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Owing to their phylogenetic position , cartilaginous fishes ( sharks , rays , skates , and chimaeras ) provide a critical reference for our understanding of vertebrate genome evolution . The relatively small genome of the elephant shark , Callorhinchus milii , a chimaera , makes it an attractive model cartilaginous fis...	Cartilaginous fishes ( sharks , rays , skates , and chimaeras ) are the phylogenetically oldest group of living jawed vertebrates . They are also an important outgroup for understanding the evolution of bony vertebrates such as human and teleost fishes . We performed survey sequencing ( 1 . 4× coverage ) of a chimaera ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "teleost", "fishes", "eukaryotes", "vertebrates", "evolutionary", "biology", "genetics", "and", "genomics" ]	2007	Survey Sequencing and Comparative Analysis of the Elephant Shark (Callorhinchus milii) Genome
DNA damage resulting from intrinsic or extrinsic sources activates DNA damage responses ( DDRs ) centered on protein kinase signaling cascades . The usual consequences of inducing DDRs include the activation of cell cycle checkpoints together with repair of the damaged DNA or induction of apoptosis . Many DNA viruses e...	As intracellular parasites , viruses often redirect cellular pathways to facilitate their own replication . Infection by DNA viruses often lead to the activation of host DNA damage response pathways , which normally function to repair damage to host chromosomes . Some DNA viruses depend on this infection-induced DNA da...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2011	An E2F1-Mediated DNA Damage Response Contributes to the Replication of Human Cytomegalovirus
Behavioural anomalies suggesting an inner ear disorder were observed in a colony of transgenic mice . Affected animals were profoundly deaf . Severe hair bundle defects were identified in all outer and inner hair cells ( OHC , IHC ) in the cochlea and in hair cells of vestibular macular organs , but hair cells in crist...	Sensory “hair” cells in the inner ear derive their name from an organised bundle of mechano-sensory “stereocilia” on their apical surface . The finger-like stereocilia are composed of actin filaments and increase in height staircase-like in one direction across the cell surface , a system which provides a defined polar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "integumentary", "system", "ears", "neuroscience", "cell", "polarity", "outer", "hair", "cells", "organ", "of", "corti", "inner", "ear", "immunologic", "techniques", "research", "and", "analysis", "metho...	2017	Disruption of SorCS2 reveals differences in the regulation of stereociliary bundle formation between hair cell types in the inner ear
DNA methylation is an epigenetic mark that is associated with transcriptional repression of transposable elements and protein-coding genes . Conversely , transcriptionally active regulatory regions are strongly correlated with histone 3 lysine 4 di- and trimethylation ( H3K4m2/m3 ) . We previously showed that Arabidops...	A number of factors contribute to the organization of eukaryotic genomes and the expression state of the underlying genes . For example , cytosine bases can be modified with the addition of a methyl-group . In the model plant Arabidopsis thaliana , methylated cytosines are typically associated with transcriptionally re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Interplay between Active Chromatin Marks and RNA-Directed DNA Methylation in Arabidopsis thaliana
Antigenic variation is employed by many pathogens to evade the host immune response , and Trypanosoma brucei has evolved a complex system to achieve this phenotype , involving sequential use of variant surface glycoprotein ( VSG ) genes encoded from a large repertoire of ~2 , 000 genes . T . brucei express multiple , s...	Antigenic variation is a system whereby pathogens switch identity of a protein that is exposed to the host adaptive immune response as a way of remaining one step ahead and avoiding being detected . African trypanosomes have evolved a spectacularly elaborate system of antigenic variation , with variants being used from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "immunology", "antigenic", "variation", "parasitic", "protozoans", "genetic", "mapping", "protozoans", "genome", "analysis", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", ...	2019	Application of long read sequencing to determine expressed antigen diversity in Trypanosoma brucei infections
Signal crosstalk within biological communication networks is common , and such crosstalk can have unexpected consequences for decision making in heterogeneous communities of cells . Here we examined crosstalk within a bacterial community composed of five strains of Bacillus subtilis , with each strain producing a varia...	Bacteria can communicate with each other using chemical signals to activate genetic expression in a process known as quorum sensing . Quorum sensing in bacteria is known to regulate a number collective behaviors in bacteria such as biofilm formation , antibiotic production and production of virulence factors which lead...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "neural", "networks", "engineering", "and", "technology", "pathogens", "signal", "processing", "bacillus", "signaling", "networks", "microbiology", "neuroscience", "prokaryotic", "model...	2019	A neural network model predicts community-level signaling states in a diverse microbial community
In eukaryotic cells , environmental and developmental signals alter chromatin structure and modulate gene expression . Heterochromatin constitutes the transcriptionally inactive state of the genome and in plants and mammals is generally characterized by DNA methylation and histone modifications such as histone H3 lysin...	The ability of eukaryotic cells to respond to external stimuli depends on the coordinated activation and repression of specific subsets of genes , often relying on chromatin structure modification . Here , we have characterized a locus-specific mechanism to repress gene expression by the action of an Arabidopsis thalia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "biology", "gene", "expression", "genetics", "plant", "genetics", "epigenetics", "biology", "dna", "modification", "plant", "cell", "biology", "molecular", "biology", "genetics", "and", "genomics", "histone", "modification" ]	2012	The SET-Domain Protein SUVR5 Mediates H3K9me2 Deposition and Silencing at Stimulus Response Genes in a DNA Methylation–Independent Manner
Typhoid and paratyphoid fever are endemic in Hongta District and their prevalence , at 113 per 100 , 000 individuals , remains the highest in China . However , the exact sources of the disease and its main epidemiological characteristics have not yet been clearly identified . Numbers of typhoid and paratyphoid cases pe...	Typhoid and paratyphoid epidemics are serious events in low-income countries; these diseases are notorious for their high infection rate , long duration , and heavy health burden . In China , typhoid and paratyphoid are considered to be under control , although the situation varies considerably from place to place . Du...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "environmental", "epidemiology", "spatial", "epidemiology", "epidemiological", "methods" ]	2013	Spatiotemporal Transmission and Determinants of Typhoid and Paratyphoid Fever in Hongta District, Yunnan Province, China
The vector-borne disease leishmaniasis is transmitted to humans by infected female sand flies , which transmits Leishmania parasites together with saliva during blood feeding . In Iran , cutaneous leishmaniasis ( CL ) is caused by Leishmania ( L . ) major and L . tropica , and their main vectors are Phlebotomus ( Ph . ...	Leishmaniasis is a vector-borne disease transmitted to humans by an infected sand fly bite , through which Leishmania parasites and saliva are co-delivered into the host skin . Despite the numerous studies performed in this area , no vaccine is yet available to control this neglected disease in humans . During the past...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ears", "immunology", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans", "otology", "ear", "infections", "protozoans", "leishmania", "insect", "vectors", "antibody", "response", "digestive", "system", "infectiou...	2019	DNA plasmid coding for Phlebotomus sergenti salivary protein PsSP9, a member of the SP15 family of proteins, protects against Leishmania tropica
Expansion of the CGG•CCG-repeat tract in the 5′ UTR of the FMR1 gene to >200 repeats leads to heterochromatinization of the promoter and gene silencing . This results in Fragile X syndrome ( FXS ) , the most common heritable form of mental retardation . The mechanism of gene silencing is unknown . We report here that a...	Fragile X syndrome is the leading cause of heritable intellectual disability . The affected gene , FMR1 , encodes FMRP , a protein that regulates the synthesis of a number of important neuronal proteins . The causative mutation is an increase in the number of CGG•CCG-repeats found at the beginning of the FMR1 gene . Al...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/transcription", "initiation", "and", "activation", "molecular", "biology/dna", "methylation", "neurological", "disorders/developmental", "and", "pediatric", "neurology", "genetics", "and", "genomics/epigenetics...	2008	SIRT1 Inhibition Alleviates Gene Silencing in Fragile X Mental Retardation Syndrome
The coordination of chromosome segregation with cell growth is fundamental to the proliferation of any organism . In most unicellular bacteria , chromosome segregation is strictly coordinated with cell division and involves ParA that moves the ParB nucleoprotein complexes bi- or unidirectionally toward the cell pole ( ...	To proliferate , cells synchronize growth and division with chromosome segregation . In unicellular bacteria , chromosomes segregate during replication by active movement of nucleoprotein complexes toward the cell pole ( s ) . Here , we asked the question how active chromosome segregation occurs in the absence of cell ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "cell", "physiology", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "fungal", "spore", "germination", "pathogens", "cell", "cycle", "and", "cell", "division", "cell", "processes", "mic...	2016	Unique Function of the Bacterial Chromosome Segregation Machinery in Apically Growing Streptomyces - Targeting the Chromosome to New Hyphal Tubes and its Anchorage at the Tips
