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Virus infections are known to induce a transient state of immune suppression often associated with an inhibition of T cell proliferation in response to mitogen or cognate-antigen stimulation . Recently , virus-induced immune suppression has been linked to responses to type 1 interferon ( IFN ) , a signal 3 cytokine tha...	Vaccines are used to protect individuals against infection with a number of different pathogens and depend on the formation of antigen specific memory cells . The efficacy of vaccines can be affected by a number of different factors . It has been known for some time now that suppression of the immune system occurs duri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "biology", "and", "life", "sciences", "immunology", "medicine", "and", "health", "sciences" ]	2014	Out-of-Sequence Signal 3 as a Mechanism for Virus-Induced Immune Suppression of CD8 T Cell Responses
A wide range of research areas in molecular biology and medical biochemistry require a reliable enzyme classification system , e . g . , drug design , metabolic network reconstruction and system biology . When research scientists in the above mentioned areas wish to unambiguously refer to an enzyme and its function , t...	The fundamental understanding of metabolism in organisms which can only be achieved by integrated studies on their biology using a systems biology approach will aid in the design of future metabolic engineering strategies . Metabolic network reconstruction provides insight into the molecular mechanisms of a particular ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "And", "Methods" ]	[ "biochemistry", "computer", "science/systems", "and", "control", "theory", "biochemistry/bioinformatics", "computational", "biology/metabolic", "networks", "computational", "biology" ]	2010	Automatic Assignment of EC Numbers
Life science technologies generate a deluge of data that hold the keys to unlocking the secrets of important biological functions and disease mechanisms . We present DEAP , Differential Expression Analysis for Pathways , which capitalizes on information about biological pathways to identify important regulatory pattern...	The data deluge represents a growing challenge for life sciences . Within this sea of data surely lie many secrets to understanding important biological and medical systems . To quantify important patterns in this data , we present DEAP ( Differential Expression Analysis for Pathways ) . DEAP amalgamates information ab...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "interactions", "statistics", "metabolic", "networks", "signaling", "networks", "computerized", "simulations", "mathematics", "biostatistics", "regulatory", "networks", "biology", "proteomics", "microarrays", "biochemistry", "computer", "science", "proteomic", "dat...	2013	Differential Expression Analysis for Pathways
To be transmitted to vertebrate hosts via the saliva of their vectors , arthropod-borne viruses have to cross several barriers in the mosquito body , including the midgut infection and escape barriers . Yellow fever virus ( YFV ) belongs to the genus Flavivirus , which includes human viruses transmitted by Aedes mosqui...	Most flaviviruses , including yellow fever virus ( YFV ) , are transmitted between hosts by mosquito bites . The yellow fever vaccine ( YFV-17D ) is one of the safest and most effective live virus vaccine ever developed . It is also used as a platform for engineering vaccines against other health-threatening flavivirus...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "animals", "viruses", "vaccines", "rna", "viruses", "infectiou...	2019	Midgut barriers prevent the replication and dissemination of the yellow fever vaccine in Aedes aegypti
Evaluating the future consequences of actions is achievable by simulating a mental search tree into the future . Expanding deep trees , however , is computationally taxing . Therefore , machines and humans use a plan-until-habit scheme that simulates the environment up to a limited depth and then exploits habitual valu...	When faced with several choices in complex environments like chess , thinking about all the potential consequences of each choice , infinitely deep into the future , is simply impossible due to time and cognitive limitations . An outstanding question is what is the best direction and depth of thinking about the future ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "decision", "making", "engineering", "and", "technology", "statistics", "applied", "mathematics", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "algorithms", "decision", "analysis", "cognitive", "neuroscience", "cognit...	2019	Optimizing the depth and the direction of prospective planning using information values
The extensive glycosylation of HIV-1 envelope ( Env ) glycoprotein leaves few glycan-free holes large enough to admit broadly neutralizing antibodies ( bnAb ) . Consequently , most bnAbs must inevitably make some glycan contacts and avoid clashes with others . To investigate how Env glycan maturation regulates HIV sens...	Here we engineered various changes in the sizes and shapes of sugars that decorate HIV surface spike proteins and tested the effects of these changes on virus susceptibility to neutralizing antibodies . In so doing , we were able to define the optimal Env-sugars recognized by prototype bnAbs that recognize various cano...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "polyacrylamide", "gel", "electrophoresis", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "blue", "native", "polyacrylamide", "gel", "electrophoresis", "293t", "cells", "pathogens", ...	2018	Glycoengineering HIV-1 Env creates ‘supercharged’ and ‘hybrid’ glycans to increase neutralizing antibody potency, breadth and saturation
Angiostrongylus costaricensis is a relatively uncharacterized nematode that causes abdominal angiostrongyliasis in Latin America , a human parasitic disease . Currently , no effective pharmacological treatment for angiostrongyliasis exists . Peptidases are known to be druggable targets for a variety of diseases and are...	A . costaricensis is a poorly studied nematode that causes abdominal angiostrongyliasis , a human parasitic disease . Peptidases perform several functions in the life cycle of parasites , including nutrition , differentiation and host invasion . The present study characterized the repertoire of peptidases in A . costar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "enzymes", "enzymology", "parasitic", "diseases", "organic", "compounds", "parasitology", "developmental", "biology", "serine", "peptide", "libraries", "acidic", "amino", "acids", "amino", "acids", "cyste...	2018	Activity profiling of peptidases in Angiostrongylus costaricensis first-stage larvae and adult worms
Decades of study have revealed more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA , yet the larger functional dynamics of this conserved system are unclear . To this end , we developed a highly precise mass spectrometric method to quantify tRNA modificatio...	While the genetic code in DNA is read from four nucleobase structures , there are more than 100 ribonucleoside structures incorporated as post-transcriptional modifications mainly in tRNA and rRNA . These structures and their biosynthetic machinery are highly conserved , with 20–30 present in any one organism , yet the...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "chemical", "biology/small", "molecule", "chemistry", "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "cell", "biology/cell", "signaling", "cell", "biology", "biochemistry/chemical", "biology", "of", "the", "cell", "biochemistry/cell", "...	2010	A Quantitative Systems Approach Reveals Dynamic Control of tRNA Modifications during Cellular Stress
The ribosome is an evolutionarily conserved organelle essential for cellular function . Ribosome construction requires assembly of approximately 80 different ribosomal proteins ( RPs ) and four different species of rRNA . As RPs co-assemble into one multi-subunit complex , mutation of the genes that encode RPs might be...	Ribosomes are composed of two subunits that each consist of a large number of proteins , and their function of translating mRNA into protein is essential for cell viability . Naturally occurring or genetically engineered mutations within an individual ribosomal protein provide a valuable resource , since the resulting ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurogenesis", "genetic", "mutation", "neuroscience", "gene", "function", "genetics", "of", "disease", "cognitive", "neuroscience", "animal", "cognition", "developmental", "neuroscience", "biology", "mutagenesis", "working", "memory", "genetic", "screens", "genetics", "b...	2013	Mutation of the Diamond-Blackfan Anemia Gene Rps7 in Mouse Results in Morphological and Neuroanatomical Phenotypes
One of the UN sustainable development goals is to achieve universal access to safe and affordable drinking water by 2030 . It is locations like Kathmandu , Nepal , a densely populated city in South Asia with endemic typhoid fever , where this goal is most pertinent . Aiming to understand the public health implications ...	Aiming to understand the ecology of municipal drinking water and measure the potential exposure to pathogens that cause typhoid fever ( Salmonella Typhi and Salmonella Paratyphi A ) in Kathmandu , Nepal , we collected water samples from 10 water sources weekly for one year and subjected them to comprehensive chemical ,...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[]	2016	The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water
During the 2014–2016 West Africa Ebola Virus Disease ( EVD ) epidemic , the public health community had concerns that sexual transmission of the Ebola virus ( EBOV ) from EVD survivors was a risk , due to EBOV persistence in body fluids of EVD survivors , particularly semen . The Sierra Leone Ebola Virus Persistence St...	The 2014–2016 West Africa Ebola Virus Disease ( EVD ) epidemic was large and widespread , affecting thousands of people across Guinea , Liberia , and Sierra Leone . Prior to this epidemic , there were limited data on persistence of Ebola virus in body fluids of EVD survivors and the potential risk that viral persistenc...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "human", "sexual", "behavior", "filoviruses", "rna"...	2017	Development of risk reduction behavioral counseling for Ebola virus disease survivors enrolled in the Sierra Leone Ebola Virus Persistence Study, 2015-2016
Advances in genomics in recent years have provided key insights into defining cancer subtypes “within-a-tissue”—that is , respecting traditional anatomically driven divisions of medicine . However , there remains a dearth of data regarding molecular profiles that are shared across tissues , an understanding of which co...	In clinical practice , the organ in which a cancer arises typically classifies it . However , developments in our understanding of cancer have revealed that this method overlooks key aspects of cancer biology relevant to both disease prevention and treatment . In fact , work characterizing the genetic make-up of cancer...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Methods" ]	[ "adenocarcinoma", "of", "the", "lung", "medicine", "and", "health", "sciences", "squamous", "cell", "lung", "carcinoma", "carcinomas", "cancers", "and", "neoplasms", "oncology", "histology", "adenocarcinomas", "epigenetics", "dna", "chromatin", "dna", "methylation", "...	2017	Comparative transcriptomes of adenocarcinomas and squamous cell carcinomas reveal molecular similarities that span classical anatomic boundaries
