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During a primary influenza infection , cytotoxic CD8+ T cells need to infiltrate the infected airways and engage virus-infected epithelial cells . The factors that regulate T cell motility in the infected airway tissue are not well known . To more precisely study T cell infiltration of the airways , we developed an exp...	Influenza virus infects the cells that line the trachea and lung airways . Virus-specific cytotoxic ( cell killing ) T cells are the first line of adaptive immunity responsible for elimination of infected cells . We studied the cell movement , or motility , of these T cells responding to infection in the mouse trachea ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "respiratory", "infections", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "pulmonology", "viruses...	2016	Live Imaging of Influenza Infection of the Trachea Reveals Dynamic Regulation of CD8+ T Cell Motility by Antigen
The identification of a new generation of potent broadly neutralizing HIV-1 antibodies ( bnAbs ) has generated substantial interest in their potential use for the prevention and/or treatment of HIV-1 infection . While combinations of bnAbs targeting distinct epitopes on the viral envelope ( Env ) will likely be require...	In recent years , a new generation of monoclonal antibodies has been isolated from HIV-1 infected individuals that exhibit broad and potent neutralizing activity when tested against diverse strains of virus . There is a high level of interest in the field in determining if these antibodies can be used to prevent or tre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "antiretrovirals", "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "immunology", "microbiology", "retroviruses", "viruses", "im...	2016	Optimal Combinations of Broadly Neutralizing Antibodies for Prevention and Treatment of HIV-1 Clade C Infection
Bacterial Toxin-Antitoxin systems ( TAS ) are involved in key biological functions including plasmid maintenance , defense against phages , persistence and virulence . They are found in nearly all phyla and classified into 6 different types based on the mode of inactivation of the toxin , with the type II TAS being the...	TASmania offers an extensive annotation of TA loci in a very large database of bacterial genomes , which represents a resource of crucial importance for the microbiology community . TASmania supports i ) the discovery of new TA families; ii ) the design of a robust experimental strategy by taking into account potential...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "markov", "models", "microbiology", "operons", "toxicology", "toxic", "agents", "mathematics", "genome", "analysis", "bacterial", "genetics", "dna", "microbi...	2019	TASmania: A bacterial Toxin-Antitoxin Systems database
The four-subunit Negative Elongation Factor ( NELF ) is a major regulator of RNA Polymerase II ( Pol II ) pausing . The subunit NELF-E contains a conserved RNA Recognition Motif ( RRM ) and is proposed to facilitate Poll II pausing through its association with nascent transcribed RNA . However , conflicting ideas have ...	RNA polymerase II ( Pol II ) is a molecular machine that is responsible for transcribing all protein coding genes in the eukaryotic genome . Transcription by Pol II is a highly regulated process consisting of several rate-limiting steps . During transcription elongation , a number of transcription factors are essential...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biomacromolecule-ligand", "interactions", "biochemistry", "rna", "genome", "analysis", "tools", "genomics", "protein", "interactions", "nucleic", "acids", "proteins", "gene", "expression", "genetics", "regulatory", "proteins", "biology", "recombinant", "pr...	2014	Defining NELF-E RNA Binding in HIV-1 and Promoter-Proximal Pause Regions
Gene duplication was prevalent during hominoid evolution , yet little is known about the functional fate of new ape gene copies . We characterized the CDC14B cell cycle gene and the functional evolution of its hominoid-specific daughter gene , CDC14Bretro . We found that CDC14B encodes four different splice isoforms th...	Many new gene copies emerged by gene duplication in human and ape ( hominoid ) ancestors . However , little is known with respect to their functional evolution . We used a combination of evolutionary analyses and cell biology experiments to unveil the adaptive evolution of the hominoid-specific CDC14Bretro gene , which...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "evolutionary", "biology" ]	2008	Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein
The organization of cells , emerging from cell–cell interactions , can give rise to collective properties . These properties are adaptive when together cells can face environmental challenges that they separately cannot . One particular challenge that is important for microorganisms is migration . In this study , we sh...	Some problems can be solved only when individuals act together . This applies to bacteria in the same way that it applies to humans . Here we study how bacteria overcome the environmental challenge of migration over a solid surface by bundling their forces . Migration can be a significant environmental challenge for ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	From Cell Differentiation to Cell Collectives: Bacillus subtilis Uses Division of Labor to Migrate
A research priority for Plasmodium vivax malaria is to improve our understanding of the spatial distribution of risk and its relationship with the burden of P . vivax disease in human populations . The aim of the research outlined in this article is to provide a contemporary evidence-based map of the global spatial ext...	Growing evidence shows that Plasmodium vivax malaria is clinically less benign than has been commonly believed . In addition , it is the most widely distributed species of human malaria and is likely to cause more illness in certain regions than the more extensively studied P . falciparum malaria . Understanding where ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "public", "health", "and", "epidemiology/global", "health" ]	2010	The International Limits and Population at Risk of Plasmodium vivax Transmission in 2009
This paper describes a general model that subsumes many parametric models for continuous data . The model comprises hidden layers of state-space or dynamic causal models , arranged so that the output of one provides input to another . The ensuing hierarchy furnishes a model for many types of data , of arbitrary complex...	Models are essential to make sense of scientific data , but they may also play a central role in how we assimilate sensory information . In this paper , we introduce a general model that generates or predicts diverse sorts of data . As such , it subsumes many common models used in data analysis and statistical testing ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "neuroscience", "neuroscience/theoretical", "neuroscience" ]	2008	Hierarchical Models in the Brain
Trachoma is thought to be common over large parts of Southern Sudan . However , many areas of the country , particularly west of the Nile , have not yet been surveyed . The aim of this study was to confirm whether trachoma extends into Western Equatoria State from neighboring Central Equatoria , where trachoma is highl...	Baseline data on trachoma prevalence is a prerequisite for intervention . Prior to the present study , all surveys in Southern Sudan reported trachoma prevalences that exceeded the threshold for large-scale intervention . This gave rise to the notion that the disease may be endemic throughout the country . The present ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	Trachoma in Western Equatoria State, Southern Sudan: Implications for National Control
In Lao People’s Democratic Republic pigs are kept in close contact with families . Human risk of infection with pig zoonoses arises from direct contact and consumption of unsafe pig products . This cross-sectional study was conducted in Luang Prabang ( north ) and Savannakhet ( central-south ) Provinces . A total of 59...	In Lao PDR , pigs are an important source of food and income and are kept by many rural residents . This study investigated five diseases that are transmitted between pigs and humans ( zoonoses ) , namely hepatitis E , Japanese encephalitis , trichinellosis , cysticercosis and taeniasis . Humans and pigs in Lao PDR wer...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "lao", "people", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "parasitic", "diseases", "animals", "mammals", "health...	2016	Endemicity of Zoonotic Diseases in Pigs and Humans in Lowland and Upland Lao PDR: Identification of Socio-cultural Risk Factors
In the Gran Chaco region , control of Triatoma infestans has been limited by persistent domestic infestations despite the efforts of the Vector Control Services . In Paraguay , this region is the highest endemic area in the country , showing high levels of indoor and outdoor infestation . Although sylvatic T . infestan...	Confirmation of sylvatic colonies of Triatoma infestans has a significant connotation for Paraguay . Prior to our findings , we believed this vector —unlike in other regions of the Gran Chaco—was living exclusively in domestic and peridomestic habitats . We never considered the possibility of sylvatic species re-infest...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "community", "ecology", "zoology", "ecology", "entomology", "biology", "species", "interactions", "biodiversity", "parasitology" ]	2011	First Report of Colonies of Sylvatic Triatoma infestans (Hemiptera: Reduviidae) in the Paraguayan Chaco, Using a Trained Dog
Clinical manifestations in onchocerciasis range from generalized onchocerciasis ( GEO ) to the rare but severe hyperreactive ( HO ) /sowda form . Since disease pathogenesis is associated with host inflammatory reactions , we investigated whether Th17 responses could be related to aggravated pathology in HO . Using flow...	Onchocerciasis , also known as river blindness is a tropical disease causing health and socioeconomic problems in endemic communities especially sub-Saharan Africa . The disease is transmitted by a filarial nematode called Onchocerca volvulus , which is spread by the bite of infected Simulium black flies . Characterist...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "tropical", "diseases", "parasitic", "diseases" ]	2015	Hyperreactive Onchocerciasis is Characterized by a Combination of Th17-Th2 Immune Responses and Reduced Regulatory T Cells
The human gene encoding the cleavage/polyadenylation ( C/P ) factor CstF-77 contains 21 exons . However , intron 3 ( In3 ) accounts for nearly half of the gene region , and contains a C/P site ( pA ) with medium strength , leading to short mRNA isoforms with no apparent protein products . This intron contains a weak 5′...	Autoregulation is commonly used in biological systems to control the homeostasis of certain activity , and cross-regulation coordinates multiple processes . We show that vertebrate genes encoding the cleavage/polyadenylation ( C/P ) factor CstF-77 contain a conserved intronic C/P site ( pA ) which regulates CstF-77 exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "rna", "rna", "processing", "nucleic", "acids", "gene", "expression", "biology", "molecular", "cell", "biology" ]	2013	The Conserved Intronic Cleavage and Polyadenylation Site of CstF-77 Gene Imparts Control of 3′ End Processing Activity through Feedback Autoregulation and by U1 snRNP