Gram-negative bacteria secrete virulence factors and assemble fibre structures on their cell surface using specialized secretion systems . Three of these , T2SS , T3SS and T4PS , are characterized by large outer membrane channels formed by proteins called secretins . Usually , a cognate lipoprotein pilot is essential f...	Pathogenic bacteria deliver toxins and virulence proteins into host cells and tissues using specialised secretion systems such as the type II and type III secretion systems . These secretion systems have a pore formed by secretin protein subunits through which the disease causing protein effectors and toxins pass . The...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biochemistry", "biology", "microbiology", "biophysics", "bacterial", "pathogens" ]	2012	Structural and Functional Insights into the Pilotin-Secretin Complex of the Type II Secretion System
To generate complex bilateral motor patterns such as those underlying birdsong , neural activity must be highly coordinated across the two cerebral hemispheres . However , it remains largely elusive how this coordination is achieved given that interhemispheric communication between song-control areas in the avian cereb...	As for all vertebrates , the songbird cerebrum has two halves ( or hemispheres ) , each of which controls mainly the muscles in one half of the body . Many motor behaviors such as singing rely on high coordination of activity in both hemispheres , yet little is known about the neural mechanisms of this coordination . B...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Rapid Interhemispheric Switching during Vocal Production in a Songbird
LXR ( Liver X Receptors ) act as “sensor” proteins that regulate cholesterol uptake , storage , and efflux . LXR signaling is known to influence proliferation of different cell types including human prostatic carcinoma ( PCa ) cell lines . This study shows that deletion of LXR in mouse fed a high-cholesterol diet recap...	Cholesterol is one of the major metabolic molecules required for a broad range of cellular processes . Recent advances in prostate cancer research have demonstrated that tumor cells need to increase their supply of cholesterol to sustain membrane building , proliferation , and survival capacities . Liver X receptors , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "models", "model", "organisms", "reproductive", "system", "biology", "anatomy", "and", "physiology", "mouse" ]	2013	Liver X Receptors Protect from Development of Prostatic Intra-Epithelial Neoplasia in Mice
Attention is a core cognitive mechanism that allows the brain to allocate limited resources depending on current task demands . A number of frontal and posterior parietal cortical areas , referred to collectively as the fronto-parietal attentional control network , are engaged during attentional allocation in both huma...	The frontal and parietal areas of the cortex control the ability to focus visuospatial attention , and damage to these areas results in profound attentional disturbances . Although much research has concentrated on where these areas are located , little is known about how these areas may function in humans . Previous s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cognitive", "neuroscience", "cognitive", "psychology", "neural", "networks", "biology", "and", "life", "sciences", "vision", "brain", "electrophysiology", "evoked", "potentials", "sensory", "perception", "cognitive", "science", "neuroscience", "neurophysiology", "attention...	2014	Dynamic Changes in Phase-Amplitude Coupling Facilitate Spatial Attention Control in Fronto-Parietal Cortex
Systems as diverse as the interacting species in a community , alleles at a genetic locus , and companies in a market are characterized by competition ( over resources , space , capital , etc ) and adaptation . Neutral theory , built around the hypothesis that individual performance is independent of group membership ,...	From fisheries and forestries to game parks and gut microbes , managing a community of organisms is much like managing a portfolio . Managers care about diversity , and calculations of risk—for extinction or financial ruin—require accurate models of the covariance between the parts of the portfolio . To model the covar...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "species", "colonization", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "invasive", "species", "neutral", "theory", "population", "genetics", "social", "sciences", "random", "variables", "covariance", "mathematics", "tongue", "...	2016	Novel Covariance-Based Neutrality Test of Time-Series Data Reveals Asymmetries in Ecological and Economic Systems
Yaws is a treponemal infection that was almost eradicated fifty years ago; however , the disease has re-emerged in a number of countries including Ghana . A single-dose of intramuscular benzathine penicillin has been the mainstay of treatment for yaws . However , intramuscular injections are painful and pose safety and...	Yaws is a tropical infection caused by a bacterium closely related to that which causes syphilis . It is transmitted from person to person through skin to skin contact and often causes papillomatous and ulcerative skin lesions , usually in young children . Without treatment , it can lead to deformities and disabilities...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "tropical", "diseases", "microbiology", "geographical", "locations", "treponematoses", "bacterial", "diseases", "signs", "and", "symptoms", "anti...	2017	A Single Dose Oral Azithromycin versus Intramuscular Benzathine Penicillin for the Treatment of Yaws-A Randomized Non Inferiority Trial in Ghana
High cost , poor compliance , and systemic toxicity have limited the use of pentavalent antimony compounds ( SbV ) , the treatment of choice for cutaneous leishmaniasis ( CL ) . Paromomycin ( PR ) has been developed as an alternative to SbV , but existing data are conflicting . We searched PubMed , Scopus , and Cochran...	Millions of people worldwide are suffering from cutaneous leishmaniasis that is caused by parasites of the genus Leishmania . Although pentavalent antimony compounds are the treatment of choice , their use is limited by high cost , poor compliance , and systemic toxicity . Paromomycin was developed to overcome such lim...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "pharmacology", "dermatology/skin", "infections" ]	2009	Is Paromomycin an Effective and Safe Treatment against Cutaneous Leishmaniasis? A Meta-Analysis of 14 Randomized Controlled Trials
Structure-specific nucleases play crucial roles in many DNA repair pathways . They must be precisely controlled to ensure optimal repair outcomes; however , mechanisms of their regulation are not fully understood . Here , we report a fission yeast protein , Pxd1 , that binds to and regulates two structure-specific nucl...	Genome stability maintenance relies on DNA repair enzymes , among which are structure-specific nucleases that cleave DNA in a sequence-independent but structure-dependent manner . It is important to understand how the activities of such nucleases are controlled , because either insufficient or excessive cleavage of DNA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "damage", "biochemistry", "genetics", "biology", "and", "life", "sciences", "dna", "dna", "repair", "dna", "recombination" ]	2014	Fission Yeast Pxd1 Promotes Proper DNA Repair by Activating Rad16XPF and Inhibiting Dna2
The eukaryotic cell cycle is the repeated sequence of events that enable the division of a cell into two daughter cells . It is divided into four phases: G1 , S , G2 , and M . Passage through the cell cycle is strictly regulated by a molecular interaction network , which involves the periodic synthesis and destruction ...	A major property of living cells is their ability to maintain mass homeostasis throughout cell divisions . It has been proposed that in order to achieve such homeostasis , some critical event ( s ) in the cell cycle will take place only when the cell has grown beyond a critical cell size . In the budding yeast Saccharo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "yeast", "and", "fungi", "microbiology", "computational", "biology", "eukaryotes", "genetics", "and", "genomics", "saccharomyces" ]	2007	Cell Size at S Phase Initiation: An Emergent Property of the G1/S Network
Melanization , an important insect defense mechanism , is mediated by clip-domain serine protease ( cSP ) cascades and is regulated by serpins . Here we show that proteolytic activation of prophenoloxidase ( PPO ) and PO-catalyzed melanization kill the baculovirus in vitro . Our quantitative proteomics and biochemical ...	Melanization is one of important modules in insect defense system . It consists of a cascade of clip-domain serine proteases ( cSPs ) that converts the zymogen prophenoloxidase ( PPO ) to active phenoloxidase ( PO ) , which is negatively regulated by serpins . PO then catalyses the formation of melanin that physically ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "molecular", "probe", "techniques", "enzymes", "immunology", "microbiology", "enzymology", "animals", "developmental", "biology", "molecular", "biology", "techniques", "...	2017	Inhibition of melanization by serpin-5 and serpin-9 promotes baculovirus infection in cotton bollworm Helicoverpa armigera
Nuclear-mitochondrial conflict ( cytonuclear incompatibility ) is a specific form of Dobzhansky-Muller incompatibility previously shown to cause reproductive isolation in two yeast species . Here , we identified two new incompatible genes , MRS1 and AIM22 , through a systematic study of F2 hybrid sterility caused by cy...	Hybrids between species are usually inviable or sterile , possibly due to functional incompatibility between genes from the different species . Incompatible genes are hypothesized to encode interacting components that cannot function properly when paired with alleles from another species . To understand how incompatibl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2010	Multiple Molecular Mechanisms Cause Reproductive Isolation between Three Yeast Species
Human Immunodeficiency Virus 1 uses for entry into host cells a receptor ( CD4 ) and one of two co-receptors ( CCR5 or CXCR4 ) . Recently , a new class of antiretroviral drugs has entered clinical practice that specifically bind to the co-receptor CCR5 , and thus inhibit virus entry . Accurate prediction of the co-rece...	Human Immunodeficiency Virus is the pathogen causing the disease AIDS . A precondition for virus entry into human cells is the contact of its glycoprotein gp120 with two cellular proteins , a receptor and a co-receptor . Depending on the viral strain , one specific co-receptor is used . The type of co-receptor used is ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "computer", "science/applications", "virology/diagnosis", "virology/immunodeficiency", "viruses", "molecular", "biology/bioinformatics", "computational", "biology/macromolecular", "sequence", "analysis", "biophysics", ...	2010	Prediction of Co-Receptor Usage of HIV-1 from Genotype