Chemotaxis is a dynamic cellular process , comprised of direction sensing , polarization and locomotion , that leads to the directed movement of eukaryotic cells along extracellular gradients . As a primary step in the response of an individual cell to a spatial stimulus , direction sensing has attracted numerous theor...	Many eukaryotic cells , including Dictyostelium discoideum ( Dicty ) , neutrophils and other cells of the immune system , can detect and reliably orient themselves in chemoattractant gradients . In Dicty , signal detection and transduction involves a G-protein-coupled receptor ( GPCR ) through which extracellular cAMP ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "signaling", "networks", "g-protein", "signaling", "network", "analysis", "cellular", "structures", "and", "organelles", "g", "protein", "coupled", "receptors", "cytosol", "computer", "and", "information", "sciences", "proteins", "ras", "signaling", ...	2016	A Model for Direction Sensing in Dictyostelium discoideum: Ras Activity and Symmetry Breaking Driven by a Gβγ-Mediated, Gα2-Ric8 -- Dependent Signal Transduction Network
Mutations in the SOD1 and TARDBP genes have been commonly identified in Amyotrophic Lateral Sclerosis ( ALS ) . Recently , mutations in the Fused in sarcoma gene ( FUS ) were identified in familial ( FALS ) ALS cases and sporadic ( SALS ) patients . Similarly to TDP-43 ( coded by TARDBP gene ) , FUS is an RNA binding p...	Mutations in the SOD1 , TARDBP , and FUS genes have been commonly identified in Amyotrophic Lateral Sclerosis ( ALS ) . However , possible interactions between these ALS–causative genetic mutations have not been examined . Here we expressed each of three human FUS mutations ( R521H , R521C , and S57Δ ) in zebrafish emb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "molecular", "neuroscience", "neurodegenerative", "diseases", "anatomy", "and", "physiology", "neuroscience", "animal", "models", "motor", "systems", "model", "organisms", "neurological", "system", "motor", "neuron", "diseases", "biology", "zebrafish", "cellul...	2011	FUS and TARDBP but Not SOD1 Interact in Genetic Models of Amyotrophic Lateral Sclerosis
Genomic imprinting is a normal process that causes genes to be expressed according to parental origin . The selective advantage conferred by imprinting is not understood but is hypothesised to act on dosage-critical genes . Here , we report a unique model in which the consequences of a single , double , and triple dosa...	Genomic imprinting , the process that causes genes to be expressed from one of the two chromosome homologues according to parental origin , is likely to act on genes whose dosage is important for their correct function . To test this , we compared the phenotype of transgenic mice expressing a double and triple dose of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/developmental", "evolution", "genetics", "and", "genomics/chromosome", "biology", "developmental", "biology/molecul...	2009	Gene Dosage Effects of the Imprinted Delta-Like Homologue 1 (Dlk1/Pref1) in Development: Implications for the Evolution of Imprinting
In order to promote infection , the blood-borne parasite Trypanosoma brucei releases factors that upregulate arginase expression and activity in myeloid cells . By screening a cDNA library of T . brucei with an antibody neutralizing the arginase-inducing activity of parasite released factors , we identified a Kinesin H...	From the first invasive step onwards , African trypanosomes can efficiently undermine the protective immune response of their mammalian host to favor their survival within the host and successful transmission by its vector , the tsetse fly . Identifying the parasite factors affecting the protective immune response is t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	A Trypanosoma brucei Kinesin Heavy Chain Promotes Parasite Growth by Triggering Host Arginase Activity
Elongator complex is required for formation of the side chains at position 5 of modified nucleosides 5-carbamoylmethyluridine ( ncm5U34 ) , 5-methoxycarbonylmethyluridine ( mcm5U34 ) , and 5-methoxycarbonylmethyl-2-thiouridine ( mcm5s2U34 ) at wobble position in tRNA . These modified nucleosides are important for effic...	Elongator is a conserved protein complex in eukaryotes . Studies in yeast , worms , and plants have revealed that Elongator complex is required for formation of mcm5 and ncm5 side chains at wobble uridines in a subset of tRNA species . The primary function of Elongator complex in yeast is to modify U34 in tRNAs . Lack ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "nucleotides", "gene", "function", "histone", "modification", "chromatin", "rna", "structure", "gene", "expression", "biology", "molecular", "biology", "biochemistry", "rna", "rna", "processing", "nucleic", "acids", "protein", "translation", "genetics", "molecular", "ce...	2011	Elongator Complex Influences Telomeric Gene Silencing and DNA Damage Response by Its Role in Wobble Uridine tRNA Modification
In the wet-dry tropics of Northern Australia , drinking water in remote communities is mostly sourced from bores accessing groundwater . Many aquifers contain naturally high levels of iron and some are shallow with surface water intrusion in the wet season . Therefore , environmental bacteria such as iron-cycling bacte...	Water providers in the wet-dry tropics of Northern Australia face additional challenges to keep drinking water microbiologically safe . The source water is often rich in iron-cycling bacteria leading to excessive biofilm formation in pipes and it can also contain the emerging opportunistic pathogen Burkholderia pseudom...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biofilms", "bacteriology", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "water", "resources", "microbiome", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "microbiology", "protozoa...	2019	Opportunistic pathogens and large microbial diversity detected in source-to-distribution drinking water of three remote communities in Northern Australia
Zaire ebolavirus ( ZEBOV ) infections are associated with high lethality in primates . ZEBOV primarily targets mononuclear phagocytes , which are activated upon infection and secrete mediators believed to trigger initial stages of pathogenesis . The characterization of the responses of target cells to ZEBOV infection m...	Ebola virus causes a severe hemorrhagic fever syndrome in man with high case-fatality rates . Following infection , monocytes and macrophages are among the first cells targeted by the virus . These cells respond by increasing expression of inflammatory cytokines and chemokines that contribute towards pathogenesis . In ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2011	Ebola Virion Attachment and Entry into Human Macrophages Profoundly Effects Early Cellular Gene Expression
Accumulating evidence indicates high risk of bias in preclinical animal research , questioning the scientific validity and reproducibility of published research findings . Systematic reviews found low rates of reporting of measures against risks of bias in the published literature ( e . g . , randomization , blinding ,...	Scientific validity of research findings depends on scientific rigor , including measures to avoid bias , such as random allocation of animals to treatment groups ( randomization ) and assessing outcome measures without knowing to which treatment groups the animals belong ( blinding ) . However , measures against bias ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "experimental", "design", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "research", "design", "cognitive", "psychology", "research", "and", "analysis", "methods", "language", "meta-research", "article", "peer", "review", "research", "assessmen...	2016	Authorization of Animal Experiments Is Based on Confidence Rather than Evidence of Scientific Rigor
Core object recognition , the ability to rapidly recognize objects despite variations in their appearance , is largely solved through the feedforward processing of visual information . Deep neural networks are shown to achieve human-level performance in these tasks , and explain the primate brain representation . On th...	In recent years , deep-learning-based computer vision algorithms have been able to achieve human-level performance in several object recognition tasks . This has also contributed in our understanding of how our brain may be solving these recognition tasks . However , object recognition under more challenging conditions...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neural", "networks", "information", "processing", "visual", "object", "recognition", "social", "sciences", "neuroscience", "learning", "and", "memory", "perception", "cognitive", "psychology", "recurrent", "neural", "networks", "human", "performance", "cognition", "brain...	2019	Beyond core object recognition: Recurrent processes account for object recognition under occlusion
Candida albicans is a medically important pathogen , and recognition by innate immune cells is critical for its clearance . Although a number of pattern recognition receptors have been shown to be involved in recognition and phagocytosis of this fungus , the relative role of these receptors has not been formally examin...	Infection by Candida albicans has increased as a result of immunosuppression associated with AIDS and organ transplantation . We assessed the role of three pattern recognition receptors , namely Dectin-1 ( a beta glucan receptor ) , the type 3 complement receptor ( CR3 ) , and the mannose receptor , in mediating uptake...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "microbiology/innate", "immunity", "immunology/innate", "immunity" ]	2008	Stage-Specific Sampling by Pattern Recognition Receptors during Candida albicans Phagocytosis
More than 220 million people worldwide are chronically infected with schistosomes , causing severe disease or even death . The major pathological damage occurring in schistosomiasis is attributable to the granulomatous inflammatory response and liver fibrosis induced by schistosome eggs . The inflammatory response is t...	Schistosomiasis is a parasitic disease that affects approximately 220 million people and causes serious morbidity and economic problems mainly in ( sub ) tropical regions . After Schistosoma japonicum or Schistosoma mansoni infection , parasite eggs are trapped in host liver and induce liver inflammation and fibrosis ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "t", "helper", "cells", "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "helminths", "immunology", "cloning", "animals", "clinical", "medicine", "molecular", "biology", "techniques", "research", "and", "ana...	2016	Blockade of PD-1 Signaling Enhances Th2 Cell Responses and Aggravates Liver Immunopathology in Mice with Schistosomiasis japonica
Despite their high degree of genomic similarity , different Salmonella enterica serovars are often associated with very different clinical presentations . In humans , for example , the typhoidal S . enterica serovar Typhi causes typhoid fever , a life-threatening systemic disease . In contrast , the non-typhoidal S . e...	Salmonella Typhimurium and Salmonella Typhi are associated with very different clinical presentations . While S . Typhimurium causes self-limiting gastroenteritis ( i . e . “food poisoning” ) , S . Typhi causes typhoid fever , a systemic , life-threatening disease . The bases for these major differences are not fully u...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "salmonella", "typhi", "salmonellosis", "epithelial", "cells", "bacterial", "diseases", "enterobacteriaceae", "bacteria", "mapk", "signaling", "cascades", "...	2017	Salmonella enterica serovar-specific transcriptional reprogramming of infected cells