Leishmania donovani is the main cause of visceral leishmaniasis ( VL ) in East Africa . Differences between northern Ethiopia/Sudan ( NE ) and southern Ethiopia ( SE ) in ecology , vectors , and patient sensitivity to drug treatment have been described , however the relationship between differences in parasite genotype...	Approximately 200 , 000–400 , 000 new cases of visceral leishmaniasis ( VL ) occur annually resulting in an estimated 40 , 000 deaths . Almost 90% of the reported cases are caused by the Leishmania donovani occurring primarily in East Africa and the Indian subcontinent . Parasites in East Africa are more polymorphic th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "spleen", "population", "genetics", "ploidy", "tropical", "diseases", "cloning", "departures", "from", "diploidy", "parasitic", "protozoans", "parasitic", "diseases", "protozoans", "leishmania", "copy", "n...	2018	Genome wide comparison of Ethiopian Leishmania donovani strains reveals differences potentially related to parasite survival
RNA-binding proteins ( RBP ) regulate numerous aspects of co- and post-transcriptional gene expression in cancer cells . Here , we demonstrate that RBP , fragile X-related protein 1 ( FXR1 ) , plays an essential role in cellular senescence by utilizing mRNA turnover pathway . We report that overexpressed FXR1 in head a...	Understanding the mechanisms underlying evasion of cellular senescence in tumor cells is expected to provide better treatment outcomes . Here , we identify RNA-binding proteins FXR1 ( Fragile X-Related protein 1 ) , that is overexpressed in oral cancer tissues and cells bypasses cellular senescence through p53/p21-depe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfection", "rna-binding", "proteins", "medicine", "and", "health", "sciences", "luciferase", "senescence", "enzymes", "cell", "cycle", "and", "cell", "division", "carcinomas", "cell", "processes", "enzymology", "cancers", "and", "neoplasms", "oncology", "physiologi...	2016	RNA-Binding Protein FXR1 Regulates p21 and TERC RNA to Bypass p53-Mediated Cellular Senescence in OSCC
The Caenorhabditis elegans spermatheca is a myoepithelial tube that stores sperm and undergoes cycles of stretching and constriction as oocytes enter , are fertilized , and exit into the uterus . FLN-1/filamin , a stretch-sensitive structural and signaling scaffold , and PLC-1/phospholipase C-ε , an enzyme that generat...	During organism development and normal physiological function cells sense , integrate , and respond to a variety of cues or signals including biochemical and mechanical stimuli . In this study we used Caenorhabditis elegans , a small transparent worm , to study filamin ( FLN-1 ) , a structural protein that may act as a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "cellular", "structures", "caenorhabditis", "elegans", "signal", "transduction", "animal", "genetics", "model", "organisms", "signaling", "in", "cellular", "processes", "genetics", "biology", "molecular", "cell", "biology", "calcium", "signaling", "g...	2013	Filamin and Phospholipase C-ε Are Required for Calcium Signaling in the Caenorhabditis elegans Spermatheca
Group A Streptococcus ( GAS ) has developed a broad arsenal of virulence factors that serve to circumvent host defense mechanisms . The virulence factor DNase Sda1 of the hyperinvasive M1T1 GAS clone degrades DNA-based neutrophil extracellular traps allowing GAS to escape extracellular killing . TLR9 is activated by un...	Group A Streptococcus ( GAS ) ranks among the top ten human pathogens causing fatal disease . GAS possesses an arsenal of virulence factors that circumvent the primary mammalian defence strategies , the innate immune system . Toll-like receptors ( TLRs ) , allow the host to detect pathogens by recognizing structures or...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	DNase Sda1 Allows Invasive M1T1 Group A Streptococcus to Prevent TLR9-Dependent Recognition
Probe-based or mixed solvent molecular dynamics simulation is a useful approach for the identification and characterization of druggable sites in drug targets . However , thus far the method has been applied only to soluble proteins . A major reason for this is the potential effect of the probe molecules on membrane st...	We introduce a simulation-based method to identify allosteric ligand binding sites in membrane-associated proteins for which existing methods are inadequate . We applied the method on two mutant forms of an oncogenic protein called K-Ras . We show that the way in which the protein interacts with membrane is an importan...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2015	pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins
Polyunsaturated fatty acids ( PUFAs ) form a class of essential micronutrients that play a vital role in development , cardiovascular health , and immunity . The influence of lipids on the immune response is both complex and diverse , with multiple studies pointing to the beneficial effects of long-chain fatty acids in...	Polyunsaturated fatty acids are vital for optimal physiological functions , including immunity . Much of these effects are mediated by eicosanoids , which are metabolites of arachidonic acid ( AA ) and eicosapentaenoic acid ( EPA ) . In mammals , PUFAs cannot be synthesized de novo . They are produced from essential di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/genetics", "of", "the", "immune", "system", "immunology/immunity", "to", "infections", "immunology/innate", "immunity" ]	2008	Gamma-Linolenic and Stearidonic Acids Are Required for Basal Immunity in Caenorhabditis elegans through Their Effects on p38 MAP Kinase Activity
In the enterobacterial species Escherichia coli and Salmonella enterica , expression of horizontally acquired genes with a higher than average AT content is repressed by the nucleoid-associated protein H-NS . A classical example of an H-NS–repressed locus is the bgl ( aryl-β , D-glucoside ) operon of E . coli . This lo...	Horizontal gene transfer , an important mechanism in bacterial adaptation and evolution , requires mechanisms to avoid uncontrolled and possibly disadvantageous expression of the transferred genes . Recently , it was shown that the protein H-NS selectively silences genes gained by horizontal transfer in enteric bacteri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "microbiology/microbial", "evolution", "and", "genomics" ]	2009	Fate of the H-NS–Repressed bgl Operon in Evolution of Escherichia coli
Praziquantel remains the drug of choice for the worldwide treatment and control of schistosomiasis . The drug is synthesized and administered as a racemate . Use of the pure active enantiomer would be desirable since the inactive enantiomer is associated with side effects and is responsible for the extremely bitter tas...	The drug praziquantel ( PZQ ) is used very widely in both animal and human medicine , where it is the mainstay of the treatment of the neglected tropical disease schistosomiasis . The drug is currently manufactured and administered as a racemate ( 1∶1 mixture of enantiomers ) but for various reasons the large-scale pro...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "medicinal", "chemistry", "stereochemistry", "organic", "chemistry", "neglected", "tropical", "diseases", "chemistry", "heterocycle", "structures", "synthetic", "chemistry", "organic", "compounds" ]	2011	Resolution of Praziquantel
Rift Valley fever virus ( RVFV ) is an arthropod-borne phlebovirus reported to be circulating in most parts of Africa . Since 2009 , RVFV has been suspected of continuously circulating in the Union of Comoros . To estimate the incidence of RVFV antibody acquisition in the Comorian ruminant population , 191 young goats ...	Rift Valley fever ( RVF ) is a viral disease transmitted by mosquitoes to ruminants . The disease may affect humans and has a great impact on the economy of the affected country . RVF occurs mostly in African countries , but epidemics have been reported in Madagascar and in the Arabian Peninsula . In the Union of Comor...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "zoonoses", "veterinary", "epidemiology", "entomology", "biology", "and", "life", "sciences", "zoology", "veterinary", "science" ]	2014	Evidence for Circulation of the Rift Valley Fever Virus among Livestock in the Union of Comoros
Over 400 , 000 people across the Americas are thought to have been infected with Zika virus as a consequence of the 2015–2016 Latin American outbreak . Official government-led case count data in Latin America are typically delayed by several weeks , making it difficult to track the disease in a timely manner . Thus , t...	In the absence of access to real-time government-reported Zika case counts , we demonstrate the ability of Internet-based data sources to track the outbreak . Our model predictions fill a critical time-gap in existing Zika surveillance , given that early interventions and real-time surveillance are necessary to curb mo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "microcephaly", "venezuela", "pathology", "and", "laboratory", "medicine", "pathogens", "sociology", "geographical", "locations", "microbiology", "social", "sciences", "social", "media", "viruses", "developmental", "biology", "rna"...	2017	Forecasting Zika Incidence in the 2016 Latin America Outbreak Combining Traditional Disease Surveillance with Search, Social Media, and News Report Data
Diarrhoea is a leading cause of death in Nigerian children under 5 years . Implementing the most cost-effective approach to diarrhoea management in Nigeria will help optimize health care resources allocation . This study evaluated the cost-effectiveness of various approaches to diarrhoea management namely: the ‘no trea...	‘‘Cost-effectiveness analysis of diarrhoea management approaches in Nigeria: a decision analytical model” was an original research carried out due to the high prevalence and mortality rate due to diarrhoea in Nigeria . The study aims to determine which treatment approach for diarrhoea would be cost-effective for Nigeri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neonatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cost-effectiveness", "analysis", "maternal", "health", "markov", "models", "economic", "analysis", "pathogens", "immunology", "geographical", "locations", "microbiology", ...	2017	Cost-effectiveness analysis of diarrhoea management approaches in Nigeria: A decision analytical model
Ubiquitination and deubiquitination are reciprocal processes that tune protein stability , function , and/or localization . The removal of ubiquitin and remodeling of ubiquitin chains is catalyzed by deubiquitinating enzymes ( DUBs ) , which are cysteine proteases or metalloproteases . Although ubiquitination has been ...	The post-translational modification of proteins by conjugation of monomers or chains of ubiquitin is a regulatory mechanism for tuning protein stability , localization and function . Given these vital functions , ubiquitination has to be highly regulated so that protein degradation and cell signaling are controlled in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/cell", "signaling", "and", "trafficking", "structures", "cell", "biology" ]	2010	A Global Census of Fission Yeast Deubiquitinating Enzyme Localization and Interaction Networks Reveals Distinct Compartmentalization Profiles and Overlapping Functions in Endocytosis and Polarity