Methotrexate ( MTX ) is widely used for the treatment of childhood acute lymphoblastic leukemia ( ALL ) . The accumulation of MTX and its active metabolites , methotrexate polyglutamates ( MTXPG ) , in ALL cells is an important determinant of its antileukemic effects . We studied 194 of 356 patients enrolled on St . Ju...	One of the primary agents used in the treatment of childhood acute lymphoblastic leukemia ( ALL ) is methotrexate ( MTX ) . By better understanding its intracellular disposition , we are able to better design treatments that circumvent drug resistance and thus help improve ALL cure rates . In this study , we develop a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics/statistics", "oncology/pediatric", "oncology", "computational", "biology/systems", "biology", "hematology/acute", "lymphoblastic", "leukemia" ]	2010	Modeling Mechanisms of In Vivo Variability in Methotrexate Accumulation and Folate Pathway Inhibition in Acute Lymphoblastic Leukemia Cells
The role of host genetic variation in the development of complicated Staphylococcus aureus bacteremia ( SAB ) is poorly understood . We used whole exome sequencing ( WES ) to examine the cumulative effect of coding variants in each gene on risk of complicated SAB in a discovery sample of 168 SAB cases ( 84 complicated ...	Complications from bloodstream infection with Staphylococcus aureus ( S . aureus ) are important causes of hospitalization , significant illness , and death . The causes of these complications are not well understood , but likely involve genetic factors rendering people more susceptible to such infections , differences...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "neurochemistry", "immune", "cells", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "immunology", "microbiology", "neuroscience", "staphylococcus", "aureus", "bacterial", "diseases", "mat...	2018	Human genetic variation in GLS2 is associated with development of complicated Staphylococcus aureus bacteremia
Borna disease virus ( BDV ) is a nonsegmented , negative-strand RNA virus that employs several unique strategies for gene expression . The shortest transcript of BDV , X/P mRNA , encodes at least three open reading frames ( ORFs ) : upstream ORF ( uORF ) , X , and P in the 5′ to 3′ direction . The X is a negative regul...	All viruses rely on host cell factors to complete their life cycles . Therefore , the replication strategies of viruses may provide not only the understanding of virus pathogenesis but also useful models to disentangle the complex machinery of host cells . Translation regulation of viral mRNA is a good example of this ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "virology/persistence", "and", "latency", "molecular", "biology/translational", "regulation", "virology/viral", "replication", "and", "gene", "regulation" ]	2009	Autogenous Translational Regulation of the Borna Disease Virus Negative Control Factor X from Polycistronic mRNA Using Host RNA Helicases
We describe methods for rapid sequencing of the entire human mitochondrial genome ( mtgenome ) , which involve long-range PCR for specific amplification of the mtgenome , pyrosequencing , quantitative mapping of sequence reads to identify sequence variants and heteroplasmy , as well as de novo sequence assembly . These...	This manuscript details a novel algorithm to evaluate high-throughput DNA sequence data from whole mitochondrial genomes purified from genomic DNA , which also contains multiple fragmented nuclear copies of mtgenomes ( numts ) . 40 samples were selected from 2 distinct reference ( HapMap ) populations of African ( YRI ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "population", "genetics", "sequence", "assembly", "tools", "algorithms", "genome", "sequencing", "genome", "analysis", "tools", "population", "biology", "mitochondrial", "diseases", "sequence", "analysis", "genetic", "polymorphism", "biology", "computer", "science", "gene...	2012	Next-Generation Sequencing of Human Mitochondrial Reference Genomes Uncovers High Heteroplasmy Frequency
The heptavalent pneumococcal conjugate vaccine ( PCV7 ) was introduced in the United States ( US ) in 2000 and has significantly reduced invasive pneumococcal disease; however , the incidence of nonvaccine serotype invasive disease , particularly due to serotype 19A , has increased . The serotype 19A increase can be ex...	The 7-valent pneumococcal conjugate vaccine is a remarkable public health success story . It has significantly reduced invasive pneumococcal disease in the United States not only by protecting vaccinated children , but also by protecting unvaccinated older children and adults by herd immunity . However , there was alwa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "microbiology", "eubacteria" ]	2007	Vaccine Escape Recombinants Emerge after Pneumococcal Vaccination in the United States
Continuous cultures of mammalian cells are complex systems displaying hallmark phenomena of nonlinear dynamics , such as multi-stability , hysteresis , as well as sharp transitions between different metabolic states . In this context mathematical models may suggest control strategies to steer the system towards desired...	While the advantages of continuous culture in the biotechnological industry have been widely advocated in the literature , its adoption over batch or fed-batch modes stalls due to the complexities of these systems . In particular , continuous cell cultures display hallmark nonlinear phenomena such as multi-stability , ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "protein", "metabolism", "biological", "cultures", "metabolic", "networks", "enzymology", "cell", "metabolism", "glucose", "metabolism", "metabolites", "network", "analysis", "enzyme", "metabolism", "cell", "cultures", "...	2019	Maximum entropy and population heterogeneity in continuous cell cultures
Caenorhabditis elegans CEP-1 and its mammalian homolog p53 are critical for responding to diverse stress signals . In this study , we found that cep-1 inactivation suppressed the prolonged lifespan of electron transport chain ( ETC ) mutants , such as isp-1 and nuo-6 , but rescued the shortened lifespan of other ETC mu...	Perturbing different components of the mitochondrial electron transport chain ( ETC ) can affect the lifespan of Caenorhabditis elegans in divergent ways . ETC dysfunction can either attenuate or extend C . elegans lifespan . Here we demonstrate that the C . elegans homolog of mammalian p53 , CEP-1 , is key in mediatin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "gene", "function" ]	2014	CEP-1, the Caenorhabditis elegans p53 Homolog, Mediates Opposing Longevity Outcomes in Mitochondrial Electron Transport Chain Mutants
We report the first genome-wide association study ( GWAS ) whose sample size ( 1 , 053 Swedish subjects ) is sufficiently powered to detect genome-wide significance ( p<1 . 5×10−7 ) for polymorphisms that modestly alter therapeutic warfarin dose . The anticoagulant drug warfarin is widely prescribed for reducing the ri...	Recently , geneticists have begun assaying hundreds of thousands of genetic markers covering the entire human genome to systematically search for and identify genes that cause disease . We have extended this “genome-wide association study” ( GWAS ) method by assaying ∼326 , 000 markers in 1 , 053 Swedish patients in or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/pharmacogenomics", "pharmacology/personalized", "medicine", "mathematics/statistics" ]	2009	A Genome-Wide Association Study Confirms VKORC1, CYP2C9, and CYP4F2 as Principal Genetic Determinants of Warfarin Dose
In 2010 and 2011 , Haiti was heavily affected by a large cholera outbreak that spread throughout the country . Although national health structure-based cholera surveillance was rapidly initiated , a substantial number of community cases might have been missed , particularly in remote areas . We conducted a community-ba...	In October 2010 , a large cholera outbreak was declared in Haiti and rapidly spread throughout the country , quickly overwhelming the existing health system . Specialized treatment structures were opened rapidly , generally in cities or large villages , and decentralized treatment units or rehydration points were gradu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Geographic Distribution and Mortality Risk Factors during the Cholera Outbreak in a Rural Region of Haiti, 2010-2011
The manner in which different distributions of synaptic weights onto cortical neurons shape their spiking activity remains open . To characterize a homogeneous neuronal population , we use the master equation for generalized leaky integrate-and-fire neurons with shot-noise synapses . We develop fast semi-analytic numer...	Neurons communicate via action potentials . Typically , depolarizations caused by presynaptic firing are small , such that many synaptic inputs are necessary to exceed the firing threshold . This is the assumption made by standard mathematical approaches such as the Fokker-Planck formalism . However , in some cases the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics
Metabolic manipulation of host cells by intracellular pathogens is currently recognized to play an important role in the pathology of infection . Nevertheless , little information is available regarding mitochondrial energy metabolism in Leishmania infected macrophages . Here , we demonstrate that during L . infantum i...	Leishmania infantum , a causative agent of visceral leishmaniasis , is able to infect host macrophages and modulate a myriad of signalling pathways that contributes to the disease outcome . In order to survive , L . infantum must compete with the host for the same metabolic resources , however scarce attention has been...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Leishmania infantum Modulates Host Macrophage Mitochondrial Metabolism by Hijacking the SIRT1-AMPK Axis
Decision-making in the real world presents the challenge of requiring flexible yet prompt behavior , a balance that has been characterized in terms of a trade-off between a slower , prospective goal-directed model-based ( MB ) strategy and a fast , retrospective habitual model-free ( MF ) strategy . Theory predicts tha...	To make good decisions , we must learn to associate actions with their true outcomes . Flexibility to changes in action/outcome relationships , therefore , is essential for optimal decision-making . For example , actions can lead to outcomes that change in value – one day , your favorite food is poorly made and thus le...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "decision", "making", "applied", "mathematics", "social", "sciences", "neuroscience", "habits", "learning", "and", "memory", "simulation", "and", "modeling", "algorithms", "cognitive", "psychology", "mathematics", "statistics", "(mathematics)", "cognition", "d...	2017	Flexibility to contingency changes distinguishes habitual and goal-directed strategies in humans
