion protein aggregates by molecular chaperone proteins . Mounting evidence indicates the J-protein Sis1 may act as an amyloid specificity factor , recognizing...	Multiple neurodegenerative disorders such as Alzheimer's , Parkinson's and Creutzfeldt-Jakob disease are associated with the accumulation of fibrous protein aggregates collectively termed ‘amyloid . ’ In the baker's yeast Saccharomyces cerevisiae , multiple proteins form intracellular amyloid aggregates known as yeast ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "cell", "biology", "proteins", "prions", "fungal", "genetics", "chaperone", "proteins", "genetics", "genetic", "elements", "biology", "and", "life", "sciences", "epigenetics", "molecular", "genetics" ]	2014	Functional Diversification of Hsp40: Distinct J-Protein Functional Requirements for Two Prions Allow for Chaperone-Dependent Prion Selection
Sapovirus , a member of the Caliciviridae family , is an important cause of acute gastroenteritis in humans and pigs . Currently , the porcine sapovirus ( PSaV ) Cowden strain remains the only cultivable member of the Sapovirus genus . While some caliciviruses are known to utilize carbohydrate receptors for entry and i...	Although enteropathogenic sapoviruses and noroviruses are leading causes of acute gastroenteritis in both humans and animals , the study of viral pathogenesis and immunity of these ubiquitous pathogens has been hampered due to the lack of a fully permissive cell culture system . Porcine sapovirus Cowden strain provides...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "veterinary", "microbiology", "biochemistry", "biology", "and", "life", "sciences", "veterinary", "science" ]	2014	Both α2,3- and α2,6-Linked Sialic Acids on O-Linked Glycoproteins Act as Functional Receptors for Porcine Sapovirus
The envelope glycoproteins ( Envs ) of HIV-1 continuously evolve in the host by random mutations and recombination events . The resulting diversity of Env variants circulating in the population and their continuing diversification process limit the efficacy of AIDS vaccines . We examined the historic changes in Env seq...	HIV-1 is the causative agent of the global AIDS pandemic . The envelope glycoproteins ( Envs ) of HIV-1 constitute a primary target for antibody-based vaccines . However , the diversity of Envs in the population limits the potential efficacy of this approach . Accurate estimates of the range of variants that currently ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "united", "states", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "pathogens", "split-decomposition", "method", "immunology", "geographical", "locations",...	2017	Accurate predictions of population-level changes in sequence and structural properties of HIV-1 Env using a volatility-controlled diffusion model
The neglected human diseases caused by trypanosomatids are currently treated with toxic therapy with limited efficacy . In search for novel anti-trypanosomatid agents , we showed previously that the Crotalus viridis viridis ( Cvv ) snake venom was active against infective forms of Trypanosoma cruzi . Here , we describe...	The pathogenic trypanosomatid parasites of the genera Leishmania and Trypanosoma infect over 20 million people worldwide , with an annual incidence of ∼3 million new infections . An additional 400 million people are at risk of infection by exposure to parasite-infected insects which act as disease vectors . Trypanosoma...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "medicine", "and", "health", "sciences", "peptides", "proteins", "biology", "and", "life", "sciences", "pharmacology", "proteomics", "tropical", "diseases", "parasitic", "diseases" ]	2014	Crovirin, a Snake Venom Cysteine-Rich Secretory Protein (CRISP) with Promising Activity against Trypanosomes and Leishmania
An effective surveillance system is critical for the elimination of canine rabies in Latin America . Brazil has made substantial progress towards canine rabies elimination , but outbreaks still occurred in the last decade in two states . Brazil uses a health information system ( SINAN ) to record patients seeking post-...	Dog-mediated rabies has declined to only a few cases in Latin America over the last decade . Brazil has the largest human and dog population of Latin America . Despite the decline of canine rabies , the country’s public health system still spends millions of dollars annually on half a million patients seeking health ca...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "post-exposure", "prophylaxis", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "dogs", "animals", "mammals", "vaccines", "preventive", "medicine", "rabies", "neglected", "tropical", "diseases", "i...	2019	An evaluation of Brazil’s surveillance and prophylaxis of canine rabies between 2008 and 2017