Fluoroquinolones are the most commonly used group of antimicrobials for the treatment of enteric fever , but no direct comparison between two fluoroquinolones has been performed in a large randomised trial . An open-label randomized trial was conducted to investigate whether gatifloxacin is more effective than ofloxaci...	Enteric fever , which comprises of typhoid and paratyphoid fevers , is common in many developing countries . It is also sometimes seen in the Western world in returning travellers . This present study of uncomplicated enteric fever in an outpatient setting in a hospital in Kathmandu , Nepal compared the newer gatifloxa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Gatifloxacin Versus Ofloxacin for the Treatment of Uncomplicated Enteric Fever in Nepal: An Open-Label, Randomized, Controlled Trial
Recent gene expression QTL ( eQTL ) mapping studies have provided considerable insight into the genetic basis for inter-individual regulatory variation . However , a limitation of all eQTL studies to date , which have used measurements of steady-state gene expression levels , is the inability to directly distinguish be...	Recent studies of functional genetic variation in humans have identified numerous loci that are associated with variation in gene expression levels , called expression quantitative trait loci ( eQTLs ) . The mechanisms by which these loci affect gene expression , however , are still largely unknown . Specifically , sin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "functional", "genomics", "rna", "stability", "genome", "analysis", "tools", "gene", "expression", "biology", "molecular", "biology", "microarrays", "genomics", "molecular", "cell", "biology", ...	2012	The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels
Pathogenesis studies of SIV infection have not been performed to date in wild monkeys due to difficulty in collecting and storing samples on site and the lack of analytical reagents covering the extensive SIV diversity . We performed a large scale study of molecular epidemiology and natural history of SIVagm infection ...	We simultaneously assessed , for the first time in a natural host , the epidemiology , diversity and natural history of SIVagmVer infection in wild vervet populations from South Africa . We report that African green monkeys ( AGMs ) have likely been infected with SIVagm for a long period , ranging from the time of thei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "transmission", "and", "infection", "immunology", "microbiology", "host-pathogen", "interaction", "immunodeficiency", "viruses", "viral", "load", "animal", "models", "of", "infection", "biology", "pathogenesis", "microbial", "ecology", "ecology", "immunity", "vir...	2013	SIVagm Infection in Wild African Green Monkeys from South Africa: Epidemiology, Natural History, and Evolutionary Considerations
Imported cases threaten rabies reemergence in rabies-free areas . During 2000–2005 , five dog and one human rabies cases were imported into France , a rabies-free country since 2001 . The Summer 2004 event led to unprecedented media warnings by the French Public Health Director . We investigated medical practice evolut...	Rabies has been eliminated from a large part of the European Union and , thus , any newly imported cases threaten its reemergence . The 2000–2005 data derived from the exhaustive surveillance system implemented in France was analyzed to evaluate the impact on demand for and delivery of antirabies prophylaxis following ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases" ]	2010	Imported Episodic Rabies Increases Patient Demand for and Physician Delivery of Antirabies Prophylaxis
Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species . We used the principle of parsimony , applied to aligned synteny blocks from 11 yeast species , to infer the gene content and gene order that existed in the genome of an extinct ancestral yea...	Genomes evolve in structure as well as in DNA sequence . We used data from 11 different yeast species to investigate the process of structural evolution of the genome on the evolutionary path leading to the bakers' yeast S . cerevisiae . We focused on an ancestor that existed about 100 million years ago . We were able ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/genomics", "evolutionary", "biology/genomics" ]	2009	Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome
Robust reference values for fecal egg count reduction ( FECR ) rates of the most widely used anthelmintic drugs in preventive chemotherapy ( PC ) programs for controlling soil-transmitted helminths ( STHs; Ascaris lumbricoides , Trichuris trichiura , and hookworm ) are still lacking . However , they are urgently needed...	Soil-transmitted helminths ( STHs; roundworms , whipworms , and hookworms ) infect millions of children in sub-tropical and tropical countries , resulting in malnutrition , growth stunting , intellectual retardation , and cognitive deficits . To fight against STH , large-scale deworming programs are implemented in whic...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "biology", "and", "life", "sciences", "microbiology", "medicine", "and", "health", "sciences" ]	2014	Assessment of Anthelmintic Efficacy of Mebendazole in School Children in Six Countries Where Soil-Transmitted Helminths Are Endemic
Animal welfare requires the adequate housing of animals to ensure health and well-being . The application of environmental enrichment is a way to improve the well-being of laboratory animals . However , it is important to know whether these enrichment items can be incorporated in experimental mouse husbandry without cr...	Adequate housing of laboratory animals is essential to guarantee their well-being . From a scientific perspective , physically and mentally healthy animals also contribute to increased validity and reproducibility of experimental results . The choice of nesting material or shelter type , referred to as environmental en...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "animal", "types", "body", "weight", "medicine", "and", "health", "sciences", "animal", "welfare", "vertebrates", "mice", "animals", "mammals", "biochemical", "analysis", "physiological", "parameters", "animal", "behavior", "bioassays", "and", "physiological", "analysis...	2018	Laboratory mouse housing conditions can be improved using common environmental enrichment without compromising data
Telomerase is expressed in early human development and then becomes silenced in most normal tissues . Because ~90% of primary human tumors express telomerase and generally maintain very short telomeres , telomerase is carefully regulated , particularly in large , long-lived mammals . In the current report , we provide ...	Telomerase is very tightly regulated in large , long-lived species such as humans . Telomerase is expressed during early human fetal development , turned off in most adult tissues , and then becomes reactivated in most human cancers . However , the exact mechanism ( s ) regulating these switches in expression are not f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "telomere", "length", "telomeres", "cell", "biology", "chromosome", "biology", "chromosome", "structure", "and", "function", "molecular", "biology", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "epigenetics", "molecular",...	2016	Regulation of the Human Telomerase Gene TERT by Telomere Position Effect—Over Long Distances (TPE-OLD): Implications for Aging and Cancer
Aedes aegypti is one of the most important mosquito vectors of human disease . The development of spatial models for Ae . aegypti provides a promising start toward model-guided vector control and risk assessment , but this will only be possible if models make reliable predictions . The reliability of model predictions ...	Dengue is one of the most important insect-vectored human viral diseases . The principal vector is Aedes aegypti , a mosquito that lives in close association with humans . Currently , there is no effective vaccine available and the only means for limiting dengue outbreaks is vector control . To help design vector contr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology/global", "health", "mathematics/statistics", "computational", "biology/ecosystem", "modeling" ]	2010	Understanding Uncertainties in Model-Based Predictions of Aedes aegypti Population Dynamics
The meiotic cell division reduces the chromosome number from diploid to haploid to form gametes for sexual reproduction . Although much progress has been made in understanding meiotic recombination and the two meiotic divisions , the processes leading up to recombination , including the prolonged pre-meiotic S phase ( ...	Sexually reproducing organisms rely on a specialized cell division called meiosis to produce genetically distinct gametes with half the chromosome number of the parent . The first stage of the meiotic cell division is the duplication of chromosomes , followed by the exchange of DNA between homologous chromosomes inheri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "chromosome", "structure", "and", "function", "centromeres", "cell", "division", "dna", "replication", "dna", "dna", "synthesis", "chromosome", "biology", "biology", "molecular", "biology", "cell", "biology", "nucleic", "acids", "dna", "recombination", "mol...	2012	Separation of DNA Replication from the Assembly of Break-Competent Meiotic Chromosomes
Herpes simplex virus type 1 causes mucocutaneous lesions , and is the leading cause of infectious blindness in the United States . Animal studies have shown that the severity of HSV-1 ocular disease is influenced by three main factors; innate immunity , host immune response and viral strain . We previously showed that ...	In addition to causing recurrent labial lesions , herpes simplex virus type 1 ( HSV-1 ) is also the primary source of infectious blindness in the United States . Animal studies have shown that the severity of infection is influenced by several factors , including viral strain . Conventional studies investigating the ge...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "herpes", "simplex", "virus", "vero", "cells", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "keratitis", "pathogens", "split-decomposition", "method", "biological", "cultures", "population", "genetics",...	2016	Quantitative Trait Locus Based Virulence Determinant Mapping of the HSV-1 Genome in Murine Ocular Infection: Genes Involved in Viral Regulatory and Innate Immune Networks Contribute to Virulence
Bacteria were thought to be devoid of tyrosine-phosphorylating enzymes . However , several tyrosine kinases without similarity to their eukaryotic counterparts have recently been identified in bacteria . They are involved in many physiological processes , but their accurate functions remain poorly understood due to slo...	An idiosyncratic new class of bacterial enzymes , bacterial tyrosine-kinases ( BY-kinases ) , has been characterized . These enzymes , which are involved in an increasing number of physiological processes ranging from stress resistance to pathogenicity , share no sequence similarities with eukaryotic kinases , and thei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "microbiology", "biophysics" ]	2008	Structural Basis for the Regulation Mechanism of the Tyrosine Kinase CapB from Staphylococcus aureus
Faithful transcription of DNA is constantly threatened by different endogenous and environmental genotoxic effects . Transcription coupled repair ( TCR ) has been described to stop transcription and quickly remove DNA lesions from the transcribed strand of active genes , permitting rapid resumption of blocked transcrip...	Our genome is continuously exposed to genotoxic attacks that generate aberrant DNA structures . These can block the transcribing DNA-dependent RNA polymerase II ( Pol II ) enzyme and can lead to deleterious cellular processes . Cells have developed several mechanisms to stop Pol II , repair the roadblocks and to restor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cellular", "stress", "responses", "genomics", "cell", "biology", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "dna", "repair", "dna", "cell", "processes", "molecular", "cell", "biology", "dna", "transcription" ]	2014	UVB Induces a Genome-Wide Acting Negative Regulatory Mechanism That Operates at the Level of Transcription Initiation in Human Cells