The RNA exosome is the major 3′-5′ RNA degradation machine of eukaryotic cells and participates in processing , surveillance and turnover of both nuclear and cytoplasmic RNA . In both yeast and human , all nuclear functions of the exosome require the RNA helicase MTR4 . We show that the Arabidopsis core exosome can ass...	Cells rely on a number of RNA degradation pathways to ensure correct and timely processing and turnover of both coding and non-coding RNAs . Another important function of RNA degradation is the rapid elimination of misprocessed RNA species , maturation by-products , and nonfunctional RNAs that are frequently produced b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rna", "interference", "brassica", "rna", "stability", "model", "organisms", "epigenetics", "plants", "research", "and", "analysis", "methods", "arabidopsis", "thaliana", "gene", "expression", "biochemistry", "rna", "plant", "and", "algal", "models", "rna", "processin...	2014	The RNA Helicases AtMTR4 and HEN2 Target Specific Subsets of Nuclear Transcripts for Degradation by the Nuclear Exosome in Arabidopsis thaliana
Approaches to identify significant pathways from high-throughput quantitative data have been developed in recent years . Still , the analysis of proteomic data stays difficult because of limited sample size . This limitation also leads to the practice of using a competitive null as common approach; which fundamentally ...	Pathway analysis is a common approach to quickly access the pathways being regulated in the experiments . There are numerous statistics to perform pathway analysis; most of them assume that the genes or proteins are independent of each other for statistical ease . This assumption , however , is unrealistic to the real ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion", "Conclusion" ]	[ "phosphorylation", "random", "variables", "covariance", "protein", "expression", "mathematics", "tcr", "signaling", "cascade", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "mapk", "signaling", "cascades", "cytoskeleton", "research", ...	2017	A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data
Leishmaniasis is a parasitic disease that is widely prevalent in many tropical and sub-tropical regions of the world . Infection with Leishmania has been recognized to induce a striking acceleration of Human Immunodeficiency Virus Type 1 ( HIV-1 ) infection in coinfected individuals through as yet incompletely understo...	Leishmaniasis is a parasitic disease that infects several human host immune cells , including neutrophils , monocytes , and macrophages . Moreover , while HIV-1 infects monocytes and macrophages , only the infected macrophages productively release viral progenies . Importantly , patients coinfected with both pathogens ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	Leishmania Induces Survival, Proliferation and Elevated Cellular dNTP Levels in Human Monocytes Promoting Acceleration of HIV Co-Infection
Medulloblastoma is the most common malignant brain tumor in children . A subset of medulloblastoma originates from granule cell precursors ( GCPs ) of the developing cerebellum and demonstrates aberrant hedgehog signaling , typically due to inactivating mutations in the receptor PTCH1 , a pathomechanism recapitulated i...	Medulloblastoma is a common pediatric brain tumor , a subtype of which is driven by aberrant hedgehog pathway activation in cerebellar granule cell precursors . Although this tumor etiology has been intensively investigated in the well-established Ptch1+/− mouse model , knowledge is still lacking about the molecular in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "oncology", "developmental", "biology", "model", "organisms", "genetics", "biology", "genomics", "morphogenesis", "genetics", "and", "genomics" ]	2012	Nos2 Inactivation Promotes the Development of Medulloblastoma in Ptch1+/− Mice by Deregulation of Gap43–Dependent Granule Cell Precursor Migration
The viruses of the family Flaviviridae possess a positive-strand RNA genome and express a single polyprotein which is processed into functional proteins . Initially , the nonstructural ( NS ) proteins , which are not part of the virions , form complexes capable of genome replication . Later on , the NS proteins also pl...	Many positive-strand RNA viruses replicate without transcribing subgenomic RNAs otherwise often used to temporally coordinate the expression of proteins involved either in genome replication ( early ) or virion formation ( late ) . Instead , the RNA genomes of the Flaviviridae are translated into a single polyprotein ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "pestivirus", "medicine", "and", "health", "sciences", "poxviruses", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "microbiology", "enzymology", "viral", "structure", "viruses", "developmental", "biology", "rna", "viruses", "dna", "viruses", "mor...	2017	A positive-strand RNA virus uses alternative protein-protein interactions within a viral protease/cofactor complex to switch between RNA replication and virion morphogenesis
Trypanosoma cruzi , the etiological agent of Chagas disease , is a polymorphic species . Evidence suggests that the majority of the T . cruzi populations isolated from afflicted humans , reservoir animals , or vectors are multiclonal . However , the extent and the complexity of multiclonality remain to be established ,...	Trypanosoma cruzi , the cause of Chagas disease , is responsible for high levels of mortality and morbidity in many countries of Latin America . This species is very polymorphic and was recently classified into six discrete typing units ( TcI-VI ) that are associated with different geographical distribution , transmiss...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "population", "genetics", "ploidy", "microbiology", "parastic", "protozoans", "dna", "genetic", "polymorphism", "dna", "amplification", "biology", "molecular", "biology", "trypanosoma", "nucleic", "acids", "genetics", "protozoology", "molecular", "cell", "biology", "genet...	2012	Unequivocal Identification of Subpopulations in Putative Multiclonal Trypanosoma cruzi Strains by FACs Single Cell Sorting and Genotyping
Lymphatic filariasis and onchocerciasis are two chronic diseases mediated by parasitic filarial worms causing long term disability and massive socioeconomic problems . Filariae are transmitted by blood-feeding mosquitoes that take up the first stage larvae from an infected host and deliver it after maturation into infe...	Lymphatic filariasis is caused by parasitic filarial worms that are transmitted by mosquitoes , requiring uptake of larvae and distribution into the blood of the host . More than 120 million people are infected and about 30% of these individuals suffer from clinical symptoms . Reduction in transmission currently depend...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "immunology", "biology", "zoology", "parasitic", "diseases", "immune", "system" ]	2012	Immunization with L. sigmodontis Microfilariae Reduces Peripheral Microfilaraemia after Challenge Infection by Inhibition of Filarial Embryogenesis
The locomotor gait in limbed animals is defined by the left-right leg coordination and locomotor speed . Coordination between left and right neural activities in the spinal cord controlling left and right legs is provided by commissural interneurons ( CINs ) . Several CIN types have been genetically identified , includ...	Movements of left and right limbs in mammals during locomotion are controlled by distinct rhythm-generating neuronal circuits in the spinal cord . Complex interactions between these circuits provide flexible coordination of limb movements in different gaits . It was shown that interactions between left and right spinal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Mechanisms of Left-Right Coordination in Mammalian Locomotor Pattern Generation Circuits: A Mathematical Modeling View
Buruli Ulcer is a tropical skin disease caused by Mycobacterium ulcerans , which , due to scarring and contractures can lead to stigma and functional limitations . However , recent advances in treatment , combined with increased public health efforts have the potential to significantly improve disease outcome . To stud...	Buruli ulcer is an infectious skin disease , mainly occurring in West Africa . It usually starts with a small nodule that over the course of weeks progresses into an ulcer . Effective treatment with antibiotics is available , but patients often report to the hospital late , and there is a serious risk of scarring , con...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "bacterial", "diseases", "infectious", "diseases", "buruli", "ulcer", "medicine", "and", "health", "sciences", "psychology", "disabilities", "behavioral", "and", "social", "aspects", "of", "health", "global", "health", "negle...	2014	Good Quality of Life in Former Buruli Ulcer Patients with Small Lesions: Long-Term Follow-up of the BURULICO Trial
Lymphatic filariasis ( LF ) is a chronic nematode infection transmitted by mosquitoes and in sub-Saharan Africa it is caused by Wuchereria bancrofti . The disease was targeted for global elimination by 2020 using repeated community-wide mass drug administration ( MDA ) distributed in endemic areas . However , recently ...	Lymphatic filariasis is a chronic human disease caused by parasitic worms and transmitted by mosquitoes . The disease is targeted for elimination by 2020 through the treatment of the entire population at risk in endemic areas using a mass drug administration ( MDA ) strategy . After several years of MDA , there is now ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "invertebrates", "medicine", "and", "health", "sciences", "landforms", "topography", "vector-borne", "diseases", "geographical", "locations", "animals", "tanzania", "molecular", "biology", "techniques", "infectious", "disease", "control", "insect", "vectors...	2017	Lymphatic filariasis transmission on Mafia Islands, Tanzania: Evidence from xenomonitoring in mosquito vectors