The phenomenology and cellular mechanisms of cortical synaptic plasticity are becoming known in increasing detail , but the computational principles by which cortical plasticity enables the development of sensory representations are unclear . Here we describe a framework for cortical synaptic plasticity termed the “Con...	The circuits of the sensory cortex are able to extract useful information from sensory inputs because of their exquisitely organized synaptic connections . These connections are wired largely through experience-dependent synaptic plasticity . Although many details of both the phenomena and cellular mechanisms of cortic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Convallis Rule for Unsupervised Learning in Cortical Networks
Insulin and related peptides play important and conserved functions in growth and metabolism . Although Drosophila has proved useful for the genetic analysis of insulin functions , little is known about the transcription factors and cell lineages involved in insulin production . Within the embryonic central nervous sys...	Genetic studies using invertebrate model organisms such as Drosophila have provided many new insights into the functions of insulin and related peptides . It has , however , been more difficult to use Drosophila to study the regulation of insulin , at least in part because the relevant insulinergic cell lineages were n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "diabetes", "and", "endocrinology", "neuroscience" ]	2008	Postmitotic Specification of Drosophila Insulinergic Neurons from Pioneer Neurons
In 2010 , 2012 , 2013 and 2014 dengue outbreaks have been reported in Dar es Salaam , Tanzania . However , there is no comprehensive data on the risk of transmission of dengue in the country . The objective of this study was to assess the risk of transmission of dengue in Dar es Salaam during the 2014 epidemic . This c...	Until 2010 , little was known about Dengue in Tanzania . Since then , four outbreaks have been reported in Dar es Salaam City . This study was therefore carried out to assess the risk of transmission of dengue in Dar es Salaam during an outbreak in 2014 . In this study adult mosquitoes were collected using carbon dioxi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	The Risk of Dengue Virus Transmission in Dar es Salaam, Tanzania during an Epidemic Period of 2014
The chromatin remodeler BRAHMA ( BRM ) is a Trithorax Group ( TrxG ) protein that antagonizes the functions of Polycomb Group ( PcG ) proteins in fly and mammals . Recent studies also implicate such a role for Arabidopsis ( Arabidopsis thaliana ) BRM but the molecular mechanisms underlying the antagonism are unclear . ...	In flowering plants , the proper transition from vegetative growth to flowering is critical for their reproductive success and must be controlled precisely . Multiple genes have been shown to regulate the floral transition in response to environmental and endogenous cues . Among them is SHORT VEGETATIVE PHASE ( SVP ) ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Arabidopsis SWI2/SNF2 Chromatin Remodeler BRAHMA Regulates Polycomb Function during Vegetative Development and Directly Activates the Flowering Repressor Gene SVP
Post kala-azar dermal leishmaniasis ( PKDL ) , a sequel to visceral leishamaniasis ( VL ) in 5–15% cases , constitutes a parasite reservoir important in disease transmission . The precise immunological cause of PKDL outcome remains obscure . However , overlapping counter regulatory responses with elevated IFN-γ and IL-...	Post kala azar dermal leishamniasis ( PKDL ) , an unusual dermatosis develops in 5–15% of apparently cured visceral leishmaniasis cases in India and in about 60% of cases in Sudan . PKDL cases assume importance since they constitute a major human reservoir for the parasite . Inadequate treatment of VL , genetics , nutr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunopathology", "immunology", "biology", "microbiology", "immune", "response", "pathogenesis" ]	2011	Foxp3 and IL-10 Expression Correlates with Parasite Burden in Lesional Tissues of Post Kala Azar Dermal Leishmaniasis (PKDL) Patients
Deciphering the specific contribution of individual motifs within cis-regulatory modules ( CRMs ) is crucial to understanding how gene expression is regulated and how this process is affected by sequence variation . But despite vast improvements in the ability to identify where transcription factors ( TFs ) bind throug...	Transcription is initiated through the binding of transcription factors ( TFs ) to specific motifs that are dispersed throughout the genome . Genomics methods have helped to discern which motifs for a TF are occupied and which are not , yet it is poorly understood why certain combinations of bound motifs , and not othe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "model", "organisms", "genetics", "synthetic", "biology", "biology" ]	2014	Subtle Changes in Motif Positioning Cause Tissue-Specific Effects on Robustness of an Enhancer's Activity