Neuroinvasion and subsequent destruction of the central nervous system by prions are typically preceded by a colonization phase in lymphoid organs . An important compartment harboring prions in lymphoid tissue is the follicular dendritic cell ( FDC ) , which requires both tumor necrosis factor receptor 1 ( TNFR1 ) and ...	Prions are unique infectious agents thought to be composed entirely of an abnormal conformer of the endogenous prion protein . Prions cause a severe neurological disorder in humans and other animals known as prion disease . Though prion disease can arise spontaneously or from genetic mutations in the gene encoding the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurobiology", "of", "disease", "and", "regeneration", "immunology", "microbiology", "lymphoid", "organs", "neuroscience", "infectious", "diseases", "biology", "pathogenesis", "immune", "system", "clinical", "immunology", "neurological", "disorders", "neurology...	2012	Lymphotoxin, but Not TNF, Is Required for Prion Invasion of Lymph Nodes
Sequence-specific transcription factors ( TFs ) represent one of the largest groups of proteins that is targeted for SUMO post-translational modification , in both yeast and humans . SUMO modification can have diverse effects , but recent studies showed that sumoylation reduces the interaction of multiple TFs with DNA ...	Transcription factors bind the genome at specific sites to control the expression of target genes . Although the DNA sequence of these sites is critical for determining where they bind , additional factors must act to ensure that only appropriate sites remain bound and regulated by transcription factors . Here we demon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "characterization", "gene", "regulation", "dna", "transcription", "fungi", "sumoylation", "sequence", "motif", "analysis", "epigenetics", "dna", "chromatin", "promoter", "regions", "research", "and", "analysis", "methods", "sequence", "analysis", "bioinformati...	2019	Sumoylation of DNA-bound transcription factor Sko1 prevents its association with nontarget promoters
Aedes aegypti is the primary vector of the four serotypes of dengue virus ( DENV1-4 ) , Chikungunya and yellow fever virus to humans . Previous population genetic studies have revealed a particular genetic structure among the vector populations in the Americas that suggests differences in the ability to transmit DENV ....	Knowledge on the population structure of Aedes aegypti , the main vector of the dengue virus ( DENV ) , is essential to improving dengue fever prevention strategies in endemic countries . In Colombia , despite the epidemiological relevance of dengue fever , the genetic population structure and phylogeography of the vec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Spatio-Temporal Distribution of Aedes aegypti (Diptera: Culicidae) Mitochondrial Lineages in Cities with Distinct Dengue Incidence Rates Suggests Complex Population Dynamics of the Dengue Vector in Colombia
The spindle checkpoint ensures that newly born cells receive one copy of each chromosome by preventing chromosomes from segregating until they are all correctly attached to the spindle . The checkpoint monitors tension to distinguish between correctly aligned chromosomes and those with both sisters attached to the same...	The spindle checkpoint monitors tension on chromosomes to distinguish between chromosomes that are correctly and incorrectly attached to the spindle . Tension is generated across a correctly attached chromosome as microtubules from opposite poles attach to and pull kinetochores apart , but are resisted by the cohesin t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Tethering Sister Centromeres to Each Other Suggests the Spindle Checkpoint Detects Stretch within the Kinetochore
Usutu virus ( USUV ) is an African mosquito-borne flavivirus closely related to West Nile virus and Japanese encephalitis virus , which host range includes mainly mosquitoes and birds , although infections in humans have been also documented , thus warning about USUV as a potential health threat . Circulation of USUV i...	The identification of cellular components and metabolic pathways involved in virus replication provides valuable information for the development of new antiviral strategies . Autophagy is one of these metabolic pathways with multiple implications during viral replication . Autophagy literally means self-digestion and c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Infection with Usutu Virus Induces an Autophagic Response in Mammalian Cells
Mutation is the engine that drives evolution and adaptation forward in that it generates the variation on which natural selection acts . Mutation is a random process that nevertheless occurs according to certain biases . Elucidating mutational biases and the way they vary across species and within genomes is crucial to...	Natural selection sorts through the variability generated by mutation and biases evolution toward fitter outcomes . However , because mutation is itself not entirely random it can also bias the direction of evolution independently of selection . For instance , it is often assumed that the extreme variation observed in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", ...	2010	Evidence That Mutation Is Universally Biased towards AT in Bacteria
Gastro-intestinal nematodes in ruminants , especially Haemonchus contortus , are a global threat to sheep and cattle farming . The emergence of drug resistance , and even multi-drug resistance to the currently available classes of broad spectrum anthelmintics , further stresses the need for new drugs active against gas...	Worldwide , sheep and cattle farming are threatened by anthelmintic-resistant gastro-intestinal nematodes . A novel chemical class of synthetic anthelmintics was recently discovered , the Amino-Acetonitrile Derivatives ( AADs ) , which exhibit excellent efficacy against various species of livestock-pathogenic nematodes...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "genetics", "and", "genomics/gene", "discovery", "molecular", "biology/rna", "splicing", "pharmacology/drug", "development" ]	2009	Haemonchus contortus Acetylcholine Receptors of the DEG-3 Subfamily and Their Role in Sensitivity to Monepantel
Mycetoma is a devastating , neglected tropical disease characterised by extensive tissue involvement resulting in destruction , deformities and disabilities in the affected patients . The hand is commonly affected by mycetoma thus compromises its functionality and hinder the patient’s daily activities of living . In th...	Hand mycetoma is a serious condition due to the complexity of the hand anatomy and functionality . The disease and the surgical intervention can both produce distortions , deformities and disabilities which interfere with patient daily activities of living . Thus producing huge burden on the patients , the families and...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "mycetoma", "tropical", "diseases", "limbs", "(anatomy)", "surgical", "and", "invasive", "medical", "procedures", "health", "care", "magnetic", "resonance",...	2016	Hand Mycetoma: The Mycetoma Research Centre Experience and Literature Review
The three dimensional conformation of the genome in the cell nucleus influences important biological processes such as gene expression regulation . Recent studies have shown a strong correlation between chromatin interactions and gene co-expression . However , predicting gene co-expression from frequent long-range chro...	Regulatory elements can target genes over large genomic distances through long-range chromatin interactions . These interactions arise as a result of the three-dimensional ( 3D ) conformation of chromosomes in the cell nucleus . This 3D conformation can also result in the co-localization of co-regulated genes . To inve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Hi-C Chromatin Interaction Networks Predict Co-expression in the Mouse Cortex
Epithelial renewal in the Drosophila intestine is orchestrated by Intestinal Stem Cells ( ISCs ) . Following damage or stress the intestinal epithelium produces ligands that activate the epidermal growth factor receptor ( EGFR ) in ISCs . This promotes their growth and division and , thereby , epithelial regeneration ....	Studies suggest that epidermal growth factor receptor ( EGFR ) signaling activation is a causal driver of many stem cell-derived epithelial cancers , including colorectal cancer . As in the human intestine , epithelial renewal in Drosophila intestine is orchestrated by intestinal stem cells ( ISCs ) . EGFR signaling al...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	EGFR/Ras Signaling Controls Drosophila Intestinal Stem Cell Proliferation via Capicua-Regulated Genes
Neisseria meningitidis is a commensal of human nasopharynx . In some circumstances , this bacteria can invade the bloodstream and , after crossing the blood brain barrier , the meninges . A filamentous phage , designated MDAΦ for Meningococcal Disease Associated , has been associated with invasive disease . In this wor...	Bacteriophages are bacterial viruses , which in some cases encode for virulence factors and increase bacterial virulence . Comparative genomic of several strains of Neisseria meningitidis , a major human pathogen , identified the presence of an 8kb prophage in strains belonging to invasive clonal complexes . The analys...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "bacteriophages", "pathogens", "endothelial", "cells", "microbiology", "pili", "and", "fimbriae", "epithelial", "cells", "viruses", "bacterial", "diseases", "cellular", "structures", ...	2017	A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation
Fungal infections have skyrocketed in immune-compromised patients lacking CD4+ T cells , underscoring the need for vaccine prevention . An understanding of the elements that promote vaccine immunity in this setting is essential . We previously demonstrated that vaccine-induced IL-17A+ CD8+ T cells ( Tc17 ) are required...	Patients with AIDS , cancer or immune suppressive treatments are vulnerable to infection with invasive fungi . We have found that even when helper CD4 T cells are profoundly reduced in a mouse model that mimics this defect in AIDS , other remaining T cells are capable of mounting vaccine immunity against a deadly funga...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Intrinsic MyD88-Akt1-mTOR Signaling Coordinates Disparate Tc17 and Tc1 Responses during Vaccine Immunity against Fungal Pneumonia
As small regulatory transcripts , microRNAs ( miRs ) act as genetic ‘fine tuners’ of posttranscriptional events , and as genetic switches to promote phenotypic switching . The miR miR26a targets the BMP signalling effector , smad1 . We show that loss of miR26a leads to hemorrhage ( a loss of vascular stability ) in viv...	The structural integrity of a blood vessel is critical to ensure proper vessel support and vascular tone . Vascular smooth cells ( vSMCs ) are a key component of the vessel wall and , in their mature state , express contractile proteins that help to constrict and relax the vessel in response to blood flow changes . vSM...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "pathology", "and", "laboratory", "medicine", "cardiovascular", "anatomy", "endothelial", "cells", "vertebrates", "animals", "epithelial", "cells", "animal", "models", "organisms", "osteichthyes", "developmental", "biology"...	2019	MicroRNA26 attenuates vascular smooth muscle maturation via endothelial BMP signalling
The natural history of infections with many human papillomavirus ( HPV ) types is poorly understood . Here , we describe for the first time the age- and sex-dependent antibody prevalence for 29 cutaneous and five mucosal HPV types from 15 species within five phylogenetic genera ( alpha , beta , gamma , mu , nu ) in a g...	Papillomaviruses ( PV ) are a large and highly diverse group of DNA viruses that infect cutaneous and mucosal epithelia of warm-blooded vertebrates . Of the more than 100 identified human PV ( HPV ) types , many cause benign lesions like warts and papillomas , and some also cervical , other anogenital , and oral cancer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/gynecologic", "infections", "microbiology/immunity", "to", "infections", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/skin", "infections", "infectious", "diseases/se...	2008	Seroprevalence of 34 Human Papillomavirus Types in the German General Population