Tuberculosis is still a major health problem worldwide . Currently it is not known what kind of immune responses lead to successful control and clearance of Mycobacterium tuberculosis . This gap in knowledge is reflected by the inability to develop sufficient diagnostic and therapeutic tools to fight tuberculosis . We ...	Tuberculosis is a common and potentially lethal lung disease spread worldwide . One third of the world's population is estimated to be infected with Mycobacterium tuberculosis , yet most individuals develop a latent disease which has the potential to reactivate . Some are thought to be able to clear the infection . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "diseases", "infectious", "diseases", "mycobacteria", "medicine", "and", "health", "sciences", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "bacterial", "pathogens" ]	2014	Adequate Th2-Type Response Associates with Restricted Bacterial Growth in Latent Mycobacterial Infection of Zebrafish
Herpesviruses include many important human pathogens such as herpes simplex virus , cytomegalovirus , varicella-zoster virus , and the oncogenic Epstein–Barr virus and Kaposi sarcoma–associated herpesvirus . Herpes virions contain a large icosahedral capsid that has a portal at a unique 5-fold vertex , similar to that ...	The herpesvirus family includes many important human pathogens such as herpes simplex viruses that cause cold-sores and human cytomegalovirus , a major cause of congenital abnormalities . Several herpes viruses are known to cause cancer . Herpes viruses assemble enveloped virus particles ( virions ) that incorporate a ...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "herpes", "simplex", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "nucleocapsids", "viral", "structure", "viruses", "dna", "viruses", "herpesviruses", "herpes", "simplex", "virus-1", "medica...	2018	Structure of the herpes simplex virus portal-vertex
Many plant bacterial pathogens including Pseudomonas species , utilize the type III secretion system ( T3SS ) to deliver effector proteins into plant cells . Genes encoding the T3SS and its effectors are repressed in nutrient-rich media but are rapidly induced after the bacteria enter a plant or are transferred into nu...	The induction of the type III secretion system ( T3SS ) is of great importance to the pathogenesis of bacterial pathogens in host plants . Pseudomonas savastanoi pv . phaseolicola ( Psph ) causes halo blight disease on beans . We discovered that the bicistronic genes in the rhpPC locus of Psph act coordinately to regul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Two components of the rhpPC operon coordinately regulate the type III secretion system and bacterial fitness in Pseudomonas savastanoi pv. phaseolicola
The surveillance of influenza activity is critical to early detection of epidemics and pandemics and the design of disease control strategies . Case reporting through a voluntary network of sentinel physicians is a commonly used method of passive surveillance for monitoring rates of influenza-like illness ( ILI ) world...	Influenza contributes substantially to global morbidity and mortality each year , and epidemiological surveillance for influenza is typically conducted by sentinel physicians and health care providers recruited to report cases of influenza-like illness . While population coverage and representativeness , and geographic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "medical", "personnel", "influenza", "atmospheric", "science", "spatial", "epidemiology", "health", "care", "health", "care", "providers", "infectious", "disease", "control", "humidity", "publi...	2018	Deploying digital health data to optimize influenza surveillance at national and local scales
Among broadly neutralizing antibodies to HIV , 10E8 exhibits greater neutralizing breadth than most . Consequently , this antibody is the focus of prophylactic/therapeutic development . The 10E8 epitope has been identified as the conserved membrane proximal external region ( MPER ) of gp41 subunit of the envelope ( Env...	The trimeric Env glycoprotein located on HIV surface is the target of broadly neutralizing antibodies and is the focus of vaccine and therapeutic approaches to prevent HIV infection . Structural studies with HIV Env trimers have shed light on the complete epitopes of several broadly neutralizing antibodies . However , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "condensed", "matter", "physics", "microbiology", "viral", "structure", "retroviruses", "viruses", "immunodefi...	2017	Lipid interactions and angle of approach to the HIV-1 viral membrane of broadly neutralizing antibody 10E8: Insights for vaccine and therapeutic design
Although it has been known for nearly a century that strains of Trypanosoma cruzi , the etiological agent for Chagas' disease , are enzootic in the southern U . S . , much remains unknown about the dynamics of its transmission in the sylvatic cycles that maintain it , including the relative importance of different tran...	The parasite Trypanosoma cruzi , transmitted by insect vectors , causes Chagas' disease , which affects millions of people throughout the Americas and over 100 other mammalian species . In the United States , infection in humans is believed rare , but prevalence is high in hosts like raccoons and opossums in the southe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "ecology/population", "ecology", "mathematics/nonlinear", "dynamics" ]	2010	Estimating Contact Process Saturation in Sylvatic Transmission of Trypanosoma cruzi in the United States
Locomotor strategies in terrestrial tetrapods have evolved from the utilisation of sinusoidal contractions of axial musculature , evident in ancestral fish species , to the reliance on powerful and complex limb muscles to provide propulsive force . Within tetrapods , a hindlimb-dominant locomotor strategy predominates ...	The transition of vertebrates from water to land is a fundamental step in the evolution of terrestrial life . Innovations that were critical to this transition were the evolution of a weight bearing pelvis , hindlimbs and their associated musculature , and the development of the “rear wheel drive” strategy that predomi...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "zebrafish", "model", "organisms", "biology", "evolutionary", "biology", "evolutionary", "developmental", "biology" ]	2011	Development and Evolution of the Muscles of the Pelvic Fin
Zika virus ( ZIKV ) and Dengue virus ( DENV ) are often co-endemic . The high protein-sequence homology of flaviviruses renders IgG induced by and directed against them highly cross-reactive against their antigen ( s ) , as observed on a large set of sera , leading to poorly reliable sero-diagnosis . We selected Domain...	The serological detection of Zika virus ( ZIKV ) is a challenge , as ZIKV infection generally leads to an immune response with a high level of cross reactivity against related viruses , such as Dengue virus . Although seroneutralization assays are the gold-standard to address specificity , a rapid and cost-effective de...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viruses", "rna", "viruses", "antibodies", "immunologic", "techniq...	2019	High specificity and sensitivity of Zika EDIII-based ELISA diagnosis highlighted by a large human reference panel
NF-κB and inflammasomes both play central roles in orchestrating anti-pathogen responses by rapidly inducing a variety of early-response cytokines and chemokines following infection . Myxoma virus ( MYXV ) , a pathogenic poxvirus of rabbits , encodes a member of the cellular pyrin domain ( PYD ) superfamily , called M0...	Myxoma virus ( MYXV ) , a rabbit-specific poxvirus pathogen , encodes diverse immunomodulatory proteins that can collectively overcome essentially all of the host immune defenses . MYXV-encoded protein M013 , a member of the cellular PYRIN domain-containing superfamily of proteins , was previously shown to be important...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "virology", "virology/immune", "evasion", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression" ]	2009	Co-Regulation of NF-κB and Inflammasome-Mediated Inflammatory Responses by Myxoma Virus Pyrin Domain-Containing Protein M013
The Hippo pathway regulates organ size , stem cell proliferation and tumorigenesis in adult organs . Whether the Hippo pathway influences establishment of stem cell niche size to accommodate changes in organ size , however , has received little attention . Here , we ask whether Hippo signaling influences the number of ...	During development , organ growth must be carefully regulated to make sure that organs achieve the correct final size needed for organ function . In organs that are made of many different types of cells , this growth regulation is likely to be particularly complex , because it is important for organs to have appropriat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Hippo Pathway Regulates Homeostatic Growth of Stem Cell Niche Precursors in the Drosophila Ovary
Validation of elimination of trachoma as a public health problem is based on clinical indicators , using the WHO simplified grading system . Chlamydia trachomatis ( Ct ) infection and anti-Ct antibody responses ( anti-Pgp3 ) have both been evaluated as alternative indicators in settings with varying levels of trachoma ...	Trachoma is a disease caused by Chlamydia trachomatis ( Ct ) . Validation of elimination of trachoma as a public health problem is based on clinical indicators . Antibody and infection data may provide a better understanding of transmission dynamics in elimination settings . Dried blood spots ( DBSs ) for antibody test...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "eye", "diseases", "sexually", "tran...	2018	Serological and PCR-based markers of ocular Chlamydia trachomatis transmission in northern Ghana after elimination of trachoma as a public health problem
Isogenic bacteria can exhibit a range of phenotypes , even in homogeneous environmental conditions . Such nongenetic individuality has been observed in a wide range of biological processes , including differentiation and stress response . A striking example is the heterogeneous response of bacteria to antibiotics , whe...	Persistence of subpopulations of bacteria to antibiotic treatments is a major problem in recurrent infections . Unlike resistance , which is passed on to the next generations , persistence is a transient trait characterized by slow growth or dormancy . It has been suggested that the existence of both persister and non-...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology" ]	2008	Nongenetic Individuality in the Host–Phage Interaction
Geographic partitioning is postulated to foster divergence of Helicobacter pylori populations as an adaptive response to local differences in predominant host physiology . H . pylori's ability to establish persistent infection despite host inflammatory responses likely involves active management of host defenses using ...	Helicobacter pylori is a genetically diverse bacterial species that infects billions of people worldwide , typically for decades . Long-term infection is a major risk factor for stomach ulcers and cancer , although most infections are benign , and the risks of various disease outcomes vary markedly among human populati...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "microbiology", "computational", "biology", "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	Helicobacter pylori Evolution: Lineage- Specific Adaptations in Homologs of Eukaryotic Sel1-Like Genes