Insulin , the primary hormone regulating the level of glucose in the bloodstream , modulates a variety of cellular and enzymatic processes in normal and diseased cells . Insulin signals are processed by a complex network of biochemical interactions which ultimately induce gene expression programs or other processes suc...	Insulin is a hormone produced by the body that regulates uptake of glucose from the bloodstream . The cellular response to insulin is governed by a complex network of intracellular interactions that ultimately influence cell growth and metabolism . Because of its central role in physiology , insulin signaling has been ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "diabetic", "endocrinology", "cancer", "risk", "factors", "signaling", "networks", "computerized", "simulations", "oncology", "mathematical", "computing", "mathematics", "hormonal", "causes", "of", "cancer", "insulin", "theoretical", "biology", "endocrinology", ...	2011	Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation
rs143383 is a C to T transition SNP located in the 5′untranslated region ( 5′UTR ) of the growth differentiation factor 5 gene GDF5 . The T allele of the SNP is associated with increased risk of osteoarthritis ( OA ) in Europeans and in Asians . This susceptibility is mediated by the T allele producing less GDF5 transc...	GDF5 is an important growth factor that plays a vital role in the development and repair of articulating joints . rs143383 is a polymorphism within the regulatory region of the GDF5 gene and has two allelic forms , C and T . Genetic studies have demonstrated that the T allele is associated with an increased risk of ost...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "rheumatology", "gene", "expression", "genetics", "gene", "regulation", "molecular", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "dna", "transcription", "gene", "function" ]	2013	The Identification of Trans-acting Factors That Regulate the Expression of GDF5 via the Osteoarthritis Susceptibility SNP rs143383
Hemorrhagic fever with renal syndrome ( HFRS ) is a rodent-borne disease caused by Hantaviruses . It is endemic in all 31 provinces , autonomous regions , and metropolitan areas in mainland China where human cases account for 90% of the total global cases . Shandong Province is among the most serious endemic areas . HF...	Hemorrhagic fever with renal syndrome ( HFRS ) , a rodent-borne disease caused by Hantaviruses , is characterized by fever , acute renal dysfunction and hemorrhagic manifestations . At present , it is endemic in all 31 provinces , autonomous regions , and metropolitan areas in mainland China where human cases account f...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/preventive", "medicine", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2010	Spatiotemporal Trends and Climatic Factors of Hemorrhagic Fever with Renal Syndrome Epidemic in Shandong Province, China
The two DNA strands of the nuclear genome are replicated asymmetrically using three DNA polymerases , α , δ , and ε . Current evidence suggests that DNA polymerase ε ( Pol ε ) is the primary leading strand replicase , whereas Pols α and δ primarily perform lagging strand replication . The fact that these polymerases di...	The stability of complex and highly organized nuclear genomes partly depends on the ability of mismatch repair ( MMR ) to correct a variety of different mismatches generated as the leading and lagging strand templates are copied by three polymerases , each with different fidelity . Here we provide the first comparison ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "microbiology", "nucleotides", "model", "organisms", "mutation", "types", "dna", "replication", "dna", "dna", "synthesis", "biology", "molecular", "biology", "mutagenesis", "biochemistry", "nucleic", "acids", "genetics", "yeast", "and", "fungal", ...	2012	Mismatch Repair Balances Leading and Lagging Strand DNA Replication Fidelity
The precision of multisensory perception improves when cues arising from the same cause are integrated , such as visual and vestibular heading cues for an observer moving through a stationary environment . In order to determine how the cues should be processed , the brain must infer the causal relationship underlying t...	As we interact with objects and people in the environment , we are constantly exposed to numerous sensory stimuli . For safe navigation and meaningful interaction with entities in the environment , our brain must determine if the sensory inputs arose from a common or different causes in order to determine whether they ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "classical", "mechanics", "applied", "mathematics", "social", "sciences", "neuroscience", "simulation", "and", "modeling", "perception", "algorithms", "optimization", "cognitive", "psychology", "mathematics", "vision", "research", "and", "analysis", "methods", "research", ...	2018	Bayesian comparison of explicit and implicit causal inference strategies in multisensory heading perception