It is generally assumed that most point mutations are fixed when damage containing template DNA undergoes replication , either right at the fork or behind the fork during gap filling . Here we provide genetic evidence for a pathway , dependent on Nucleotide Excision Repair , that induces mutations when processing close...	In this paper , we report the surprising finding that in addition to the well-known properties of Nucleotide Excision Repair ( NER ) in efficiently repairing a large number of DNA lesions , NER entails a mutagenic sub-pathway . Our data suggest that closely spaced lesions are processed by NER into a toxic DNA intermedi...	[ "Abstract", "Introduction", "Results", "and", "discussion" ]	[ "mutagenesis", "biochemistry", "mutation", "dna", "damage", "point", "mutation", "dna", "polymerase", "mutant", "strains", "polymerases", "dna", "replication", "nucleic", "acids", "proteins", "genetics", "biology", "and", "life", "sciences", "dna", "dna-binding", "pro...	2017	Processing closely spaced lesions during Nucleotide Excision Repair triggers mutagenesis in E. coli
Cytosine methylation is one of the most important epigenetic marks that regulate the process of gene expression . Here , we have examined the effect of epigenetic DNA methylation on nucleosomal stability using molecular dynamics simulations and elastic deformation models . We found that methylation of CpG steps destabi...	In Eukaryotic cells , control of the patterns of DNA cytosine methylation – a mechanism that acts on top of the genetic code – plays a key role in the regulation of gene expression . The large prevalence of DNA methylation in vivo , suggests a connection between the physical properties of methylated and un-methylated D...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2013	Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
Prevalence is a common epidemiological measure for assessing soil-transmitted helminth burden and forms the basis for much public-health decision-making . Standard diagnostic techniques are based on egg detection in stool samples through microscopy and these techniques are known to have poor sensitivity for individuals...	Current diagnostic methods for assessing prevalence of soil-transmitted helminths ( STHs ) largely rely on microscopic visualization of helminth eggs , an inexpensive but insensitive method of detection . However , growing interest in going beyond control to break transmission of STH through mass drug administration wi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "cost-effectiveness", "analysis", "decision", "making", "engineering", "and", "technology", "economic", "analysis", "tropical", "diseases", "social", "sciences", "neuroscience", "parasitic", "diseases", "cognitive", "psychology", "...	2019	Calculating the prevalence of soil-transmitted helminth infection through pooling of stool samples: Choosing and optimizing the pooling strategy
Tools for plague diagnosis and surveillance are not always available and affordable in most of the countries affected by the disease . Yersinia pestis isolation for confirmation is time-consuming and difficult to perform under field conditions . Serologic tests like ELISA require specific equipments not always availabl...	Plague is due to the bacterium Yersinia pestis . It is accidentally transmitted to humans by the bite of infected fleas . Currently , approximately 20 developing countries with very limited infrastructure are still affected . A plague case was defined according to clinical , epidemiological and biological features . Ra...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "developmental", "biology", "immunology/immune", "response" ]	2009	Development and Evaluation of Two Simple, Rapid Immunochromatographic Tests for the Detection of Yersinia pestis Antibodies in Humans and Reservoirs
Although antibody responses to dengue virus ( DENV ) in naturally infected individuals have been extensively studied , the functionality of DENV specific memory T cell responses in relation to clinical disease severity is incompletely understood . Using ex vivo IFNγ ELISpot assays , and by determining cytokines produce...	Although dengue viral infections cause severe clinical disease , the majority of individuals infected with the dengue virus ( DENV ) develop asymptomatic infection . The function of DENV specific memory T cells in relation to past clinical disease severity is incompletely understood . In this study , we sought to inves...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Functionality of Dengue Virus Specific Memory T Cell Responses in Individuals Who Were Hospitalized or Who Had Mild or Subclinical Dengue Infection
Quantitatively understanding the robustness , adaptivity and efficiency of cell cycle dynamics under the influence of noise is a fundamental but difficult question to answer for most eukaryotic organisms . Using a simplified budding yeast cell cycle model perturbed by intrinsic noise , we systematically explore these i...	Quantitatively understanding the dynamic behavior of the yeast cell cycle process under noise perturbations is a fundamental problem in theoretical biology . By constructing a global energy landscape for a simplified yeast cell-cycle regulatory network , we provide a systematic study of this issue . Our results demonst...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Energy Landscape Reveals That the Budding Yeast Cell Cycle Is a Robust and Adaptive Multi-stage Process
Computational protein design ( CPD ) is a powerful technique to engineer existing proteins or to design novel ones that display desired properties . Rosetta is a software suite including algorithms for computational modeling and analysis of protein structures and offers many elaborate protocols created to solve highly ...	Protein engineering , i . e . the targeted modification or design of proteins has tremendous potential for medical and industrial applications . One generally applicable strategy for protein engineering is rational protein design: based on detailed knowledge of structure and function , computer programs like Rosetta pr...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "comparative", "sequence", "analysis", "crystal", "structure", "applied", "mathematics", "condensed", "matter", "physics", "simulation", "and", "modeling", "algorithms", "optimization", "mathematics", "protein", "structure", "crystallography", "research", "and", "analysis",...	2017	Rosetta:MSF: a modular framework for multi-state computational protein design
HIV infection induces phenotypic and functional changes to CD8+ T cells defined by the coordinated upregulation of a series of negative checkpoint receptors that eventually result in T cell exhaustion and failure to control viral replication . We report that effector CD8+ T cells during HIV infection in blood and SIV i...	HIV-1 infection contributes substantially to global morbidity and mortality , with no immediate promise of an effective vaccine . One major obstacle to vaccine development and therapy is to understand why HIV-1 replication persists in a person despite the presence of viral specific immune responses . The emerging conse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	TIGIT Marks Exhausted T Cells, Correlates with Disease Progression, and Serves as a Target for Immune Restoration in HIV and SIV Infection
Borrelia burgdorferi , the Lyme disease spirochete , dramatically alters its transcriptome and proteome as it cycles between the arthropod vector and mammalian host . During this enzootic cycle , a novel regulatory network , the Rrp2-RpoN-RpoS pathway ( also known as the σ54–σS sigma factor cascade ) , plays a central ...	Borrelia burgdorferi , the causative agent of Lyme disease , is maintained in nature in a complex enzootic cycle involving Ixodes ticks and mammals . A novel regulatory network , the Rrp2-RpoN-RpoS pathway , which governs differential expression of numerous genes of B . burgdorferi , is essential for this complex life ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "physiology", "and", "metabolism", "microbiology/medical", "microbiology" ]	2010	Role of Acetyl-Phosphate in Activation of the Rrp2-RpoN-RpoS Pathway in Borrelia burgdorferi
Genomes contain tandem repeats that are at risk of internal rearrangements and a threat to genome integrity . Here , we investigated the behavior of the human subtelomeric minisatellites HRAS1 , CEB1 , and CEB25 in Saccharomyces cerevisiae . In mitotically growing wild-type cells , these GC–rich tandem arrays stimulate...	All genomes contain particular DNA sequences that are prone to break and rearrange . They can be lost or rescued at the expense of sequence variations and complex rearrangements . Using a sensitive yeast model system , we examined the fragility of the HRAS1 , CEB1 , and CEB25 GC-rich human minisatellites ( tandem repet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "metabolism", "genetic", "mutation", "small", "molecules", "microbiology", "model", "organisms", "mutation", "types", "dna", "dna", "structure", "biology", "molecular", "biology", "mutagenesis", "biochemistry", "nucleic", "acids", "genetics", "yeast", "and", "f...	2012	Stimulation of Gross Chromosomal Rearrangements by the Human CEB1 and CEB25 Minisatellites in Saccharomyces cerevisiae Depends on G-Quadruplexes or Cdc13
The human protozoan parasites Leishmania are prototrophic for pyrimidines with the ability of both de novo biosynthesis and uptake of pyrimidines . Five independent L . infantum mutants were selected for resistance to the pyrimidine analogue 5-fluorouracil ( 5-FU ) in the hope to better understand the metabolism of pyr...	The human protozoan parasites Leishmania present the ability of both de novo biosynthesis and uptake of pyrimidines . The pyrimidine pathway is not well understood in these parasites . In the hope to better understand the pyrimidine pathway in Leishmania , five independent L . infantum mutants were selected for resista...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Gene Amplification and Point Mutations in Pyrimidine Metabolic Genes in 5-Fluorouracil Resistant Leishmania infantum
DNA signatures are nucleotide sequences that can be used to detect the presence of an organism and to distinguish that organism from all other species . Here we describe Insignia , a new , comprehensive system for the rapid identification of signatures in the genomes of bacteria and viruses . With the availability of h...	Now that the genome sequences of hundreds of bacteria and viruses are known , we can design tests that will rapidly detect the presence of these species based solely on their DNA . Such tests have a wide range of applications , from diagnosing infections to detecting harmful microbes in a water supply . These tests can...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "infectious", "diseases", "none", "microbiology", "computational", "biology", "molecular", "biology" ]	2007	Comprehensive DNA Signature Discovery and Validation