Wolbachia bacteria are now being introduced into Aedes aegypti mosquito populations for dengue control . When Wolbachia infections are at a high frequency , they influence the local transmission of dengue by direct virus blocking as well as deleterious effects on vector mosquito populations . However , the effectivenes...	Aedes aegypti mosquitoes infected with Wolbachia symbionts are being deployed in the tropics as a way of reducing disease transmission . Some Wolbachia strains are vulnerable to high temperatures but these effects have not been evaluated outside of a laboratory setting . We reared Ae . aegypti infected with the wMel st...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "classical", "mechanics", "geographical", "locations", "australia", "mechanical", "stress", "light", "animals", "wolbachia", "electromagnetic", "radiation", "developmental", "biology", "infectious", "disease", "contr...	2019	Loss of cytoplasmic incompatibility in Wolbachia-infected Aedes aegypti under field conditions
UNC-6/Netrin is a conserved axon guidance cue that directs growth cone migrations in the dorsal-ventral axis of C . elegans and in the vertebrate spinal cord . UNC-6/Netrin is expressed in ventral cells , and growth cones migrate ventrally toward or dorsally away from UNC-6/Netrin . Recent studies of growth cone behavi...	Neural circuits are formed by precise connections between axons . During axon formation , the growth cone leads the axon to its proper target in a process called axon guidance . Growth cone outgrowth involves asymmetric protrusion driven by extracellular cues that stimulate and inhibit protrusion . How guidance cues re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "microtubules", "caenorhabditis", "enzymes", "enzymology", "neuroscience", "animals", "cell", "polarity", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems", "genetic", "interac...	2019	RHO-1 and the Rho GEF RHGF-1 interact with UNC-6/Netrin signaling to regulate growth cone protrusion and microtubule organization in Caenorhabditis elegans
Cytoplasmic transport of organelles , nucleic acids and proteins on microtubules is usually bidirectional with dynein and kinesin motors mediating the delivery of cargoes in the cytoplasm . Here we combine live cell microscopy , single virus tracking and trajectory segmentation to systematically identify the parameters...	Molecular motors , due to their transportation function , are essential to the cell , but they are often hijacked by viruses to reach their replication site . Imaging of virus trajectories provides information about the patterns of virus transport in the cytoplasm , leading to improved understanding of the underlying m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "virology", "computational", "biology/systems", "biology", "computational", "biology" ]	2009	A Stochastic Model for Microtubule Motors Describes the In Vivo Cytoplasmic Transport of Human Adenovirus
Dengue is a serious vector-borne disease , and incidence rates have significantly increased during the past few years , particularly in 2014 in Guangzhou . The current situation is more complicated , due to various factors such as climate warming , urbanization , population increase , and human mobility . The purpose o...	Dengue transmission is a spatio-temporal process with interactions between hosts , vectors , and viruses . Its transmission also involves multiple complex or even hidden factors , such as climate , social environment , vector ecology , and host mobility . These complexities make the underlying process of dengue transmi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "china", "vector-borne", "diseases", "geographical", "locations", "social", "sciences", "spatial", "epidemiology", "human", "mobility", "animals", "infectious", "disease", "...	2016	Inferring the Spatio-temporal Patterns of Dengue Transmission from Surveillance Data in Guangzhou, China
Neutrophils and dendritic cells ( DCs ) converge at localized sites of acute inflammation in the skin following pathogen deposition by the bites of arthropod vectors or by needle injection . Prior studies in mice have shown that neutrophils are the predominant recruited and infected cells during the earliest stage of L...	Prior studies in mice have shown that the inoculation of Leishmania major into the skin by sand fly bite or by needle provokes a massive recruitment of neutrophils that take up the parasite , and that this response somehow suppresses immunity since neutrophil depletion results in better control of the infection . We in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology" ]	2012	Efficient Capture of Infected Neutrophils by Dendritic Cells in the Skin Inhibits the Early Anti-Leishmania Response
YAP1 is a major effector of the Hippo pathway and a well-established oncogene . Elevated YAP1 activity due to mutations in Hippo pathway components or YAP1 amplification is observed in several types of human cancers . Here we investigated its genomic binding landscape in YAP1-activated cancer cells , as well as in non-...	The YAP1/Hippo signaling pathway is a key regulator of organ size and tissue homeostasis , and its dysregulation is linked to cancer development . Elevated activity of YAP1 , a transcriptional coactivator and well-established oncogene has been reported to occur in human cancers . Comprehensive identification of YAP1 re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	YAP1 Exerts Its Transcriptional Control via TEAD-Mediated Activation of Enhancers
Kaposi's sarcoma-associated herpesvirus ( KSHV ) is an oncogenic herpesvirus associated with multiple AIDS-related malignancies . Like other herpesviruses , KSHV has a biphasic life cycle and both the lytic and latent phases are required for tumorigenesis . Evidence suggests that KSHV lytic replication can cause genome...	The hallmarks of cancer comprise the essential elements that permit the formation and development of human tumours . Genome instability is an enabling characteristic that allows the progression of tumorigenesis through genetic mutation and therefore , understanding the molecular causes of genome instability in all canc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "medicine", "and", "health", "sciences", "rna", "transport", "cell", "biology", "nucleic", "acids", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "virology", "viruses", "and", "cancer", "biology", "and", "life", ...	2014	A Novel Mechanism Inducing Genome Instability in Kaposi's Sarcoma-Associated Herpesvirus Infected Cells
The fixation of into living matter sustains all life on Earth , and embeds the biosphere within geochemistry . The six known chemical pathways used by extant organisms for this function are recognized to have overlaps , but their evolution is incompletely understood . Here we reconstruct the complete early evolutionary...	The existence of the biosphere today depends on its capacity to fix inorganic into living matter . A wide range of evidence also suggests that the earliest life forms on Earth likewise derived their carbon from . From these two observations one can assume that the global biological carbon cycle has always been based on...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "systems", "biology", "biochemistry", "microbial", "metabolism", "evolutionary", "biology", "microbial", "evolution", "origin", "of", "life", "biology", "computational", "biology", "metabolic", "networks", "metabolism", "microbiology", "genetics", "and", "genomics" ]	2012	The Emergence and Early Evolution of Biological Carbon-Fixation
Leprosy Type 1 ( T1R ) reactions are immune-mediated events leading to nerve damage and preventable disability affecting hands , feet and eyes . Type 1 Reactions are treated with oral corticosteroids . There is little evidence on alternative treatments for patients who do not respond to steroids or experience steroid a...	Leprosy infection is cured with multi-drug therapy ( MDT ) , but patients may develop immune mediated skin and nerve lesions . These immunological reactions lead to disability and deformity secondary to neuropathy . Prednisolone is the main drug used to treat reactions but is only partially effective and patients have ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "nervous", "system", "tropical", "diseases", "social", "sciences", "neuroscience", "health", "care", "research", ...	2016	A Randomized Controlled Double Blind Trial of Ciclosporin versus Prednisolone in the Management of Leprosy Patients with New Type 1 Reaction, in Ethiopia
The Gram-negative bacterium , Legionella pneumophila , is a protozoan parasite and accidental intracellular pathogen of humans . We propose a model in which cycling through multiple protozoan hosts in the environment holds L . pneumophila in a state of evolutionary stasis as a broad host-range pathogen . Using an exper...	Legionella pneumophila is an accidental pathogen of humans , responsible for the severe , often-fatal pneumonia known as Legionnaires' disease . In the environment , L . pneumophila survives and replicates within protozoa by co-opting the intracellular machinery of these microbial predators . These freshwater encounter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "genomics", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Experimental Evolution of Legionella pneumophila in Mouse Macrophages Leads to Strains with Altered Determinants of Environmental Survival
The intuitive response to an invading pathogen is to start disease management as rapidly as possible , since this would be expected to minimise the future impacts of disease . However , since more spread data become available as an outbreak unfolds , processes underpinning pathogen transmission can almost always be cha...	Infectious disease outbreaks in human , animal and plant populations can have devastating consequences . Where and how much control should be deployed are difficult questions to answer . However , mathematical modelling is increasingly used by policy-makers to underpin these–sometimes contentious–decisions . When to ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "applied", "mathematics", "pathogens", "immunology", "simulation", "and", "modeling", "algorithms", "preventive", "medicine", "mathematics", "in...	2018	Control fast or control smart: When should invading pathogens be controlled?