Protein homeostasis is critical for cell survival and functions during stress and is regulated at both RNA and protein levels . However , how the cell integrates RNA-processing programs with post-translational protein quality control systems is unknown . Transactive response DNA-binding protein ( TARDBP/TDP-43 ) is an ...	TDP-43 is linked to pathogenesis of major neurodegenerative diseases , including amyotrophic lateral sclerosis ( ALS ) and frontotemporal dementia ( FTD ) . How TDP-43 contributes to the development of these degenerative diseases remains unsolved , and the full range of TDP-43 functions has yet to be established . In t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "biology", "biology", "and", "life", "sciences", "molecular", "biology" ]	2014	RNA-Processing Protein TDP-43 Regulates FOXO-Dependent Protein Quality Control in Stress Response
Suppressor of cytokine signaling ( SOCS ) proteins are inducible feedback inhibitors of cytokine signaling . SOCS1−/− mice die within three weeks postnatally due to IFN-γ-induced hyperinflammation . Since it is well established that IFN-γ is dispensable for protection against influenza infection , we generated SOCS1−/−...	Cytokines are critical in regulating the balance between protective immunity and detrimental inflammation during influenza infection . Suppressor of cytokine signaling ( SOCS ) proteins are inducible feedback inhibitors of cytokine signaling . Using gene-deficient and infectious animal models , we determined how SOCS1 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "immunology" ]	2014	Expression of Suppressor of Cytokine Signaling 1 (SOCS1) Impairs Viral Clearance and Exacerbates Lung Injury during Influenza Infection
There are economic and physical limitations when applying prevention and control strategies for urban vector borne diseases . Consequently , there are increasing concerns and interest in designing efficient strategies and regulations that health agencies can follow in order to reduce the imminent impact of viruses like...	A disease is called vector-borne when it is not transmitted directly among humans , but in a human-vector-human way . Examples of major importance , due to its epidemiological magnitude , are Dengue , Chikungunya and Zika tropical diseases , for which the main vector is the Aedes aegypti mosquito . Usually , some index...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "neighborhoods", "vector-borne", "diseases", "social", "sciences", "human", "mobility", "animals", "population", "biology", "infectious", "disease", "contr...	2018	Vector-borne disease risk indexes in spatially structured populations
Due to their remarkable parasitocidal activity , artemisinins represent the key components of first-line therapies against Plasmodium falciparum malaria . However , the decline in efficacy of artemisinin-based drugs jeopardizes global efforts to control and ultimately eradicate the disease . To better understand the re...	The emergence of artemisinin resistance within and beyond Southeast Asia is a looming threat that needs to be promptly addressed . With this in mind , we derived several artemisinin-resistant parasite lines in vitro in order to fully characterize the resistance phenotype at the cellular and molecular levels . In additi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "gene", "regulation", "regulatory", "proteins", "microbiology", "dna-binding", "proteins", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "genome",...	2018	Oxidative stress and protein damage responses mediate artemisinin resistance in malaria parasites
The insulin/IGF signaling pathway is a highly conserved regulator of metabolism in flies and mammals , regulating multiple physiological functions including lipid metabolism . Although insulin signaling is known to regulate the activity of a number of enzymes in metabolic pathways , a comprehensive understanding of how...	Type 2 diabetes , which is reaching epidemic proportions worldwide , is often associated with obesity and an imbalance in organismal lipid homeostasis . Therefore , understanding how insulin regulates lipid biosynthesis and breakdown is necessary . Surprisingly , the molecular mechanisms by which insulin regulates fatt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "development", "biology" ]	2012	Insulin Signaling Regulates Fatty Acid Catabolism at the Level of CoA Activation
Understanding the role of humans in the dispersal of predominately animal pathogens is essential for their control . We used newly developed Bayesian phylogeographic methods to unravel the dynamics and determinants of the spread of dog rabies virus ( RABV ) in North Africa . Each of the countries studied exhibited larg...	At least 15 million doses of anti-rabies post-exposure prophylaxis are administered annually worldwide , and an estimated 55 , 000 people die of rabies every year . Over 99% of these deaths occur in developing countries , predominantly in Asia and in Africa where rabies is endemic in domestic dogs . Despite the global ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "computational", "biology/evolutionary", "modeling", "infectious", "diseases/viral", "infections", "public", "health", "and"...	2010	Phylodynamics and Human-Mediated Dispersal of a Zoonotic Virus
Amino acid substitutions in protein structures often require subtle backbone adjustments that are difficult to model in atomic detail . An improved ability to predict realistic backbone changes in response to engineered mutations would be of great utility for the blossoming field of rational protein design . One model ...	Protein design has the potential to generate useful molecules for medicine and chemistry , including sensors , drugs , and catalysts for arbitrary reactions . When protein design is carried out starting from an experimentally determined structure , as is often the case , one important aspect to consider is backbone fle...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "structure", "biology", "computational", "biology", "macromolecular", "structure", "analysis" ]	2012	The Role of Local Backrub Motions in Evolved and Designed Mutations
Phlebotomine sand flies are blood-sucking insects transmitting Leishmania parasites . In bitten hosts , sand fly saliva elicits specific immune response and the humoral immunity was shown to reflect the intensity of sand fly exposure . Thus , anti-saliva antibodies were suggested as the potential risk marker of Leishma...	Leishmania major is the causative agent of zoonotic cutaneous leishmaniasis and Phlebotomus papatasi serve as the major vector . In endemic foci , rodents are the natural reservoirs of this disease . Thus , we studied anti-P . papatasi saliva antibody response in BALB/c and C57BL/6 mice that are commonly used as model ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "models", "model", "organisms", "parasitology", "immunology", "biology", "zoology", "mouse", "immune", "response" ]	2012	Kinetics of Antibody Response in BALB/c and C57BL/6 Mice Bitten by Phlebotomus papatasi
Stimulus properties , attention , and behavioral context influence correlations between the spike times produced by a pair of neurons . However , the biophysical mechanisms that modulate these correlations are poorly understood . With a combined theoretical and experimental approach , we show that the rate of balanced ...	Neurons in sensory , motor , and cognitive regions of the nervous system integrate synaptic input and output trains of action potentials ( spikes ) . A critical feature of neural computation is the ability for neurons to modulate their spike train response to a given input , allowing task context or past history to aff...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "statistical", "mechanics", "computational", "neuroscience", "single", "neuron", "function", "biology", "sensory", "systems", "neuroscience", "coding", "mechanisms" ]	2011	Balanced Synaptic Input Shapes the Correlation between Neural Spike Trains
Although it is generally believed that CD4+ T cells play important roles in anti-Leishmania immunity , some studies suggest that they may be dispensable , and that MHC II-restricted CD3+CD4−CD8− ( double negative , DN ) T cells may be more important in regulating primary anti-Leishmania immunity . In addition , while t...	Although it is generally believed that CD4+ T cells mediate anti-Leishmania immunity , some studies suggest that CD3+CD4−CD8− ( double negative , DN ) T cells may play a more important role in regulating primary anti-Leishmania immunity . Here , we report that DN T cells extensively proliferate and produce effector cyt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "microbiology", "parasitology" ]	2014	MHC Class II Restricted Innate-Like Double Negative T Cells Contribute to Optimal Primary and Secondary Immunity to Leishmania major
The 2009 H1N1 pandemic ( H1N1pdm ) viruses have evolved to contain an E47K substitution in the HA2 subunit of the stalk region of the hemagglutinin ( HA ) protein . The biological significance of this single amino acid change was investigated by comparing A/California/7/2009 ( HA2-E47 ) with a later strain , A/Brisbane...	Influenza viruses cause seasonal epidemics and occasional pandemics , representing a threat to public health . The trimeric hemagglutinin ( HA ) surface glycoprotein mediates viral entry and plays important roles in viral host restriction , transmission and pathogenesis . The HA protein binds to the receptor on the cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	A Single Amino Acid in the Stalk Region of the H1N1pdm Influenza Virus HA Protein Affects Viral Fusion, Stability and Infectivity
Chromosomal translocations between loci encoding MALT1 and c-IAP2 are common in MALT lymphomas . The resulting fusion proteins lack the c-IAP2 RING domain , the region responsible for its ubiquitin protein ligase ( E3 ) activity . Ectopic expression of the fusion protein activates the canonical NF-κB signaling cascade ...	MALT ( mucosal associated lymphoid tissue ) lymphomas commonly express a mutant protein that contains a portion of the ubiquitin protein ligase cellular Inhibitor of Apoptosis 2 ( c-IAP2 ) and a portion of the paracaspase MALT1 . Expression of this fusion protein activates the anti-apoptotic transcription factor NF-κB ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/leukocyte", "signaling", "and", "gene", "expression", "oncology/gastrointestinal", "cancers", "cell", "biology/cell", "signaling" ]	2010	Non-Canonical NF-κB Activation and Abnormal B Cell Accumulation in Mice Expressing Ubiquitin Protein Ligase-Inactive c-IAP2
The epidemic tendency of hemorrhagic fever with renal syndrome ( HFRS ) is on the rise in recent years in Guangzhou . This study aimed to explore the associations between meteorological factors and HFRS epidemic risk in Guangzhou for the period from 2006–2015 . We obtained data of HFRS cases in Guangzhou from the Natio...	The prevalence of HFRS was on the rise in recent years , especially in the large and medium-sized cities in China . We obtained data of HFRS cases in Guangzhou from the National Notifiable Disease Report System ( NNDRS ) during the period of 2006–2015 . Meteorological data were obtained from the Guangzhou Meteorologica...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "china", "atmospheric", "science", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "viruses", "hemorrhagic", "fever", "wi...	2018	Meteorological factors and risk of hemorrhagic fever with renal syndrome in Guangzhou, southern China, 2006–2015