Leptospirosis , an emerging zoonotic disease with worldwide distribution , is caused by spirochetes belonging to the genus Leptospira . More than 500 , 000 cases of severe leptospirosis are reported annually , with >10% of these being fatal . Leptospires can survive for weeks in suitably moist conditions before encount...	Leptospirosis , a global disease caused by the unusual bacterium Leptospira , is transmitted from animals to humans . Pathogenic species of Leptospira are excreted in urine from infected animals and can continue to survive in suitable environments before coming into contact with a new reservoir or accidental host . Lep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "host-pathogen", "interaction", "microbiology", "bacterial", "diseases", "emerging", "infectious", "diseases", "neglected", "tropical", "diseases", "microbial", "growth", "and", "development", "bacterial", "pathogens", "veterinary", "science", "infectious", "dis...	2014	A Model System for Studying the Transcriptomic and Physiological Changes Associated with Mammalian Host-Adaptation by Leptospira interrogans Serovar Copenhageni
In previous studies , we suggested that Acanthamoeba is a new aero-allergen and that patients who showed positive results for the skin-prick test response to Acanthamoeba cross-reacted with several pollen allergens . Additionally , patients with common antibodies reacted to the 13–15 kDa Acanthamoeba unknown allergen ....	Recently , the number of asthma patients have increased sharply . Among patients with asthma have a high serum IgE titer , but despite this , some of these patients do not react to known allergens in skin prick tests , that suggests the presence of unknown environmental allergens . The protozoa Acanthamoeba live in ver...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "plant", "anatomy", "cell", "motility", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "aspergillus", "enzymes", "immunology", "enzymology", "parasitic", "protozoans", "fungal", "molds", "acanthamoeb...	2018	Acanthamoeba profilin elicits allergic airway inflammation in mice
Elite controllers ( ECs ) are a rare subset of HIV-1 slow progressors characterized by prolonged viremia suppression . HLA alleles B27 and B57 promote the cytotoxic T lymphocyte ( CTL ) -mediated depletion of infected cells in ECs , leading to the emergence of escape mutations in the viral capsid ( CA ) . Whether those...	Some HIV-1-infected individuals show a natural capacity to control viral propagation . In individuals that have the HLA B27 or B57 allele , HIV-1 control is associated with mutations in viral proteins that arise as a result of immune pressure from cytotoxic T lymphocytes . HIV-1 capsid protein mutations found in these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "293t", "cells", "pathogens", "biological", "cultures", "vector-borne", "diseases", "microbiology", "rna", "extraction", "retroviruses", "...	2018	HIV-1 capsids from B27/B57+ elite controllers escape Mx2 but are targeted by TRIM5α, leading to the induction of an antiviral state
The majority of invasive human fungal pathogens gain access to their human hosts via the inhalation of spores from the environment into the lung , but relatively little is known about this infectious process . Among human fungal pathogens the most frequent cause of inhaled fatal fungal disease is Cryptococcus , which c...	Little is known about how inhaled spores from human fungal pathogens cause infections and spread to other parts of the body . The most frequent cause of inhaled fatal fungal disease is Cryptococcus , which causes meningitis . To understand how Cryptococcus causes disease , we evaluated pathogenesis of two types of cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "fungal", "spores", "medicine", "and", "health", "sciences", "yeast", "infections", "cryptococcus", "immune", "cells", "fungal", "spore", "germination", "immunology", "cell", "processes", "animal", "models", "fungi", "model", "organisms", "lymph", ...	2019	Infectious particle identity determines dissemination and disease outcome for the inhaled human fungal pathogen Cryptococcus
Infections with high-risk human papillomaviruses ( HR-HPV ) such as HPV16 and 31 can lead to ano-genital and oropharyngeal cancers and HPV types from the beta genus have been implicated in the development of non-melanoma skin cancer . HPV replicate as nuclear extrachromosomal plasmids at low copy numbers in undifferent...	Human papillomaviruses ( HPV ) have been shown to cause ano-genital and oropharyngeal cancers and have been also implicated in non-melanoma skin cancer . HPV have a two-stage replication cycle: in undifferentiated keratinocytes only a low level of genome replication without virus production can be observed whereas in d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "microbiology", "plasmid", "construction", "viruses", "dna", "replication", "dna", "viruses", "hpv-31", "dna", "construction", "molecular", "biology...	2016	Interaction of NCOR/SMRT Repressor Complexes with Papillomavirus E8^E2C Proteins Inhibits Viral Replication
Introns are key regulators of eukaryotic gene expression and present a potentially powerful tool for the design of synthetic eukaryotic gene expression systems . However , intronic control over gene expression is governed by a multitude of complex , incompletely understood , regulatory mechanisms . Despite this lack of...	Synthetic biology is gradually expanding our capability to engineer biology through rational genetic engineering of synthetic gene expression systems . These developments are already paving the way for the accelerated study of biology and applying engineered biological systems to major environmental and health problems...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bioengineering", "biological", "systems", "engineering", "engineering", "and", "technology", "synthetic", "biology", "biology", "and", "life", "sciences" ]	2014	Accurate, Model-Based Tuning of Synthetic Gene Expression Using Introns in S. cerevisiae
The ecdysis behavioral sequence in insects is a classic fixed action pattern ( FAP ) initiated by hormonal signaling . Ecdysis triggering hormones ( ETHs ) release the FAP through direct actions on the CNS . Here we present evidence implicating two groups of central ETH receptor ( ETHR ) neurons in scheduling the first...	In Drosophila , the pupal ecdysis behavioral sequence is composed of three distinct steps: pre-ecdysis , ecdysis , and post-ecdysis . We hypothesize that release of ecdysis-triggering-hormone ( ETH ) from endocrine Inka cells drives these stereotypical behaviors through sequential activation of peptidergic ETH receptor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Rescheduling Behavioral Subunits of a Fixed Action Pattern by Genetic Manipulation of Peptidergic Signaling
Many animals can choose between different developmental fates to maximize fitness . Despite the complexity of environmental cues and life history , different developmental fates are executed in a robust fashion . The nematode Caenorhabditis elegans serves as a powerful model to examine this phenomenon because it can ad...	During development , many animals choose between mutually exclusive fates , such as workers , soldiers , or queens in bees or ants . The choice between states is uniform throughout the animal since mixtures of these fates are not observed in the wild . The nematode Caenorhabditis elegans larvae integrate environmental ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "organism", "development", "gene", "expression", "genetics", "biology", "genetics", "and", "genomics", "dna", "transcription", "gene", "function" ]	2012	Hormonal Signal Amplification Mediates Environmental Conditions during Development and Controls an Irreversible Commitment to Adulthood
Throughout evolution , one of the most ancient forms of aggression between cells or organisms has been the production of proteins or peptides affecting the permeability of the target cell membrane . This class of virulence factors includes the largest family of bacterial toxins , the pore-forming toxins ( PFTs ) . PFTs...	Many pathogenic bacteria produce proteins , called pore-forming toxins , designed to perforate the plasma membrane of target cells thus perturbing host cell integrity and functionality . It is , however , important that these toxins do not form pores in the producing bacterium . To prevent this , bacteria initially pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "transmembrane", "proteins", "proteins", "protein", "folding", "protein", "structure", "biology", "microbiology", "host-pathogen", "interaction", "biophysics" ]	2011	Dual Chaperone Role of the C-Terminal Propeptide in Folding and Oligomerization of the Pore-Forming Toxin Aerolysin
Persistent infection with the hepatitis C virus ( HCV ) is a major risk factor for the development of liver cirrhosis and hepatocellular carcinoma . With an estimated about 3% of the world population infected with this virus , the lack of a prophylactic vaccine and a selective therapy , chronic hepatitis C currently is...	The hepatitis C virus ( HCV ) is a major cause of acute and chronic liver diseases worldwide . In spite of high medical need there is no selective antiviral therapy available and a prophylactic vaccine is not in sight . Their development requires cellular replication systems that have become available just recently . O...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/viral", "replication", "and", "gene", "regulation", "virology/virion", "structure,", "assembly,", "and", "egress", "gastroenterology", "and", "hepatology/hepatology", "cell", "biology", "virology", "infectious", ...	2008	Essential Role of Domain III of Nonstructural Protein 5A for Hepatitis C Virus Infectious Particle Assembly
Follicular thyroid carcinoma ( FTC ) and benign follicular adenoma ( FA ) are indistinguishable by preoperative diagnosis due to their similar histological features . Here we report the first RNA sequencing study of these tumors , with data for 30 minimally invasive FTCs ( miFTCs ) and 25 FAs . We also compared 77 clas...	Recently , The Cancer Genome Atlas proposed an improved classification of the subtypes of papillary thyroid carcinoma ( PTC ) based on gene expression profiles , which better represents cell signaling and differentiation . However , a molecular characterization of follicular thyroid carcinoma ( FTC ) , which has a grea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "endocrine", "tumors", "carcinomas", "cancers", "and", "neoplasms", "oncology", "mutation", "histology", "signaling", "cascades", "gene", "types", "mapk", "signaling", "cascades", "chromosome", "biology", "lung", "and", "intrat...	2016	Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers
Currently , the predominant onchocerciasis control strategy in Africa is annual mass drug administration ( MDA ) with ivermectin . However , there is a consensus among the global health community , supported by mathematical modelling , that onchocerciasis in Africa will not be eliminated within proposed time frameworks...	Novel and alternative strategies are required to meet the demanding control and elimination ( of infection ) goals for human onchocerciasis ( river blindness ) in Africa . Due to the overlapping distribution of onchocerciasis and loiasis ( African eye worm ) in forested areas of central Africa , millions of people livi...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion", "Scenario", "2:", "Potential", "Influence", "on", "Infection", "Resurgence" ]	[]	2015	Human Onchocerciasis: Modelling the Potential Long-term Consequences of a Vaccination Programme
Most mosquito control efforts are primarily focused on reducing the adult population size mediated by reductions in the larval population , which should lower risk of disease transmission . Although the aim of larviciding is to reduce larval abundance and thus recruitment of adults , nonlethal effects on adults are pos...	Effective control of mosquito-borne diseases like dengue fever has historically been achieved by controlling vector populations . The use of larvicides that kill the larval stages of the yellow fever mosquito is a critical component of effective control . However , larvicides may act together with other components of t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "larvicides", "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "animals", "viruses", "age", "groups", "developmental", "biology", "adults", "rna", ...	2016	Transstadial Effects of Bti on Traits of Aedes aegypti and Infection with Dengue Virus