How does education affect cortical organization ? All literate adults possess a region specialized for letter strings , the visual word form area ( VWFA ) , within the mosaic of ventral regions involved in processing other visual categories such as objects , places , faces , or body parts . Therefore , the acquisition ...	Reading acquisition is a major landmark in child development . We examined how it changes the child’s brain . Ten young children were scanned repeatedly , once every 2 months , before , during , and after their first year of school . In the scanner , they watched images of faces , tools , bodies , houses , numbers , an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "education", "sociology", "brain", "social", "sciences", "neuroscience", "cerebral", "hemispheres", "learning", "and", "memory", "left", "he...	2018	The emergence of the visual word form: Longitudinal evolution of category-specific ventral visual areas during reading acquisition
The type VI secretion system ( T6SS ) is a widespread protein secretion system found in many Gram-negative bacteria . T6SSs are highly regulated by various regulatory systems at multiple levels , including post-translational regulation via threonine ( Thr ) phosphorylation . The Ser/Thr protein kinase PpkA is responsib...	The bacterial type VI secretion system ( T6SS ) resembles a contractile phage tail structure and functions to deliver effectors to eukaryotic or prokaryotic target cells for the survival of many pathogenic bacteria . T6SS is highly regulated by various regulatory systems at multiple levels in response to environmental ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "plant", "biochemistry", "transmembrane", "proteins", "protein", "interactions", "plant", "microbiology", "proteins", "regulatory", "proteins", "biology", "microbiology", "bacterial", "pathogens" ]	2014	Fha Interaction with Phosphothreonine of TssL Activates Type VI Secretion in Agrobacterium tumefaciens
Understanding how a pathogen colonizes and adapts to a new host environment is a primary aim in studying emerging infectious diseases . Adaptive mutations arise among the thousands of variants generated during RNA virus infection , and identifying these variants will shed light onto how changes in tropism and species j...	When RNA viruses replicate , they do so with a high rate of error; hence , their populations are not composed of a single genotype , but of a swarm of different , yet related , genomes . This mutant spectrum has been described as the viral quasispecies , and its composition has important consequences for evolution , ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Group Selection and Contribution of Minority Variants during Virus Adaptation Determines Virus Fitness and Phenotype
Eukaryotic striatin forms striatin-interacting phosphatase and kinase ( STRIPAK ) complexes that control many cellular processes including development , cellular transport , signal transduction , stem cell differentiation and cardiac functions . However , detailed knowledge of complex assembly and its roles in stress r...	The multisubunit STRIPAK complex has been studied from yeast to human and plays a range of roles from cell-cycle arrest , fruit body formation to neuronal functions . Molecular assembly of the STRIPAK complex and its roles in stress responses are not well-documented . Fungi , with an estimated 1 . 5 million members are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cell", "fusion", "cellular", "stress", "responses", "aspergillus", "cell", "processes", "fungal", "molds", "aspergillus", "nidulans", "developmental", "biology", "fungi", "model", "organisms", "experimental", "organism", "systems", "morphogenesis", ...	2019	Assembly of a heptameric STRIPAK complex is required for coordination of light-dependent multicellular fungal development with secondary metabolism in Aspergillus nidulans
Gram-negative bacterial pathogens of plants and animals employ type III secreted effectors to suppress innate immunity . Most characterized effectors work through modification of host proteins or transcriptional regulators , although a few are known to modify small molecule targets . The Xanthomonas type III secreted a...	Infectious bacteria have many strategies to weaken the defenses of their hosts . One common strategy is to inject proteins called effectors into the host cells . Many effectors inactivate proteins that transmit defense signals , disabling the alarm systems that alert the plant to defend against the pathogen . In this p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "medicine", "and", "health", "sciences", "yeast", "infections", "pathology", "and", "laboratory", "medicine", "immunology", "immune", "suppression", "toxicology", "toxicity", "fungi", "plant", "science", "rice", "model", "organisms", "metabolites", ...	2017	The effector AvrRxo1 phosphorylates NAD in planta
Identifying environmentally-specific genetic effects is a key challenge in understanding the structure of complex traits . Model organisms play a crucial role in the identification of such gene-by-environment interactions , as a result of the unique ability to observe genetically similar individuals across multiple dis...	Identifying gene-by-environment interactions is important for understand the architecture of a complex trait . Discovering gene-by-environment interaction requires the observation of the same phenotype in individuals under different environments . Model organism studies are often conducted under different environments ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "genome-wide", "association", "studies", "biology", "animal", "genetics" ]	2014	Meta-Analysis Identifies Gene-by-Environment Interactions as Demonstrated in a Study of 4,965 Mice
Cryptosporidium are parasitic protozoa that infect humans , domestic animals , and wildlife globally . In the United States , cryptosporidiosis occurs in an estimated 750 , 000 persons annually , and is primarily caused by either of the Cryptosporidium parvum genotypes 1 and 2 , exposure to which occurs through ingesti...	We examined if and how social inequality in the United States influences seropositivity to Cryptosporidium parvum . By using nationwide data on parasite seropositivity , demographics , and household metrics of socioeconomic status provided through the National Health and Nutritional Examination Survey , we quantified h...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Household Socioeconomic and Demographic Correlates of Cryptosporidium Seropositivity in the United States
The World Health Organization ( WHO ) in collaboration with partners is developing a toolkit of resources to guide lymphatic filariasis ( LF ) morbidity management and disability prevention ( MMDP ) implementation and evaluation . Direct health facility inspection is the preferred method for documenting the readiness o...	Prior to this assessment , there was a need for clearly defined , measurable indicators for global lymphoedema management programmes to use to evaluate their lymphoedema morbidity management and disability prevention services . The results presented in this report outline a framework for indicators to assess healthcare...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "hydrocele", "pathology", "and", "laboratory", "medicine", "education", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "health", "care", "health", "services", "administration", "and", "managem...	2018	A Delphi consultation to assess indicators of readiness to provide quality health facility-based lymphoedema management services
Hepatitis C virus ( HCV ) naturally infects only humans and chimpanzees . The determinants responsible for this narrow species tropism are not well defined . Virus cell entry involves human scavenger receptor class B type I ( SR-BI ) , CD81 , claudin-1 and occludin . Among these , at least CD81 and occludin are utilize...	The hepatitis C virus ( HCV ) infects only humans and chimpanzees , which has hampered development of suitable animal models . The inability of HCV to penetrate non-human cells is primarily due to inefficient usage of non-human CD81 and occludin . In this study we adapted HCV to mouse CD81 . Efficient utilization of mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/animal", "models", "of", "infection", "virology/host", "invasion", "and", "cell", "entry" ]	2010	Adaptation of Hepatitis C Virus to Mouse CD81 Permits Infection of Mouse Cells in the Absence of Human Entry Factors
Hosts are likely to respond to parasitic infections by a combination of resistance ( expulsion of pathogens ) and tolerance ( active mitigation of pathology ) . Of these strategies , the basis of tolerance in animal hosts is relatively poorly understood , with especially little known about how tolerance is manifested i...	Hosts do not always resist parasites . And once infection establishes , relatively little is known of how naturally occurring hosts tolerate ( mitigate for ) adverse effects , or what the life history consequences of this tolerance may be . In this article we demonstrate a pattern of tolerance to parasitic worms and ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "immunology", "ecology", "and", "environmental", "sciences" ]	2014	An Immunological Marker of Tolerance to Infection in Wild Rodents
Buruli ulcer ( BU ) is a chronic necrotizing infectious skin disease caused by Mycobacterium ulcerans . The treatment with BU-specific antibiotics is initiated after clinical suspicion based on the WHO clinical and epidemiological criteria . This study aimed to estimate the predictive values of these criteria and how t...	Buruli ulcer ( BU ) is a neglected necrotizing skin disease caused by Mycobacterium ulcerans . The treatment with BU-specific antibiotics is initiated after clinical suspicion based on WHO diagnostic criteria . In this study we evaluated the WHO diagnostic guidelines for BU and how these criteria could be improved . A ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "smell", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "carcinomas", "tropical", "diseases", "cancers", "and", "neoplasms", "social", "sciences", "geographical", "locations", "neuroscience", "oncology", "bacterial", "diseases", "...	2018	Improving clinical and epidemiological predictors of Buruli ulcer