Infection with the human gastric pathogen Helicobacter pylori is associated with a spectrum of diseases including gastritis , peptic ulcers , gastric adenocarcinoma , and gastric mucosa–associated lymphoid tissue lymphoma . The cytotoxin-associated gene A ( CagA ) protein of H . pylori , which is translocated into host...	Like many pathogens , the human gastric bacterium Helicobacter pylori orchestrates infection through the activity of proteins that it translocates into host cells . The H . pylori translocated protein , CagA , which shares no homology to any other proteins , is a significant risk factor for H . pylori–associated diseas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "genetics", "and", "genomics/gene", "function" ]	2008	A Transgenic Drosophila Model Demonstrates That the Helicobacter pylori CagA Protein Functions as a Eukaryotic Gab Adaptor
The archaeal RNA polymerase ( RNAP ) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation . To deepen our knowledge of cellular transcription , we have determined the structure of the 13-subunit DNA-directed RNAP from Sul...	Transcription , the process of converting DNA into RNA ( which in turn is translated into proteins by ribosomes ) is carried out by the multisubunit RNA polymerase ( RNAP ) enzyme . Transcription is fundamental to all organisms across the three kingdoms of life—Eukarya , Bacteria , and Archaea—and can be divided into t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biochemistry" ]	2009	Evolution of Complex RNA Polymerases: The Complete Archaeal RNA Polymerase Structure
The suppression of protective Type 2 immunity is a principal factor driving the chronicity of helminth infections , and has been attributed to a range of Th2 cell-extrinsic immune-regulators . However , the intrinsic fate of parasite-specific Th2 cells within a chronic immune down-regulatory environment , and the resul...	Helminth parasites mount chronic infections in over 1 billion people worldwide , of which filarial nematode infections account for 120 million . A major barrier to the development of protective Th2 immunity lies in the dominant down-regulatory immune responses invoked during infection . Although this immune suppression...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunomodulation", "adaptive", "immunity", "immune", "cells", "immunity", "t", "cells", "immune", "defense", "immunology", "biology", "immune", "suppression", "immunity", "to", "infections", "immunoregulation", "immune", "response" ]	2013	Th2 Cell-Intrinsic Hypo-Responsiveness Determines Susceptibility to Helminth Infection
Excessive accumulation of bone marrow adipocytes observed in senile osteoporosis or age-related osteopenia is caused by the unbalanced differentiation of MSCs into bone marrow adipocytes or osteoblasts . Several transcription factors are known to regulate the balance between adipocyte and osteoblast differentiation . H...	Increased bone marrow adiposity is observed in the bone marrow of senile osteoporosis patients . This is caused by unbalanced differentiation of mesenchymal stem cells ( MSCs ) into osteoblast or adipocyte . Previous reports have indicated that several transcription factors play important roles in determining the direc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/stem", "cells", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "developmental", "biology/cell", "differentiation", "genetics", "and", "genomics/gene", "function", "cell", "bi...	2010	Id4, a New Candidate Gene for Senile Osteoporosis, Acts as a Molecular Switch Promoting Osteoblast Differentiation
SARS-coronavirus ( SARS-CoV ) genome expression depends on the synthesis of a set of mRNAs , which presumably are capped at their 5′ end and direct the synthesis of all viral proteins in the infected cell . Sixteen viral non-structural proteins ( nsp1 to nsp16 ) constitute an unusually large replicase complex , which i...	In 2003 , an emerging coronavirus ( CoV ) was identified as the etiological agent of severe acute respiratory syndrome ( SARS ) . SARS-CoV replicates and transcribes its large RNA genome using a membrane-bound enzyme complex containing a variety of viral nonstructural proteins . A critical step during RNA synthesis is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/emerging", "viral", "diseases", "virology/viral", "replication", "and", "gene", "regulation", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance" ]	2010	In Vitro Reconstitution of SARS-Coronavirus mRNA Cap Methylation
Cationic and heavy metal toxicity is involved in a substantial number of diseases in mammals and crop plants . Therefore , the understanding of tightly regulated transporter activities , as well as conceiving the interplay of regulatory mechanisms , is of substantial interest . A generalized thermodynamic description i...	Metals , and particularly their positively charged ions ( cations ) , are an integral part of our environment , and all living organisms are exposed to metals in their natural habitat . Even though significant efforts have already been made by experimental and theoretical analysis of the individual components of transp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protons", "medicine", "and", "health", "sciences", "chemical", "compounds", "membrane", "potential", "ions", "electrophysiology", "carbohydrates", "organic", "compounds", "glucose", "sodium", "organisms", "fungi", "model", "organisms", "biological", "transport", "cations...	2016	A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae
Exchange of O2 and CO2 of plants with their environment is essential for metabolic processes such as photosynthesis and respiration . In some fruits such as pears , which are typically stored under a controlled atmosphere with reduced O2 and increased CO2 levels to extend their commercial storage life , anoxia may occu...	Respiration plays an important role in the overall metabolism of plants , and certainly is related to gas exchange of plants with the environment . In roots and bulky storage organs such as fruit and tubers , where the length of the diffusion path may be considerable , anoxic conditions may even occur . This is of part...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-environment", "interactions", "plant", "biology/plant", "biochemistry", "and", "physiology" ]	2008	A Continuum Model for Metabolic Gas Exchange in Pear Fruit
Many tumors are characterized by genetic instability , producing an assortment of genetic variants of tumor cells called subclones . These tumors and their surrounding environments form complex multi-cellular ecosystems , where subclones compete for resources and cooperate to perform multiple tasks , including cancer i...	Cancer is an elusive disease due to the wide variety of cancer types and adaptability to treatment . How is this adaptability accomplished ? Loss of genetic stability , a hallmark of cancer , leads to the emergence of many different types of cancer cells within a tumor . This creates a complex ecosystem where cancer ce...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "vegf", "signaling", "population", "dynamics", "cancer", "treatment", "cancers", "and", "neoplasms", "oncology", "systems", "science", "mathematics", "population", "biology", "conser...	2018	The complex ecosystem in non small cell lung cancer invasion
Asymmetric segregation of damaged proteins at cell division generates a cell that retains damage and a clean cell that supports population survival . In cells that divide asymmetrically , such as Saccharomyces cerevisiae , segregation of damaged proteins is achieved by retention and active transport . We have previousl...	During their lifetime , cells accumulate damage that is inherited by the daughter cells when the mother cell divides . The amount of inherited damage determines how long the daughter cell will live and how fast it will age . We have discovered fusion of protein aggregates as a new strategy that cells use to apportion d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "and", "information", "sciences", "mathematical", "computing", "model", "organisms", "mathematics", "cell", "biology", "theoretical", "biology", "biology", "and", "life", "sciences", "computing", "methods", "physical", "sciences", "yeast", "and", "fungal", ...	2014	Fusion of Protein Aggregates Facilitates Asymmetric Damage Segregation
Specialized microenvironments called niches regulate tissue homeostasis by controlling the balance between stem cell self-renewal and the differentiation of stem cell daughters . However the mechanisms that govern the formation , size and signaling of in vivo niches remain poorly understood . Loss of the highly conserv...	The mechanisms that govern the formation , size and signaling output of in vivo niches remain poorly understood . Studies of Drosophila germline stem cells ( GSCs ) have suggested that chromatin programming greatly influences the behavior of these cells and their progeny . Previous work has shown that loss of the highl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "fate", "determination", "model", "organisms", "stem", "cells", "molecular", "development", "gene", "expression", "genetics", "epigenetics", "biology", "cell", "differentiation" ]	2014	Lsd1 Restricts the Number of Germline Stem Cells by Regulating Multiple Targets in Escort Cells
Coral snakes of the genus Micrurus have a high diversity and wide distribution in the Americas . Despite envenomings by these animals being uncommon , accidents are often severe and may result in death . Producing an antivenom to treat these envenomings has been challenging since coral snakes are difficult to catch , p...	Coral snakes are distributed in the Americas form Southern United States to Argentina . These snakes cause envenomings that , despite not being common , often lead to death . The antivenoms currently produced to treat accidents caused by these snakes have limitations regarding the number of species venoms they could ne...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "toxins", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "vertebrates", "animals", "mammals", "toxicology", "toxic", "agents", "toxicity", "routes", "of", "administrati...	2019	A polyvalent coral snake antivenom with broad neutralization capacity
Cerebral malaria , a major cause of death during malaria infection , is characterised by the sequestration of infected red blood cells ( IRBC ) in brain microvessels . Most of the molecules implicated in the adhesion of IRBC on endothelial cells ( EC ) are already described; however , the structure of the IRBC/EC junct...	Cerebral malaria , a major cause of death during malaria infection , is characterised by the sequestration of infected red blood cells ( IRBC ) in brain microvessels . This study describes the interactions between plasmodium infected red blood cell and human brain endothelial cells . It highlights the activation of a t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "cell", "biology", "microbiology/parasitology", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "microbiology/cellular", "microbiology", "and", "pathogenesis", "cell", ...	2010	Plasmodium falciparum Adhesion on Human Brain Microvascular Endothelial Cells Involves Transmigration-Like Cup Formation and Induces Opening of Intercellular Junctions