As the Lyme disease bacterium Borrelia burgdorferi traverses its enzootic cycle , alternating between a tick vector and a vertebrate host , the spirochete must adapt and persist in the tick midgut under prolonged nutrient stress between blood meals . In this study , we examined the role of the stringent response in tic...	Borrelia burgdorferi , the spirochete responsible for causing Lyme disease , is maintained in nature via cycling between an Ixodes tick vector and a vertebrate host . The spirochete must adapt to and survive extreme nutrient deprivation , which may last months between blood meals , to persist in the midgut of the tick ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation
Recently diverged species typically have incomplete reproductive barriers , allowing introgression of genetic material from one species into the genomic background of the other . The role of natural selection in preventing or promoting introgression remains contentious . Because of genomic co-adaptation , some chromoso...	The role of natural selection in promoting or preventing genomic divergence between nascent species remains highly debated . As long as reproductive barriers remain incomplete , genetic material from one species is indeed exposed to natural selection into the genomic background of the other species . In some cases , ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "evolutionary", "biology/genomics", "evolutionary", "biology/plant", "genomes", "and", "evolution", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	Repeated Adaptive Introgression at a Gene under Multiallelic Balancing Selection
Escherichia coli pol V ( UmuD′2C ) , the main translesion DNA polymerase , ensures continued nascent strand extension when the cellular replicase is blocked by unrepaired DNA lesions . Pol V is characterized by low sugar selectivity , which can be further reduced by a Y11A “steric-gate” substitution in UmuC that enable...	E . coli pol V , a complex formed by umuC and umuD gene products , is a “founding” member of the Y-family of DNA polymerases that have been identified in all domains of life . The primary cellular function of Y-family polymerases is the replication of damaged DNA . We discovered that pol V is characterized by unusually...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Mechanisms Employed by Escherichia coli to Prevent Ribonucleotide Incorporation into Genomic DNA by Pol V
Collectively classified as white-rot fungi , certain basidiomycetes efficiently degrade the major structural polymers of wood cell walls . A small subset of these Agaricomycetes , exemplified by Phlebiopsis gigantea , is capable of colonizing freshly exposed conifer sapwood despite its high content of extractives , whi...	The wood decay fungus Phlebiopsis gigantea degrades all components of plant cell walls and is uniquely able to rapidly colonize freshly exposed conifer sapwood . However , mechanisms underlying its conversion of lignocellulose and resinous extractives have not been explored . We report here analyses of the genetic repe...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "sequencing", "techniques", "genome", "expression", "analysis", "functional", "genomics", "gene", "regulation", "microbiology", "genome", "sequencing", "fungi", "genome", "analysis", "molecular", "genetics", "molecular", "biology", "techniques", "applied", ...	2014	Analysis of the Phlebiopsis gigantea Genome, Transcriptome and Secretome Provides Insight into Its Pioneer Colonization Strategies of Wood
We present a computational method for the reaction-based de novo design of drug-like molecules . The software DOGS ( Design of Genuine Structures ) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds . The quality of the designed compounds is assessed by a graph ...	The computer program DOGS aims at the automated generation of new bioactive compounds . Only a single known reference compound is required to have the computer come up with suggestions for potentially isofunctional molecules . A specific feature of the algorithm is its capability to propose a synthesis plan for each de...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "biotechnology", "computer", "applications", "computer", "science", "medicinal", "chemistry", "organic", "chemistry", "chemistry", "biology" ]	2012	DOGS: Reaction-Driven de novo Design of Bioactive Compounds
The photoreceptors of the Drosophila compound eye are a classical model for studying cell fate specification . Photoreceptors ( PRs ) are organized in bundles of eight cells with two major types – inner PRs involved in color vision and outer PRs involved in motion detection . In wild type flies , most PRs express a sin...	Complex networks of genetic interactions govern the development of multicellular organisms . One of the best-characterized networks governs the development of the fruit-fly retina , a highly organized , three-dimensional organ composed of a hexagonal grid of eight types of photoreceptor neurons . Each photoreceptor res...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "developmental", "biology", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Stochastic De-repression of Rhodopsins in Single Photoreceptors of the Fly Retina
Drug resistance of Salmonella enterica serovar Typhi ( Salmonella Typhi ) to first-line antibiotics is emerging in Central Africa . Although increased use of fluoroquinolones is associated with spread of resistance , Salmonella Typhi with decreased ciprofloxacin susceptibility ( DCS ) has rarely been reported in Centra...	Typhoid fever , caused by infection with Salmonella enterica serovar Typhi ( Salmonella Typhi ) , is an important health problem in sub-Saharan Africa . Multidrug resistance of Salmonella Typhi to the first line antibiotics is spreading and treatment of typhoid fever increasingly relies on fluoroquinolone antibiotics s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "salmonellosis", "salmonella" ]	2012	Salmonella Typhi in the Democratic Republic of the Congo: Fluoroquinolone Decreased Susceptibility on the Rise
The important human pathogen Pseudomonas aeruginosa has been linked to numerous biofilm-related chronic infections . Here , we demonstrate that biofilm formation following the transition to the surface attached lifestyle is regulated by three previously undescribed two-component systems: BfiSR ( PA4196-4197 ) harboring...	Biofilms are complex communities of microorganisms encased in a matrix and attached to surfaces . It is well recognized that biofilm cells differ from their free swimming counterparts with respect to gene expression , protein production , and resistance to antibiotics and the human immune system . However , little is k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "microbiology/microbial", "physiology", "and", "metabolism", "genetics", "and", "genomics/gene", "function", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "infectious", "diseases/bacterial", "infections", "micro...	2009	A Novel Signaling Network Essential for Regulating Pseudomonas aeruginosa Biofilm Development
O-linked glycosylation is an important post-translational modification of mucin-type protein , changes to which are important biomarkers of cancer . For this study of the enzymes of O-glycosylation , we developed a shorthand notation for representing GalNAc-linked oligosaccharides , a method for their graphical interpr...	Our objective being to model the enzymes of mucin-type O-linked glycosylation , we first developed a model language to represent O-glycan structures succinctly in linear string form , to which a set of pattern-matching rules was then applied to simulate the activities of a set of 25 glycosyltransferase and sulfotransfe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "linguistics", "chemical", "compounds", "enzymes", "enzymology", "social", "sciences", "carbohydrates", "neuroscience", "organic", "compounds", "cognitive", "psychology", "glycosylation", "glycoproteins", "language", "proteins", "chemistry", "grammar", "biochemistry", "enzyme...	2016	A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts
Feedback modules , which appear ubiquitously in biological regulations , are often subject to disturbances from the input , leading to fluctuations in the output . Thus , the question becomes how a feedback system can produce a faithful response with a noisy input . We employed multiple time scale analysis , Fluctuatio...	Many biological systems use feedback loops to regulate dynamic interactions among different genes and proteins . Here , we ask how interlinked feedback loops control the timing of signal transductions and responses and , consequently , attenuate noise . Drawing on simple modeling along with both analytical insights and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/signaling", "networks", "mathematics", "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2010	A Critical Quantity for Noise Attenuation in Feedback Systems
The Wolbachia strategy aims to manipulate mosquito populations to make them incapable of transmitting dengue viruses between people . To test its efficacy , this strategy requires field trials . Public consultation and engagement are recognized as critical to the future success of these programs , but questions remain ...	In recent years , a number of new strategies using novel technologies for the control of dengue fever control have emerged . These strategies are notably different from their predecessors and not without controversy . Many also require open release field trials to test their efficacy . Public consultation and engagemen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "public", "and", "occupational", "health", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "sociology", "social", "sciences", "anthropology" ]	2014	Designing a Community Engagement Framework for a New Dengue Control Method: A Case Study from Central Vietnam
Plasmodium knowlesi , a malaria parasite originally thought to be restricted to macaques in Southeast Asia , has recently been recognized as a significant cause of human malaria . Unlike the benign and morphologically similar P . malariae , these parasites can lead to fatal infections . Malaria parasites , including P ...	We recently described the first focus of human infections with P . knowlesi , a malaria parasite of monkeys , and subsequently reported that these infections can be fatal . Whether mosquito transmission of infection depended on the monkey reservoir or was maintained by the human population was unknown . In the area of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "organismal", "evolution", "public", "health", "and", "epidemiology", "ecology", "epidemiology", "biology", "evolutionary", "biology", "zoology", "parasitology" ]	2011	Plasmodium knowlesi: Reservoir Hosts and Tracking the Emergence in Humans and Macaques
Genotype I ( GI ) virus has replaced genotype III ( GIII ) virus as the dominant Japanese encephalitis virus ( JEV ) in the epidemic area of Asia . The mechanism underlying the genotype replacement remains unclear . Therefore , we focused our current study on investigating the roles of mosquito vector and amplifying ho...	Flaviviral vertebrate amplifying host ( s ) , invertebrate vector ( s ) , genetics , and environmental factors shape the viral geographical distribution and epidemic disease pattern . Newly emerging dengue virus genotypes , West Nile virus clades , or Zika virus strains exhibited an enhancement in mosquito vector compe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "urology", "invertebrates", "medicine", "and", "health", "sciences", "microbiology", "vertebrates", "animals", "mammals", "viruses", "rna", "viruses", "insect", "vectors", "infectious", "diseases", "swine", "birds", "gamefowl", "viral", "replication", "fowl", "disease",...	2019	NS2B/NS3 mutations enhance the infectivity of genotype I Japanese encephalitis virus in amplifying hosts