Zika virus ( ZIKV ) is a mosquito-borne pathogen which has recently spread beyond Africa and into Pacific and South American regions . Despite first being detected in 1947 , very little information is known about the virus , and its spread has been associated with increases in Guillain-Barre syndrome and microcephaly ....	Since first being recognised in 1947 , Zika virus ( ZIKV ) has mainly been associated with a mild illness with symptoms including a limited fever and rash . In 2007 the virus spread from Africa into French Polynesia and then onwards across Pacific regions and into South America . In these new regions , ZIKV has been as...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "immune", "physiology", "microcephaly", "pathology", "and", "laboratory", "medicine", "body", "fluids", "viral", "transmission", "and", "infection", "spleen", "pathogens", "animal", "models", "of", "di...	2016	A Susceptible Mouse Model for Zika Virus Infection
The therapeutic strategy for advanced nasopharyngeal carcinoma ( NPC ) is still challenging . It is an urgent need to uncover novel treatment targets for NPC . Therefore , understanding the mechanisms underlying NPC tumorigenesis and progression is essential for the development of new therapeutic strategies . Here , we...	The therapeutic strategy for advanced nasopharyngeal carcinoma ( NPC ) is still challenging . The most urgent need for NPC is novel treatment targets . Therefore , understanding the mechanisms underlying NPC tumorigenesis and progression is essential for the development of new therapeutic strategies . Here , we identif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "gene", "regulation", "carcinomas", "cell", "processes", "cancers", "and", "neoplasms", "oncology", "micrornas", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "research", "and", ...	2016	Overexpression of Mitochondria Mediator Gene TRIAP1 by miR-320b Loss Is Associated with Progression in Nasopharyngeal Carcinoma
Risk assessment of tick-borne and zoonotic disease emergence necessitates sound knowledge of the particular microorganisms circulating within the communities of these major vectors . Assessment of pathogens carried by wild ticks must be performed without a priori , to allow for the detection of new or unexpected agents...	Diseases transmitted by ticks have diverse etiology ( viral , bacterial , parasitic ) and are responsible for high morbidity and mortality rates around the world , both in humans and animals . The emergence or re-emergence of tick-borne diseases is increasingly becoming a problem as the geographical distribution of sev...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biology", "and", "life", "sciences", "veterinary", "science", "medicine", "and", "health", "sciences" ]	2014	Identification of Parasitic Communities within European Ticks Using Next-Generation Sequencing
The reliable response to weak biological signals requires that they be amplified with fidelity . In E . coli , the flagellar motors that control swimming can switch direction in response to very small changes in the concentration of the signaling protein CheY-P , but how this works is not well understood . A recently p...	Bacteria swim to find nutrients or to avoid toxins . Their swimming is powered by the rotation of flagella ( hair-like structures ) that act as propellers . Each flagellum is driven by a rotary molecular engine ( the bacterial flagellar motor ) that can rotate in either a counterclockwise or clockwise direction and swi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "theoretical", "biology", "biology", "computational", "biology", "biophysics" ]	2012	Conformational Spread in the Flagellar Motor Switch: A Model Study
An analysis of gene expression variability can provide an insightful window into how regulatory control is distributed across the transcriptome . In a single cell analysis , the inter-cellular variability of gene expression measures the consistency of transcript copy numbers observed between cells in the same populatio...	In order to function properly , cells express specific sets of genes that are regulated via complex transcriptional programs . During early stages of development , when an embryo consists of only a handful of cells , it is vital that these cells work together so that the embryo can develop into a healthy baby . Single ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development