DNA methylation is involved in gene silencing and genome stability in organisms from fungi to mammals . Genetic studies in Neurospora crassa previously showed that the CUL4-DDB1 E3 ubiquitin ligase regulates DNA methylation via histone H3K9 trimethylation . However , the substrate-specific adaptors of this ligase that ...	DNA associates with histones to form chromatin in eukaryotes . Epigenetics refers to DNA and histone modifications in chromatin that persist from one cell generation to the next , controlling gene expression and genome stability . These epigenetic changes are crucial for the development and differentiation of the vario...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "growth", "and", "development", "genetics", "and", "genomics/epigenetics", "biochemistry/protein", "chemistry" ]	2010	DCAF26, an Adaptor Protein of Cul4-Based E3, Is Essential for DNA Methylation in Neurospora crassa
Charcot-Marie-Tooth disease type 2D ( CMT2D ) is a dominantly inherited peripheral neuropathy caused by missense mutations in the glycyl-tRNA synthetase gene ( GARS ) . In addition to GARS , mutations in three other tRNA synthetase genes cause similar neuropathies , although the underlying mechanisms are not fully unde...	Mutations in the glycyl-tRNA synthetase gene ( GARS ) cause Charcot-Marie-Tooth disease type 2D , a disease characterized by neuronal axon loss in the arms and legs , resulting in weakness and sensory problems . The GARS protein is essential for protein synthesis in every cell , and it has been difficult to determine w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurobiology", "of", "disease", "and", "regeneration", "animal", "genetics", "genetic", "mutation", "neuroscience", "gene", "function", "mutation", "types", "biology", "neurological", "disorders", "neurology", "neuromuscular", "diseases", "genetics", "genetic...	2011	Charcot-Marie-Tooth–Linked Mutant GARS Is Toxic to Peripheral Neurons Independent of Wild-Type GARS Levels
Rabies is an ancient neglected tropical disease that causes tens of thousands of human deaths and millions of cattle deaths annually . In order to develop a new vaccine for potential use in bats , a reservoir of rabies infection for humans and animals alike , an in silico antigen designer tool was used to create a mosa...	Rabies remains a significant and costly zoonotic disease worldwide . While control of canine rabies can significantly diminish the threat to human health , spillover of rabies and related lyssaviruses from bats into terrestrial animals and humans continues to be an important issue . Here we describe the development of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "viruses", "vaccines", "preventive", "medicine", "rabies"...	2017	Protection of bats (Eptesicus fuscus) against rabies following topical or oronasal exposure to a recombinant raccoon poxvirus vaccine
Chikungunya virus ( CHIKV ) is a reemerging mosquito-borne pathogen that has recently caused devastating urban epidemics of severe and sometimes chronic arthralgia . As with most other mosquito-borne viral diseases , control relies on reducing mosquito populations and their contact with people , which has been ineffect...	Chikungunya virus ( CHIKV ) is a mosquito-borne alphavirus that has reemerged since 2004 to cause millions of cases of severe and often persistent arthralgia . Because no licensed vaccine exists to prevent this disease , we utilized an attenuation approach to produce a live CHIKV vaccine candidate that elicits a robust...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "global", "health", "genetics", "immunology", "biology", "microbiology", "genetics", "and", "genomics" ]	2011	Novel Chikungunya Vaccine Candidate with an IRES-Based Attenuation and Host Range Alteration Mechanism
Human decisions are based on accumulating evidence over time for different options . Here we ask a simple question: How is the accumulation of evidence affected by the level of awareness of the information ? We examined the influence of awareness on decision-making using combined behavioral methods and magneto-encephal...	When making a decision , we gather evidence for the different options and ultimately choose on the basis of the accumulated evidence . A fundamental question is whether and how conscious awareness of the evidence changes this decision-making process . Here , we examined the influence of sensory awareness on decision-ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cognitive", "neuroscience", "cognition", "decision", "making", "consciousness", "biology", "neuroscience", "neuroimaging" ]	2011	How Awareness Changes the Relative Weights of Evidence During Human Decision-Making
Hereditary hypertrichoses are a group of hair overgrowth syndromes that are extremely rare in humans . We have previously demonstrated that a position effect on TRPS1 is associated with hypertrichosis in humans and mice . To gain insight into the functional role of Trps1 , we analyzed the late morphogenesis vibrissae p...	The various ectodermal appendages found in nature have evolved over time to allow organisms to better adapt to their environment . These include hair , feathers , scales , nails , teeth , beaks , horns , and a wide array of eccrine glands . The hair follicle is an ectodermal appendage unique to mammals that serves a wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "growth", "control", "gene", "networks", "animal", "genetics", "genetic", "mutation", "functional", "genomics", "chromosome", "structure", "and", "function", "gene", "regulation", "dna", "transcription", "gene", "function", "animal", "models", "genetics", "of", "disea...	2012	Trps1 and Its Target Gene Sox9 Regulate Epithelial Proliferation in the Developing Hair Follicle and Are Associated with Hypertrichosis
The 2015-16 Zika virus pandemic originating in Latin America led to predictions of a catastrophic global spread of the disease . Since the current outbreak began in Brazil in May 2015 local transmission of Zika has been reported in over 60 countries and territories , with over 750 thousand confirmed and suspected cases...	Between 1952 , when the Zika virus was first found in humans , and 2007 Zika disease outbreaks were limited to small isolated epidemics in equatorial Africa and tropical Asia . However , the recent outbreak , which began in Brazil in May 2015 , resulted over 750 thousand estimated cases and confirmed local transmission...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chikungunya", "infection", "engineering", "and", "technology", "transportation", "pathogens", "geographical", "locations", "microbiology", "tropical", "diseases", "anima...	2017	Vector status of Aedes species determines geographical risk of autochthonous Zika virus establishment
Apicomplexan parasites are responsible for numerous important human diseases including toxoplasmosis , cryptosporidiosis , and most importantly malaria . There is a constant need for new antimalarials , and one of most keenly pursued drug targets is an ancient algal endosymbiont , the apicoplast . The apicoplast is ess...	The apicoplast is an essential parasite organelle derived from an algal endosymbiont . Most apicoplast proteins are nuclear encoded and post-translationally imported . Part of this journey utilizes the endoplasmic reticulum associated degradation or ERAD system of the algal endosymbiont . Typically , the ERAD system is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parasitology", "biology", "microbiology" ]	2013	An Apicoplast Localized Ubiquitylation System Is Required for the Import of Nuclear-encoded Plastid Proteins
Genetic strategies that reduce or block pathogen transmission by mosquitoes have been proposed as a means of augmenting current control measures to reduce the growing burden of vector-borne diseases . The endosymbiotic bacterium Wolbachia has long been promoted as a potential vehicle for introducing disease-resistance ...	Dengue fever and its associated condition , dengue hemorrhagic fever , are emerging globally as the most important arboviral diseases currently threatening human populations . Dengue virus is transmitted to humans by aedine mosquitoes , primarily Aedes aegypti and , to a lesser extent , Aedes albopictus . No treatment ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology/applied", "microbiology", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/global", "health", "microbiology/applied", "microbiology", "infectious", "diseases/tropical", ...	2010	The Endosymbiotic Bacterium Wolbachia Induces Resistance to Dengue Virus in Aedes aegypti
Coronaviruses raise serious concerns as emerging zoonotic viruses without specific antiviral drugs available . Here we screened a collection of 16671 diverse compounds for anti-human coronavirus 229E activity and identified an inhibitor , designated K22 , that specifically targets membrane-bound coronaviral RNA synthes...	Viruses that replicate in the host cell cytoplasm have evolved to employ host cell-derived membranes to compartmentalize genome replication and transcription . Specifically for positive-stranded RNA viruses , accumulating knowledge concerning the involvement , rearrangement and requirement of cellular membranes for RNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "respiratory", "infections", "sars", "veterinary", "virology", "common", "cold", "biology", "and", "life", "sciences", "viral", "diseases", "pulmonology", "veterinar...	2014	Targeting Membrane-Bound Viral RNA Synthesis Reveals Potent Inhibition of Diverse Coronaviruses Including the Middle East Respiratory Syndrome Virus
The complement C3-like protein TEP1 of the mosquito Anopheles gambiae is required for defense against malaria parasites and bacteria . Two forms of TEP1 are present in the mosquito hemolymph , the full-length TEP1-F and the proteolytically processed TEP1cut that is part of a complex including the leucine-rich repeat pr...	Mosquitoes are vectors of numerous human diseases including malaria . Disease transmission requires that microbes overcome the robust mosquito immune system . In the African malaria mosquito , the TEP1 protein that is homologous to mammalian complement factor C3 is shown to play a central role in mosquito immunity to m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "complement", "system", "immunity", "vector", "biology", "innate", "immunity", "anopheles", "immune", "defense", "immunology", "biology", "microbiology", "parasitology", "immune", "system" ]	2013	The CLIP-Domain Serine Protease Homolog SPCLIP1 Regulates Complement Recruitment to Microbial Surfaces in the Malaria Mosquito Anopheles gambiae
Disruption of gene regulation is known to play major roles in carcinogenesis and tumour progression . Here , we comprehensively characterize the mutational profiles of diverse transcription factor binding sites ( TFBSs ) across 1 , 574 completely sequenced cancer genomes encompassing 11 tumour types . We assess the rel...	Regulatory regions of the genome are important players in cancer initiation and progression . Here , we study the patterns of mutations accumulating at short DNA segments bound by regulatory proteins ( transcription factor binding sites ) across many cancer types and in the human population . We find strikingly high ra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cancer", "genomics", "sequencing", "techniques", "medicine", "and", "health", "sciences", "basic", "cancer", "research", "oncology", "substitution", "mutation", "mutation", "sequence", "motif", "analysis", "epigenetics", "molecular", "biology", "techniques", "chromatin",...	2016	Mutational Biases Drive Elevated Rates of Substitution at Regulatory Sites across Cancer Types