Prior to the meiotic divisions , dynamic chromosome reorganizations including pairing , synapsis , and recombination of maternal and paternal chromosome pairs must occur in a highly regulated fashion during meiotic prophase . How chromosomes identify each other's homology and exclusively pair and synapse with their hom...	Meiosis creates gametes by distributing diploid genomes containing homologous chromosome pairs into daughter cells that receive only one of each chromosome . To segregate correctly at the first meiotic division , chromosomes must pair and synapse with their homologous partners , and undergo crossover recombination , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "cell", "biology", "synapsis", "chromosome", "biology", "cell", "cycle", "and", "cell", "division", "biology", "and", "life", "sciences", "cell", "processes", "meiotic", "prophase" ]	2014	Protein Phosphatase 4 Promotes Chromosome Pairing and Synapsis, and Contributes to Maintaining Crossover Competence with Increasing Age
The seed maturation program only occurs during late embryogenesis , and repression of the program is pivotal for seedling development . However , the mechanism through which this repression is achieved in vegetative tissues is poorly understood . Here we report a microRNA ( miRNA ) –mediated repression mechanism operat...	Seed development can be conceptually divided into two phases: namely the morphogenesis phase , in which cell division is active and all the major organs are formed , and the maturation phase , in which cells enlarge and storage reserves are synthesized and accumulated . Expression of the seed maturation program is tigh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "growth", "and", "development", "plant", "biology", "plant", "genetics", "biology" ]	2012	MicroRNA–Mediated Repression of the Seed Maturation Program during Vegetative Development in Arabidopsis
Nigeria carries the highest burden and diversity of neglected tropical diseases ( NTDs ) in sub-Saharan Africa and is preparing to scale up its efforts to control/eliminate these diseases . To achieve this it will require a range of internal technical support and expertise for mapping , monitoring and evaluating , oper...	Nigeria carries the highest burden and diversity of neglected tropical diseases ( NTDs ) in sub-Saharan Africa and is preparing to increase the control and elimination of these diseases . The aim of this study was to provide information on the disease focus and type of studies carried out by scientists working on lymph...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "medicine", "and", "health", "sciences", "disease", "eradication", "global", "health", "vector-borne", "diseases", "infectious", "disease", "control" ]	2014	Neglected Tropical Diseases: A Systematic Evaluation of Research Capacity in Nigeria
Schistosomiasis is the most important helminthic disease of humanity in terms of morbidity and mortality . Facile manipulation of schistosomes using lentiviruses would enable advances in functional genomics in these and related neglected tropical diseases pathogens including tapeworms , and including their non-dividing...	Schistosomiasis is a major neglected tropical disease ( NTD ) , which afflicts > 200 million people in developing countries . The genome sequence of the schistosome parasite has been decoded; it includes > 10 , 000 genes . New approaches to control this NTD are sought and genomic information may provide targets for new...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "helminths", "pathogens", "microbiology", "viral", "structure", "genomic", "library", "construction",...	2016	HIV-1 Integrates Widely throughout the Genome of the Human Blood Fluke Schistosoma mansoni
The lack of a deep understanding of how proteins interact remains an important roadblock in advancing efforts to identify binding partners and uncover the corresponding regulatory mechanisms of the functions they mediate . Understanding protein-protein interactions is also essential for designing specific chemical modi...	Protein–protein interactions are key to understand the molecular level mechanisms of regulation in the cell . However , there is still a limited understanding of what distinguishes a protein-protein binding site from the rest of the surface . This lack of knowledge is manifested in the relatively low accuracy of comput...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "chemical", "characterization", "medicine", "and", "health", "sciences", "immune", "physiology", "protein", "interactions", "statistics", "immunology", "mathematics", "forecasting", "receptor-ligand", "binding", "assay", "protein", "structure", "prediction", "protein", "str...	2019	Protein—protein binding supersites
Hepatitis C virus ( HCV ) is a positive-strand RNA virus that frequently causes persistent infections and is uniquely associated with the development of hepatocellular carcinoma . While the mechanism ( s ) by which the virus promotes cancer are poorly defined , previous studies indicate that the HCV RNA-dependent RNA p...	Persons infected with hepatitis C virus ( HCV ) are at increased risk for liver cancer . This is remarkable because HCV is an RNA virus with replication confined to the cytoplasm and no potential for integration of its genome into host cell DNA . While it is likely that chronic inflammation contributes to liver cancer ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "oncology", "viruses", "infectious", "diseases", "hepatitis", "ubiqutin", "ligase", "cell", "biology", "gastroenterology", "and", "hepatology", "virology", "rna", "polymerase", "hepatocellular", "carcinoma" ]	2007	Hepatitis C Virus Induces E6AP-Dependent Degradation of the Retinoblastoma Protein
Centromere behavior is specialized in meiosis I , so that sister chromatids of homologous chromosomes are pulled toward the same side of the spindle ( through kinetochore mono-orientation ) and chromosome number is reduced . Factors required for mono-orientation have been identified in yeast . However , comparatively l...	There are two types of cell division in eukaryotes . Mitosis produces cells with identical copies of the genome , while meiosis produces gametes with half the number of chromosomes found in the parent cell . Faithful genome inheritance is controlled by centromeres , chromosomal structures that allow duplicated chromoso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "plant", "science", "molecular", "cell", "biology", "cell", "biology", "chromosome", "biology", "plant", "biology", "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	Meiosis-Specific Loading of the Centromere-Specific Histone CENH3 in Arabidopsis thaliana
Insulin-like peptides ( ILPs ) play highly conserved roles in development and physiology . Most animal genomes encode multiple ILPs . Here we identify mechanisms for how the forty Caenorhabditis elegans ILPs coordinate diverse processes , including development , reproduction , longevity and several specific stress resp...	Insulin signaling is widely implicated in regulating diverse physiological processes ranging from metabolism to longevity across many animal species . Many animals have multiple insulin-like peptides that can regulate the activity of this signaling pathway . For example , while humans have ten , including the well-stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "neurochemistry", "immune", "physiology", "caenorhabditis", "gene", "regulation", "animals", "hormones", "gene", "function", "endocrine", "physiology", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "organ...	2014	An Insulin-to-Insulin Regulatory Network Orchestrates Phenotypic Specificity in Development and Physiology
Mass drug administration ( MDA ) is part of the current trachoma control strategy , but it can be costly and results in many uninfected individuals receiving treatment . Here we explore whether alternative , targeted approaches are effective antibiotic-sparing strategies . We analysed data on the prevalence of ocular i...	Repeated ocular infection with the bacterium Chlamydia trachomatis leads to the development of trachoma , a major cause of infectious blindness worldwide . Mass distribution of antibiotics , a component of the current trachoma control strategy , has had success in reducing infection in some areas , but results in a lar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "ophthalmology/eye", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Targeting Antibiotics to Households for Trachoma Control
Five independent groups have reported microarray studies that identify dozens of rhythmically expressed genes in the fruit fly Drosophila melanogaster . Limited overlap among the lists of discovered genes makes it difficult to determine which , if any , exhibit truly rhythmic patterns of expression . We reanalyzed data...	Circadian genes regulate many of life's most essential processes , from sleeping and eating to cellular metabolism , learning , and much more . Many of these genes exhibit cyclic transcript expression , a characteristic utilized by an ever-expanding corpus of microarray-based studies to discover additional circadian ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "mathematics", "cell", "biology", "computational", "biology", "neuroscience", "drosophila", "genetics", "and", "genomics" ]	2007	Meta-Analysis of Drosophila Circadian Microarray Studies Identifies a Novel Set of Rhythmically Expressed Genes
The development of classically activated monocytic cells ( M1 ) is a prerequisite for effective elimination of parasites , including African trypanosomes . However , persistent activation of M1 that produce pathogenic molecules such as TNF and NO contributes to the development of trypanosome infection-associated tissue...	Most infections are associated with host inflammatory responses that can result in multiple organ failure and death . It is therefore essential to understand the mechanisms balancing host immune response and tissue damage . Mouse models of African trypanosome infection represent valuable tools to study the mechanisms c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immunity", "to", "infections", "pathology/immunology" ]	2010	Tip-DC Development during Parasitic Infection Is Regulated by IL-10 and Requires CCL2/CCR2, IFN-γ and MyD88 Signaling
The human body is a complex organism , the gross mechanical properties of which are enabled by an interconnected musculoskeletal network controlled by the nervous system . The nature of musculoskeletal interconnection facilitates stability , voluntary movement , and robustness to injury . However , a fundamental unders...	While network science is frequently used to characterize networks from genomics , proteomics , and connectomics , its utility in understanding biomechanics , orthopedics , and physical therapy has remained largely unexplored . Indeed , current clinical practice and knowledge regarding the musculoskeletal system largely...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "eye", "muscles", "traumatic", "injury", "medicine", "and", "health", "sciences", "ocular", "anatomy", "mathematical", "models", "bone", "network", "analysis", "bioassays", "and", "physiological", "analysis", "muscle", "functions", "research", "and", "analysis", "meth...	2018	Structure, function, and control of the human musculoskeletal network