A key priority in infectious disease research is to understand the ecological and evolutionary drivers of viral diseases from data on disease incidence as well as viral genetic and antigenic variation . We propose using a simulation-based , Bayesian method known as Approximate Bayesian Computation ( ABC ) to fit and as...	The infectious disease dynamics of many viral pathogens like influenza , norovirus and coronavirus are inextricably tied to their evolution . This interaction between evolutionary and ecological processes complicates our ability to understand the infectious disease behavior of rapidly evolving pathogens . Most statisti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "evolutionary", "ecology", "mathematics", "ecology", "evolutionary", "biology", "epidemiology", "statistics", "theoretical", "ecology", "biology", "population", "biology", "statistical", "methods" ]	2012	Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study
Insecticidal crystal toxins derived from the soil bacterium Bacillus thuringiensis ( Bt ) are widely used as biopesticide sprays or expressed in transgenic crops to control insect pests . However , large-scale use of Bt has led to field-evolved resistance in several lepidopteran pests . Resistance to Bt Cry1Ac toxin in...	Biopesticide and transgenic crops based on Bacillus thuringiensis ( Bt ) Cry toxins are widely used worldwide , yet the development of field resistance seriously threatens their sustainability . Unraveling these resistance mechanisms are of great importance for delaying insect field resistance evolution . The diamondba...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	MAPK Signaling Pathway Alters Expression of Midgut ALP and ABCC Genes and Causes Resistance to Bacillus thuringiensis Cry1Ac Toxin in Diamondback Moth
Soil-transmitted helminths colonize more than 1 . 5 billion people worldwide , yet little is known about how they interact with bacterial communities in the gut microbiota . Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of helminths ...	Soil-transmitted helminths are carried by large numbers of people in developing countries . These parasites live in the gut and may interact with bacterial communities in the gut , also called the gut microbiota . To determine whether there are alterations to the gut microbiota that are associated with helminth infecti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "infectious", "diseases", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "tropical", "diseases", "soil-transmitted", "helminthiases", "parasitic", "diseases" ]	2014	Helminth Colonization Is Associated with Increased Diversity of the Gut Microbiota
In October 2013 , a locally-acquired case of dengue virus ( DENV ) infection was reported in Western Australia ( WA ) where local dengue transmission has not occurred for over 70 years . Laboratory testing confirmed recent DENV infection and the case demonstrated a clinically compatible illness . The infection was most...	Dengue fever transmission in Western Australia ceased in the 1940s and there are currently no known dengue vector species present . Despite this , a locally acquired of dengue fever was reported in 2013 with the most likely location of exposure the township of Point Samson in Pilbara region in the north-west of the Sta...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Investigation of the First Case of Dengue Virus Infection Acquired in Western Australia in Seven Decades: Evidence of Importation of Infected Mosquitoes?
The membrane-associated and membrane-spanning constituents of the Schistosoma mansoni tegument surface , the parasite's principal interface with the host bloodstream , have recently been characterized using proteomic techniques . Biotinylation of live worms using membrane-impermeant probes revealed that only a small su...	Adult schistosome parasites can reside in the host bloodstream for decades surrounded by components of the immune system . It was originally proposed that their survival depended on the secretion of an inert bilayer , the membranocalyx , to protect the underlying plasma membrane from attack . We have investigated wheth...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/helminth", "infections", "chemical", "biology/protein", "chemistry", "and", "proteomics" ]	2011	Enzymatic Shaving of the Tegument Surface of Live Schistosomes for Proteomic Analysis: A Rational Approach to Select Vaccine Candidates
The Type III Secretion System ( T3SS ) is a macromolecular complex used by Gram-negative bacteria to secrete effector proteins from the cytoplasm across the bacterial envelope in a single step . For many pathogens , the T3SS is an essential virulence factor that enables the bacteria to interact with and manipulate thei...	Type III Secretion Systems ( T3SS ) secrete bacterial effector proteins from the cytoplasm across the cell wall , but mechanistic details of this process remain mostly elusive . We locked the T3SS of Shigella flexneri in an actively secreting state by expression of substrate fusions that consist of a functional translo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "shigellosis", "infections", "protein", "interactions", "macromolecular", "assemblies", "host-pathogen", "interaction", "microbiology", "globular", "proteins", "bacterial", "biochemistry", "protein", "classes", "bacterial", "diseases", "protein", "...	2014	A Substrate-Fusion Protein Is Trapped inside the Type III Secretion System Channel in Shigella flexneri