In Arabidopsis , micro ( mi ) RNAs and trans-acting ( ta-si ) RNAs synthesized directly or indirectly through the DICER-LIKE-1 ( DCL1 ) ribonuclease have roles in patterning and hormonal responses , while DCL2 , 3 , 4-dependent small-interfering ( si ) RNAs are mainly involved in silencing of transposable elements and ...	In the plant and animal RNA silencing pathways , small RNA molecules known as micro ( mi ) RNA and short-interfering ( si ) RNAs have key roles in development and antiviral defense , respectively . In turn , viruses counteract this defense by deploying specific virulence factors , referred to as Viral Suppressors of RN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "biology", "molecular", "cell", "biology" ]	2011	Misregulation of AUXIN RESPONSE FACTOR 8 Underlies the Developmental Abnormalities Caused by Three Distinct Viral Silencing Suppressors in Arabidopsis
Cysteine ( Cys ) residues often play critical roles in proteins , for example , in the formation of structural disulfide bonds , metal binding , targeting proteins to the membranes , and various catalytic functions . However , the structural determinants for various Cys functions are not clear . Thiol oxidoreductases ,...	Among the 20 amino acids commonly found in proteins , cysteine ( Cys ) is special in that it is present more often than other residues in functionally important locations within proteins . Some of these functions include metal binding , catalysis , structural stability , and posttranslational modifications . Identifyin...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biochemistry/biocatalysis", "biochemistry/bioinformatics", "biochemistry/structural", "genomics" ]	2009	A Structure-Based Approach for Detection of Thiol Oxidoreductases and Their Catalytic Redox-Active Cysteine Residues
Electron microscopy ( EM ) achieves the highest spatial resolution in protein localization , but specific protein EM labeling has lacked generally applicable genetically encoded tags for in situ visualization in cells and tissues . Here we introduce “miniSOG” ( for mini Singlet Oxygen Generator ) , a fluorescent flavop...	Electron microscopy ( EM ) once revolutionized cell biology by revealing subcellular anatomy at resolutions of tens of nanometers , well below the diffraction limit of light microscopy . Over the past two decades , light microscopy has been revitalized by the development of spontaneously fluorescent proteins , which al...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bioengineering", "biochemistry", "biology", "molecular", "cell", "biology", "neuroscience", "engineering" ]	2011	A Genetically Encoded Tag for Correlated Light and Electron Microscopy of Intact Cells, Tissues, and Organisms
Glycolytic potential ( GP ) in skeletal muscle is economically important in the pig industry because of its effect on pork processing yield . We have previously mapped a major quantitative trait loci ( QTL ) for GP on chromosome 3 in a White Duroc × Erhualian F2 intercross . We herein performed a systems genetic analys...	Glycogen storage diseases ( GSD ) are a group of inherited disorders characterized by storage of excess glycogen , which are mainly caused by the abnormality of a particular enzyme essential for releasing glucose from glycogen . GSD-like conditions have been described in a wide variety of species . Pigs are a valuable ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "animal", "genetics" ]	2014	A Splice Mutation in the PHKG1 Gene Causes High Glycogen Content and Low Meat Quality in Pig Skeletal Muscle
Germline mutations of the Liver Kinase b1 ( LKB1/STK11 ) tumor suppressor gene have been linked to Peutz-Jeghers Syndrome ( PJS ) , an autosomal-dominant , cancer-prone disorder in which patients develop neoplasms in several organs , including the oviduct , ovary , and cervix . We have conditionally deleted Lkb1 in Mül...	Peutz-Jeghers Syndrome patients have autosomal dominant mutations in the LKB1/STK11 gene and are prone to developing cancer , predominantly in the intestinal tract but also in other tissues , including the reproductive tracts and gonads . To elucidate the mechanisms disrupted by the loss of LKB1 in the reproductive tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "gene", "networks", "cancer", "genetics", "genetic", "mutation", "obstetrics", "and", "gynecology", "cancer", "risk", "factors", "cancers", "and", "neoplasms", "animal", "models", "oncology", "model", "organisms", "biology", "gynecological", "tumors", "mou...	2012	Stromal Liver Kinase B1 [STK11] Signaling Loss Induces Oviductal Adenomas and Endometrial Cancer by Activating Mammalian Target of Rapamycin Complex 1
Despite the fact that tRNA abundances are thought to play a major role in determining translation error rates , their distribution across the genetic code and the resulting implications have received little attention . In general , studies of codon usage bias ( CUB ) assume that codons with higher tRNA abundance have l...	Codon usage bias ( CUB ) is a ubiquitous and important phenomenon . CUB is thought to be driven primarily due to selection against missense errors . For over 30 years , the standard model of translation errors has implicitly assumed that the relationship between translation errors and tRNA abundances are inversely rela...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry/molecular", "evolution", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/bioinformatics" ]	2010	Effect of Correlated tRNA Abundances on Translation Errors and Evolution of Codon Usage Bias
Schistosomiasis in humans along the lower Mekong River has proven a persistent public health problem in the region . The causative agent is the parasite Schistosoma mekongi ( Trematoda: Digenea ) . A new transmission focus is reported , as well as the first study of genetic variation among S . mekongi populations . The...	Schistosomiasis is a disease caused by parasitic worms of the genus Schistosoma . In the lower Mekong river , schistosomiasis in humans is called Mekong schistosomiasis and is caused by Schistosoma mekongi . In the past , Mekong schistosomiasis was known only from the lower Mekong river . Here DNA-sequence variation is...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "genetics", "and", "genomics/population", "genetics", "evolutionary", "biology/evolutionary", "ecology", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	DNA-Sequence Variation Among Schistosoma mekongi Populations and Related Taxa; Phylogeography and the Current Distribution of Asian Schistosomiasis
Post-transcriptional modifications of transfer RNAs ( tRNAs ) have long been recognized to play crucial roles in regulating the rate and fidelity of translation . However , the extent to which they determine global protein production remains poorly understood . Here we use quantitative proteomics to show a direct link ...	Here we present evidence for a more complicated role for transfer RNAs ( tRNAs ) than as mere adapters that link the genetic code in messenger RNA ( mRNA ) to the amino acid sequence of a protein during translation . tRNAs have long been known to be modified with dozens of different chemical structures other than the 4...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation
Respiratory syncytial virus ( RSV ) RNA synthesis occurs in cytoplasmic inclusion bodies ( IBs ) in which all the components of the viral RNA polymerase are concentrated . In this work , we show that RSV P protein recruits the essential RSV transcription factor M2-1 to IBs independently of the phosphorylation state of ...	Respiratory syncytial virus ( RSV ) is the leading cause of lower respiratory tract illness in infants . Since no vaccine and no potent antivirals are available against RSV , it is essential to better understand the mechanisms of viral replication to develop new antiviral strategies . Here we have investigated the mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "luciferase", "nucleic", "acid", "synthesis", "enzymes", "messenger", "rna", "enzymology", "dna-binding", "proteins", "phosphatases", "dna", "transcription", "polymerases", "sequence", "motif", "analysis", "rna", "synthesis", "chemical", "synthesis", "r...	2018	RSV hijacks cellular protein phosphatase 1 to regulate M2-1 phosphorylation and viral transcription
The Notch signaling pathway is a highly evolutionarily-conserved cell-cell signaling pathway that regulates many events during development . It plays a pivotal role in the regulation of fundamental cellular processes , such as cell proliferation , stem cell maintenance , and differentiation during embryonic and adult d...	Mosquitoes transmit many devastating diseases , including malaria , dengue , and Zika , which together are responsible for over one million deaths per year . Major reasons for this tragic situation are the unavailability of effective vaccines and drugs for most mosquito-borne diseases , increased resistance of vectors ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "phosphorylation", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "animals", "notch", "signaling", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "popu...	2018	The non-canonical Notch signaling is essential for the control of fertility in Aedes aegypti
Spinster ( Spin ) in Drosophila or Spinster homolog 1 ( Spns1 ) in vertebrates is a putative lysosomal H+-carbohydrate transporter , which functions at a late stage of autophagy . The Spin/Spns1 defect induces aberrant autolysosome formation that leads to embryonic senescence and accelerated aging symptoms , but little...	Spinster homolog 1 ( Spns1 ) in vertebrates , as well as Spinster ( Spin ) in Drosophila , is a hypothetical lysosomal H+-carbohydrate transporter , which functions at a late stage of autophagy . The Spin/Spns1 defect induces aberrant autolysosome formation that leads to embryonic senescence and accelerated aging sympt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Aberrant Autolysosomal Regulation Is Linked to The Induction of Embryonic Senescence: Differential Roles of Beclin 1 and p53 in Vertebrate Spns1 Deficiency
Adaptation is likely to be an important determinant of the success of many pathogens , for example when colonizing a new host species , when challenged by antibiotic treatment , or in governing the establishment and progress of long-term chronic infection . Yet , the genomic basis of adaptation is poorly understood in ...	Pathogens face a hostile and often novel environment when infecting a new host , and adaptation to this environment can be critical to a pathogen's survival . The genetic basis of pathogen adaptation is in turn important for treatment , since the consistency with which therapies succeed may depend on the extent to whic...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "microbial", "evolution", "microbial", "pathogens", "biology", "evolutionary", "biology", "microbiology", "evolutionary", "genetics" ]	2012	Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa
Upon phagocytosis , Legionella pneumophila translocates numerous effector proteins into host cells to perturb cellular metabolism and immunity , ultimately establishing intracellular survival and growth . VipD of L . pneumophila belongs to a family of bacterial effectors that contain the N-terminal lipase domain and th...	Legionella pneumophila is a pathogen bacterium that causes Legionnaires' disease accompanied by severe pneumonia . Surprisingly , this pathogen invades and replicates inside macrophages , whose major function is to detect and destroy invading microorganisms . How L . pneumophila can be “immune” to this primary immune c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "protein", "structure", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2012	VipD of Legionella pneumophila Targets Activated Rab5 and Rab22 to Interfere with Endosomal Trafficking in Macrophages