The N-linked glycosylation motif at amino acid position 154–156 of the envelope ( E ) protein of West Nile virus ( WNV ) is linked to enhanced murine neuroinvasiveness , avian pathogenicity and vector competence . Naturally occurring isolates with altered E protein glycosylation patterns have been observed in WNV isola...	West Nile virus ( WNV ) has been responsible for the largest human encephalitis epidemics in the continental United States . Avians and Culex mosquitoes are the primary hosts for WNV natural transmission cycles . The envelope ( E ) protein for WNV contains a variable N-linked glycosylation motif which influences avian ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "saliva", "animals", "viruses", "rna", "viruses", "sequence", "motif", "analysis", "glycosylation", "ins...	2019	N-linked glycosylation of the West Nile virus envelope protein is not a requisite for avian virulence or vector competence
Craniofacial abnormalities , including facial skeletal defects , comprise approximately one-third of all birth defects in humans . Since most bones in the face derive from cranial neural crest cells ( CNCCs ) , which are multipotent stem cells , craniofacial bone disorders are largely attributed to defects in CNCCs . H...	Craniofacial abnormalities , including facial skeletal defects , comprise approximately one-third of all birth defects in humans . Since most bones in the face derive from neural crest cells , which are multipotent stem cells , craniofacial bone disorders are largely attributed to defects in neural crest cells . Howeve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "face", "cancer", "risk", "factors", "neuroscience", "oncology", "dna", "damage", "developmental", "biology", "frontal", "bones", "organism", "development", "stem", "cells", "skeleton", "dna", "embryos", "bone", "development", ...	2018	BRCA1 and BRCA2 tumor suppressors in neural crest cells are essential for craniofacial bone development
The environmental pathogen , Mycobacterium ulcerans ( MU ) can infect both humans and animals and cause Buruli ulcer ( BU ) disease . However , its mode ( s ) of transmission from the colonized environment to human/animal hosts remain unclear . In Australia , MU can infect both wildlife and domestic mammals . Till date...	Buruli ulcer ( BU ) remains a major Public Health problem in rural communities in sub-Saharan Africa . There are several reports of the occurrence of BU in Wildlife as well as domestic animals in Australia leading to the suggestion that animals may play a role in the transmission of MU to humans . Report of BU in anima...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "ruminants", "domestic", "animals", "geographical", "locations", "tropical", "diseases", "vertebrates", "dogs", "animals", "mammals", "bacterial", "diseases", "sign...	2018	Domestic animals infected with Mycobacterium ulcerans—Implications for transmission to humans
Influenza viruses cause seasonal flu each year and pandemics or epidemic sporadically , posing a major threat to public health . Recently , a new influenza D virus ( IDV ) was isolated from pigs and cattle . Here , we reveal that the IDV utilizes 9-O-acetylated sialic acids as its receptor for virus entry . Then , we d...	Of the Orthomyxoviridae family of viruses , influenza A , B and C viruses all can cause disease in humans . Recently , a novel influenza D virus ( IDV ) with approximately 50% amino acid identity to human influenza C virus ( ICV ) is found in pigs and cattle . This novel virus can establish infection in other mammals i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "livestock", "medicine", "and", "health", "sciences", "chemical", "characterization", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "ruminants", "enzymes", "pathogens", "condensed", "matter", "physics", "enzymology", "vertebrates", "microbiology", ...	2016	An Open Receptor-Binding Cavity of Hemagglutinin-Esterase-Fusion Glycoprotein from Newly-Identified Influenza D Virus: Basis for Its Broad Cell Tropism
We describe the rudolph mouse , a mutant with striking defects in both central nervous system and skeletal development . Rudolph is an allele of the cholesterol biosynthetic enzyme , hydroxysteroid ( 17-beta ) dehydrogenase 7 , which is an intriguing finding given the recent implication of oxysterols in mediating intra...	The molecules and signaling pathways that regulate growth and patterning of the developing embryo are still being elucidated , and one valuable experimental approach is the use of animal models , such as the mouse . We have identified a recessive mutation in the mouse , rudolph , that causes abnormal forebrain developm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "biochemistry", "developmental", "biology", "lipids", "embryology", "model", "organisms", "genetic", "mutation", "genetics", "biology", "morphogenesis", "sterols", "genetics", "and", "genomics" ]	2011	Cholesterol Metabolism Is Required for Intracellular Hedgehog Signal Transduction In Vivo
Gonad differentiation is a crucial step conditioning the future fertility of individuals and most of the master genes involved in this process have been investigated in detail . However , transcriptomic analyses of developing gonads from different animal models have revealed that hundreds of genes present sexually dimo...	DMXL2 gene dysfunction underlies various human diseases , including breast cancer , non-syndromic hearing loss , and polyendocrine-polyneuropathy syndrome , demonstrating the large range of potential actions of DMXL2 . We show here that Dmxl2 expression is crucial for survival in mice , as neonates die within hours of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "epithelial", "cells", "germ", "cells", "sertoli", "cells", "developmental", "biology", "sperm", "animal", "cells", "gene", "expression", "biological", "tissue", "testes", "ovaries", "anatomy...	2019	Dual role of DMXL2 in olfactory information transmission and the first wave of spermatogenesis
Several studies have suggested investigation of health beliefs in children to be an important pre-condition for primary prevention of disease . However , little effort has been made to understand these in the context of podoconiosis . This study therefore aimed to explore the health beliefs of school-age rural children...	Podoconiosis is an example of a lifestyle-related disease that develops after childhood and affects millions of people with little experience of preventive behaviour . It is caused by prolonged barefoot exposure to irritant mineral particles , accompanied by inherited susceptibility . Children with a family history of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "biological", "locomotion", "pediatrics", "age", "groups", "human", "families", "neglected", "tropical", "diseases", "families", "pub...	2017	Health beliefs of school-age rural children in podoconiosis-affected families: A qualitative study in Southern Ethiopia
Group A streptococcus ( GAS ) causes a wide variety of human diseases , and at the same time , GAS can also circulate without producing symptoms , similar to its close commensal relative , group G streptococcus ( GGS ) . We previously identified , by transposon-tagged mutagenesis , the streptococcal invasion locus ( si...	Cell-to-cell communication in bacteria is termed quorum-sensing ( QS ) , which is triggered by signaling molecules called autoinducers . In streptococci , autoinducers are synthesized as immature peptides that are processed , secreted , and then sensed by two-component systems ( TCSs ) . As a result , the autoinducer's...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "genetics", "and", "genomics/bioinformatics", "microbiology/medical", "microbiology" ]	2009	Functional Analysis of the Quorum-Sensing Streptococcal Invasion Locus (sil)
Alpha-synuclein ( aSyn ) is the main component of proteinaceous inclusions known as Lewy bodies ( LBs ) , the typical pathological hallmark of Parkinson's disease ( PD ) and other synucleinopathies . Although aSyn is phosphorylated at low levels under physiological conditions , it is estimated that ∼90% of aSyn in LBs ...	Protein aggregation is a common hallmark in neurodegenerative disorders , but is also associated with phenotypic plasticity in a variety of organisms , including yeasts . Alpha-synuclein ( aSyn ) forms aggregates that are typical of synucleinopathies , and is phosphorylated at S129 , but the significance of phosphoryla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "cellular", "neuroscience", "model", "organisms", "biology", "and", "life", "sciences", "yeast", "and", "fungal", "models", "neuroscience", "research", "and", "analysis", "methods" ]	2014	Phosphorylation Modulates Clearance of Alpha-Synuclein Inclusions in a Yeast Model of Parkinson's Disease
Living in a social environment requires the ability to respond to specific social stimuli and to incorporate information obtained from prior interactions into future ones . One of the mechanisms that facilitates social interaction is pheromone-based communication . In Drosophila melanogaster , the male-specific pheromo...	In this work , we used Drosophila melanogaster as a model organism to explore a basic question in neuroscience: why do different individuals experience the same sensory stimuli , such as smell differently , and moreover , why does one individual experience identical stimuli differently on different occasions ? Focusing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "rna", "extraction", "neuroscience", "odorant", "binding", "proteins", "extraction", "techniques", "research", "and", "analysis", "methods", "aggression", "transcriptional", "control", "animal", "cells", "proteins", "behavior", "gene", "expression", ...	2018	Odorant binding protein 69a connects social interaction to modulation of social responsiveness in Drosophila
We experimentally and numerically investigate the evolutionary dynamics of four competing strains of E . coli with differing expansion velocities in radially expanding colonies . We compare experimental measurements of the average fraction , correlation functions between strains , and the relative rates of genetic doma...	Population expansions occur naturally during the spread of invasive species and have played a role in our evolutionary history when humans migrated out of Africa . We use a colony of non-motile bacteria expanding into unoccupied , nutrient-rich territory on an agar plate as a model system to explore how an expanding po...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "heterozygosity", "organismal", "evolution", "population", "genetics", "radii", "microbiology", "mathematical", "models", "geometry", "simulation", "and", "modeling", "luminescent", "proteins", "mathematics", "yellow", "fluorescent", "protein", "microbial", ...	2017	Genetic drift and selection in many-allele range expansions
Schistosome infection begins with the penetration of cercariae through healthy unbroken host skin . This process leads to the transformation of the free-living larvae into obligate parasites called schistosomula . This irreversible transformation , which occurs in as little as two hours , involves casting the cercaria ...	Schistosomiasis is an endemic parasitic disease affecting ∼200 million people in the most socioeconomically deprived regions of the world . Human infection occurs during water contact where free-living larvae called cercariae penetrate host skin and become parasitic organisms called schistosomula . This stage represent...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome", "expression", "analysis", "gene", "expression", "genetics", "biology", "genomics", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "parasitology" ]	2013	Comparative Study of Transcriptome Profiles of Mechanical- and Skin-Transformed Schistosoma mansoni Schistosomula

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