Helminth infections have proven recalcitrant to control by chemotherapy in many parts of Southeast Asia and indeed farther afield . This study isolates and examines the influence of different aspects of the physical and social environment , and uneven intervention effort contributing to the pathogenic landscape of huma...	Many of the large-scale helminth control programs around the world have primarily relied upon drug treatment . Reliance on drug treatment alone does not deal with the ultimate causes of infection , resulting in reduced infection levels only in the short-term . Re-emergence of infections and possibly even development of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "rivers", "demography", "cancer", "treatment", "clinical", "oncology", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "health", "care", "freshwater", "fis...	2016	Uncovering the Pathogenic Landscape of Helminth (Opisthorchis viverrini) Infections: A Cross-Sectional Study on Contributions of Physical and Social Environment and Healthcare Interventions
Leptospirosis is the most common bacterial zoonoses and has been identified as an important emerging global public health problem in Southeast Asia . Rodents are important reservoirs for human leptospirosis , but epidemiological data is lacking . We sampled rodents living in different habitats from seven localities dis...	Leptospirosis is the most prevalent bacterial zoonosis worldwide . Rodents are believed to be the main reservoirs of Leptospira , yet little epidemiological research has been conducted on rodents from Southeast Asia . Previous studies suggest that activities which place humans in microenvironments shared by rodents inc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "leptospirosis", "bacterial", "diseases", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "environmental", "epidemiology", "epidemiology", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "...	2014	Epidemiology of Leptospira Transmitted by Rodents in Southeast Asia
The presence of amyloid deposits consisting primarily of Amyloid-β ( Aβ ) fibril in the brain is a hallmark of Alzheimer's disease ( AD ) . The morphologies of these fibrils are exquisitely sensitive to environmental conditions . Using molecular dynamics simulations combined with data from previously published solid-st...	Amyloid diseases are characterized by the presence of amyloid fibrils on organs and tissue in the body . Alzheimer's disease , Parkinson's diseases and Type II Diabetes are all examples of amyloid diseases . Determining the structure of amyloid fibrils is critical for understanding the mechanism of fibril formation as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/molecular", "dynamics", "public", "health", "and", "epidemiology/global", "health", "biophysics/protein", "folding" ]	2010	Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils
The resident skin microbiota plays an important role in restricting pathogenic bacteria , thereby protecting the host . Scabies mites ( Sarcoptes scabiei ) are thought to promote bacterial infections by breaching the skin barrier and excreting molecules that inhibit host innate immune responses . Epidemiological studie...	Scabies is a neglected , contagious skin disease caused by a parasitic mite Sarcoptes scabiei . It is highly prevalent world-wide , and now recognized as a possible underlying factor for secondary bacterial infections with potential serious downstream complications . There is currently few experimental data demonstrati...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "ecology", "staphylococcus", "medical", "microbiology", "host-pathogen", "interactions", "microbial", "pathogens", "parasitology", "biology", "and", "life", "sciences", "microbiology", ...	2014	Scabies Mites Alter the Skin Microbiome and Promote Growth of Opportunistic Pathogens in a Porcine Model
The pathogenesis of persistent viral infections depends critically on long-term viral loads . Yet what determines these loads is largely unknown . Here , we show that a single CD8+ T cell epitope sets the long-term latent load of a lymphotropic gamma-herpesvirus , Murid herpesvirus-4 ( MuHV-4 ) . The MuHV-4 M2 latency ...	Persistent viruses present a major challenge to the immune response . Gamma-herpesviruses are a prime example , and the archetypal family member , Epstein-Barr virus ( EBV ) , has been studied for many years . A major unanswered question with EBV is why long-term virus loads—a key pathogenesis outcome—vary so widely be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/persistence", "and", "latency", "immunology/immunity", "to", "infections", "virology/animal", "models", "of", "infection" ]	2008	A Single CD8+ T Cell Epitope Sets the Long-Term Latent Load of a Murid Herpesvirus

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