Lymphatic filariasis is a major tropical disease caused by the parasite Brugia malayi . Microfilariae ( Mf ) circulate in the peripheral blood for 2–3 hours in synchronisation with maximal feeding of the mosquito vector . When absent from the peripheral blood , Mf sequester in the capillaries of the lungs . Mf are ther...	Brugia malayi is a nematode which causes lymphatic filariasis in South and South-East Asia . Most infected people harbour many millions of the microfilarial stage of the parasite in their blood stream and yet they show few visible symptoms of disease . Vascular endothelial cells ( EC ) line the blood vessels and are th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "filariasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Live Brugia malayi Microfilariae Inhibit Transendothelial Migration of Neutrophils and Monocytes
SMYD4 belongs to a family of lysine methyltransferases . We analyzed the role of smyd4 in zebrafish development by generating a smyd4 mutant zebrafish line ( smyd4L544Efs1 ) using the CRISPR/Cas9 technology . The maternal and zygotic smyd4L544Efs1 mutants demonstrated severe cardiac malformations , including defects ...	SMYD4 belongs to a SET and MYND domain-containing lysine methyltransferase . In zebrafish , smyd4 is ubiquitously expressed in early embryos and becomes enriched in the developing heart at 48 hours post-fertilization ( hpf ) . We generated a smyd4 mutant zebrafish line ( smyd4L544Efs*1 ) using the CRISPR/Cas9 technolog...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "enzymes", "cardiac", "ventricles", "enzymology", "vertebrates", "dna-binding", "proteins", "animals", "animal", "models", "osteichthyes", "organisms", "developmental", "biology", "model", "orga...	2018	The roles of SMYD4 in epigenetic regulation of cardiac development in zebrafish
Some pathogens have evolved mechanisms to overcome host immune defenses by inhibiting host defense signaling pathways and suppressing the expression of host defense effectors . We present evidence that Pseudomonas aeruginosa is able to suppress the expression of a subset of immune defense genes in the animal host Caeno...	Bacterial pathogens have evolved mechanisms to overcome the immune defenses that animals and plants deploy against them . In some cases , this involves directly interfering with the proper functioning of the immune system . Because pathogens that employ these strategies are often the most deadly and difficult to treat ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "immunology/immunomodulation", "genetics", "and", "genomics/gene", "expression", "immunology/innate", "immunity", "microbiology/cellular", "microbiology", "and"...	2008	Pseudomonas aeruginosa Suppresses Host Immunity by Activating the DAF-2 Insulin-Like Signaling Pathway in Caenorhabditis elegans
The reciprocal differentiation of T helper 17 ( TH17 ) cells and induced regulatory T ( iTreg ) cells plays a critical role in both the pathogenesis and resolution of diverse human inflammatory diseases . Although initial studies suggested a stable commitment to either the TH17 or the iTreg lineage , recent results rev...	In order to perform complex functions upon pathogenic challenges , the immune system needs to efficiently deploy a repertoire of specialized cells by inducing the differentiation of precursor cells into effector cells . In a critical process of the adaptive immune system , one common type of precursor cell can give ris...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "theoretical", "biology", "immunology", "biology", "computational", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	A Mathematical Model for the Reciprocal Differentiation of T Helper 17 Cells and Induced Regulatory T Cells
In Uganda , control of intestinal schistosomiasis with preventive chemotherapy is typically focused towards treatment of school-aged children; the needs of younger children are presently being investigated as in lakeshore communities very young children can be infected . In the context of future epidemiological monitor...	In sub-Saharan Africa , intestinal schistosomiasis is a debilitating disease caused by a worm infection . To arrest disease progression , de-worming medications are given out , often en masse , to school-aged children . In Uganda , however , much younger children can be infected , and in lakeshore communities both infa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "evidence-based", "healthcare", "pediatrics", "and", "child", "health" ]	2011	Schistosoma mansoni Infections in Young Children: When Are Schistosome Antigens in Urine, Eggs in Stool and Antibodies to Eggs First Detectable?
Half of the human population is at risk of infection by an arthropod-borne virus . Many of these arboviruses , such as West Nile , dengue , and Zika viruses , infect humans by way of a bite from an infected mosquito . This infectious inoculum is insect cell-derived giving the virus particles distinct qualities not pres...	Many emerging viruses of public health concern are arthropod-borne , including tick-borne encephalitis , dengue , Zika , chikungunya , and West Nile viruses . The arboviruses are maintained in nature via virus-specific transmission cycles , involving arthropod ( e . g . mosquitos , midges , and ticks ) and vertebrate a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "transfection", "invertebrates", "medicine", "and", "health", "sciences", "luciferase", "body", "fluids", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "microbiology", "enzymology", "animals", "viruses", "lymph", "nodes", "rna", "viruses", "lymph...	2017	Mosquito cell-derived West Nile virus replicon particles mimic arbovirus inoculum and have reduced spread in mice
Inhibition of N-myristoyltransferase has been validated pre-clinically as a target for the treatment of fungal and trypanosome infections , using species-specific inhibitors . In order to identify inhibitors of protozoan NMTs , we chose to screen a diverse subset of the Pfizer corporate collection against Plasmodium fa...	Inhibition of N-myristoyltransferase has been validated pre-clinically as a target for the treatment of fungal and trypanosome infections , using species-specific inhibitors . In order to identify inhibitors of protozoan NMTs , we chose to screen a diverse subset of the Pfizer corporate collection against Plasmodium fa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicinal", "chemistry", "emerging", "infectious", "diseases", "chemistry", "biology", "microbiology", "parasitology", "parasite", "physiology" ]	2012	Selective Inhibitors of Protozoan Protein N-myristoyltransferases as Starting Points for Tropical Disease Medicinal Chemistry Programs
Genotype III ( GIII ) Japanese encephalitis virus ( JEV ) predominance has gradually been replaced by genotype I ( GI ) over the last 20 years in many Asian countries . This genotype shift raises concerns about the protective efficacy of Japanese encephalitis ( JE ) vaccines , as all of the currently licensed JE vaccin...	Japanese encephalitis virus ( JEV ) is a mosquito-borne flavivirus that causes Japanese encephalitis ( JE ) in humans and reproductive disorders in pigs . JEV is phylogenetically classified into five genotypes . JEV genotype III ( GIII ) was historically dominant throughout most of Asia , but has been replaced by genot...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "urology", "viral", "vaccines", "medicine", "and", "health", "sciences", "immune", "physiology", "viral", "transmission", "and", "infection", "immunology", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "vaccines", "preventive", "medicin...	2019	Partial cross-protection between Japanese encephalitis virus genotype I and III in mice
Studies of the immunogenicity of the killed bivalent whole cell oral cholera vaccine , Shanchol , have been performed in historically cholera-endemic areas of Asia . There is a need to assess the immunogenicity of the vaccine in Haiti and other populations without historical exposure to Vibrio cholerae . We measured im...	Studies evaluating the ability of the killed bivalent whole cell oral cholera vaccine , Shanchol , to elicit an immune response have been performed in historically cholera-endemic areas of Asia . There is a need to assess whether the vaccine is able to elicit an immune response in Haiti and other populations without hi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "medicine", "and", "health", "sciences", "global", "health", "biology", "and", "life", "sciences", "immunology" ]	2014	Immunogenicity of a Killed Bivalent (O1 and O139) Whole Cell Oral Cholera Vaccine, Shanchol, in Haiti
Humans who experience a primary dengue virus ( DENV ) infection develop antibodies that preferentially neutralize the homologous serotype responsible for infection . Affected individuals also generate cross-reactive antibodies against heterologous DENV serotypes , which are non-neutralizing . Dengue cross-reactive , no...	Dengue is a mosquito-borne viral disease of humans . The dengue virus complex is made up of four viruses designated as serotypes . People experiencing their first infection develop immune responses that prevent re-infection with the same serotype only . People experiencing a second infection with a new serotype face a ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "medicine", "infectious", "diseases", "immunity", "immunology", "biology", "microbiology", "viral", "diseases", "dengue", "immune", "response", "immunoglobulins" ]	2011	In-Depth Analysis of the Antibody Response of Individuals Exposed to Primary Dengue Virus Infection
The formation of mature cells by blood stem cells is very well understood at the cellular level and we know many of the key transcription factors that control fate decisions . However , many upstream signalling and downstream effector processes are only partially understood . Genome wide association studies ( GWAS ) ha...	In this manuscript we report on a follow-up study of the GWAS loci associated with the platelet size and number . A GWAS meta-analysis identified 68 genetic loci controlling platelet size and number . Only a quarter of those genes , however , are known regulators of hematopoiesis . To determine function of the remainin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "medicine", "and", "health", "sciences", "body", "fluids", "blood", "anatomy", "platelets", "biology", "and", "life", "sciences", "hematology" ]	2014	A Loss of Function Screen of Identified Genome-Wide Association Study Loci Reveals New Genes Controlling Hematopoiesis
In eukaryotes , the spatial and temporal organization of genome duplication gives rise to distinctive profiles of replication origin usage along the chromosomes . While it has become increasingly clear that these programs are important for cellular physiology , the mechanisms by which they are determined and modulated ...	The duplication of the genetic material is a highly conserved and tightly regulated process that is essential for cell proliferation . DNA synthesis initiates at sites called origins that are distributed throughout the genome . Replication origins are not all used equivalently , and their patterns of activation along t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "nucleic", "acid", "synthesis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "fungi", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "dna", "mammalian", "genomics", "synthesis", "phase", "schizosaccharomyces", "d...	2018	CDK activity provides temporal and quantitative cues for organizing genome duplication

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