A molecular diagnostic platform with DANP-anchored hairpin primer was developed and evaluated for the rapid and cost-effective detection of Chikungunya virus ( CHIKV ) with high sensitivity and specificity . The molecule 2 , 7-diamino-1 , 8-naphthyridine ( DANP ) binds to a cytosine-bulge and emits fluorescence at 450 ...	Chikungunya has reemerged as an important mosquito-borne infection with global health significance . Rapid diagnosis plays an important role in early clinical management of patients due to lack of a vaccine and effective treatment . Laboratory diagnosis is generally accomplished by blood tests to detect virus-specific ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "fluorescence", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical"...	2016	Development of 2, 7-Diamino-1, 8-Naphthyridine (DANP) Anchored Hairpin Primers for RT-PCR Detection of Chikungunya Virus Infection
The analysis of microcircuitry ( the connectivity at the level of individual neuronal processes and synapses ) , which is indispensable for our understanding of brain function , is based on serial transmission electron microscopy ( TEM ) or one of its modern variants . Due to technical limitations , most previous studi...	Brains contain a vast number of connections between neurons , termed synapses . The precise patterns of these synaptic contacts form the structural underpinning of electrical microcircuits responsible for animal behavior . Due to their small size , synaptic contacts can be conclusively shown using only high-resolution ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/neurodevelopment" ]	2010	An Integrated Micro- and Macroarchitectural Analysis of the Drosophila Brain by Computer-Assisted Serial Section Electron Microscopy
Treponema pallidum is a highly invasive pathogen that undergoes rapid dissemination to establish widespread infection . Previous investigations identified the T . pallidum adhesin , pallilysin , as an HEXXH-containing metalloprotease that undergoes autocatalytic cleavage and degrades laminin and fibrinogen . In the cur...	Syphilis , caused by the spirochete Treponema pallidum , is a chronic sexually transmitted disease which infects 12 million people annually . Treponema pallidum is highly invasive and undergoes widespread dissemination via the circulatory system . Similar to other invasive pathogens , T . pallidum has been shown to exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "basement", "membrane", "molecular", "cell", "biology", "cell", "biology", "proteins", "extracellular", "matrix", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "extracellular", "matrix", "adhesions", "bacterial", "patho...	2012	Activation and Proteolytic Activity of the Treponema pallidum Metalloprotease, Pallilysin
Tumors develop through multiple stages , implicating multiple effectors , but the tools to assess how candidate genes contribute to stepwise tumor progression have been limited . We have developed a novel system in which progression of phenotypes in a mouse model of pancreatic islet cell tumorigenesis can be used to me...	Cancer cells accumulate multiple genetic alterations . Some of these contribute to tumor development while others are a mere by-product of genomic instability . To determine whether a candidate gene can promote tumor development , we have developed a novel experimental system using engineered viruses to deliver genes i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "oncology", "biochemistry" ]	2007	Assessing Tumor Progression Factors by Somatic Gene Transfer into a Mouse Model: Bcl-xL Promotes Islet Tumor Cell Invasion
The development of vaccines against fungi and other intracellular microbes is impeded in part by a lack of suitable adjuvants . While most current vaccines against infectious diseases preferentially induce production of antibodies , cellular immunity is essential for the resolution of fungal infections . Microbes such ...	Despite several million new systemic fungal infections annually worldwide , there are no commercial vaccines available . The lack of appropriate adjuvants is one major impediment to developing safe and effective vaccines against infections with fungal pathogens . Current vaccines against infectious diseases preferentia...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "graduates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "alumni", "vaccines", ...	2017	Ligation of Dectin-2 with a novel microbial ligand promotes adjuvant activity for vaccination
Human adenoviruses from multiple species bind to coagulation factor X ( FX ) , yet the importance of this interaction in adenovirus dissemination is unknown . Upon contact with blood , vectors based on adenovirus serotype 5 ( Ad5 ) binds to FX via the hexon protein with nanomolar affinity , leading to selective uptake ...	Adenoviruses can infect many cell types and cause a range of illnesses in humans , including respiratory , ocular and gastrointestinal disorders . These illnesses are rarely fatal; however , in immunocompromised individuals , especially young children , disseminated adenovirus infections can cause serious and life-thre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/host", "invasion", "and", "cell", "entry" ]	2010	Requirements for Receptor Engagement during Infection by Adenovirus Complexed with Blood Coagulation Factor X
Aggregation of misfolded proteins or peptides is a common feature of neurodegenerative diseases including Alzheimer’s , Parkinson’s , Huntington’s , prion and other diseases . Recent years have witnessed a growing number of reports of overlap in neuropathological features that were once thought to be unique to only one...	Aggregation of misfolded proteins or peptides is a common feature of neurodegenerative diseases . Recent years have witnessed a growing number of reports of overlap in neuropathological features specific to two or more neurodegenerative diseases in individual patients . However , the origin for the overlap remains uncl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "hela", "cells", "prions", "biological", "cultures", "brain", "vertebrates", "animals", "mammals", "cell", "cultures", "research", "and", "analysis", "methods", "hamsters", "infectious", "diseases", "specimen", "preparation", "...	2017	Cross-seeding of prions by aggregated α-synuclein leads to transmissible spongiform encephalopathy
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy . Here we present biobeam , an open-source software package that enables simulation of operational light-sheet microscopes by combining data from 105–106 multiplexed and GPU-accelerated point-spread-function calculation...	Modern microscopes permit to acquire high quality images of large fields of view , which is the result of a decade-long development of computer aided optical design . However , this high image quality can only be obtained at the very surface of biological specimens: when trying to penetrate deeper into biological tissu...	[ "Abstract", "Introduction", "Design", "and", "implementation", "Results", "Discussion", "Availability", "and", "future", "directions" ]	[ "fluorescence", "imaging", "chemical", "characterization", "diffraction", "digital", "video", "imaging", "microscopy", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "light", "microscopy", "light", "electromagnetic", "radiation", "simulation", ...	2018	Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy
Spike-timing-dependent plasticity ( STDP ) , a form of Hebbian plasticity , is inherently stabilizing . Whether and how GABAergic inhibition influences STDP is not well understood . Using a model neuron driven by converging inputs modifiable by STDP , we determined that a sufficient level of inhibition was critical to ...	Evidence suggests that maturation of inhibition is required for the development of plasticity to proceed in the visual cortex . However , the mechanisms by which increased inhibition promotes plasticity are not clear . Here we characterized the maturation of synaptic and intrinsic ionic properties of parvalbumin-positi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neuroscience/theoretical", "neuroscience", "neuroscience/neurodevelopment", "neuroscience/sensory", "systems" ]	2010	Maturation of GABAergic Inhibition Promotes Strengthening of Temporally Coherent Inputs among Convergent Pathways
Tissue-encysting coccidia , including Toxoplasma gondii and Sarcocystis neurona , are heterogamous parasites with sexual and asexual life stages in definitive and intermediate hosts , respectively . During its sexual life stage , T . gondii reproduces either by genetic out-crossing or via clonal amplification of a sing...	The parasites Toxoplasma gondii and Sarcocystis neurona have lifecycles that include a sexual stage in a definitive host and an asexual stage in intermediate hosts . For T . gondii , laboratory studies have demonstrated that the sexual stage can serve the dual purpose of producing new , virulent genotypes through recom...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2010	Self-Mating in the Definitive Host Potentiates Clonal Outbreaks of the Apicomplexan Parasites Sarcocystis neurona and Toxoplasma gondii
Human fungal pathogens like Candida albicans respond to host immune surveillance by rapidly adapting their transcriptional programs . Chromatin assembly factors are involved in the regulation of stress genes by modulating the histone density at these loci . Here , we report a novel role for the chromatin assembly-assoc...	Candida albicans is the most prevalent fungal pathogen infecting humans , causing life-threatening infections in immunocompromised individuals . Host immune surveillance imposes stress conditions upon C . albicans , to which it has to adapt quickly to escape host killing . This can involve regulation of specific genes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Candida albicans Histone Acetyltransferase Hat1 Regulates Stress Resistance and Virulence via Distinct Chromatin Assembly Pathways
Small RNAs regulate diverse biological processes by directing effector proteins called Argonautes to silence complementary mRNAs . Maturation of some classes of small RNAs involves terminal 2′-O-methylation to prevent degradation . This modification is catalyzed by members of the conserved HEN1 RNA methyltransferase fa...	Small RNAs serve as sentinels of the genome , policing activity of selfish genetic elements , modulating chromatin dynamics , and fine-tuning gene expression . Nowhere is this more important than in the germline , where endogenous small interfering RNAs ( endo-siRNAs ) and Piwi-interacting RNAs ( piRNAs ) promote forma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "gene", "regulation", "rna", "stability", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "epigenetics", "molecular", "genetics", "gene", "expression", "biology", "molecular", "biology", "rna", "rna", "processing", "nucleic"...	2012	The Caenorhabditis elegans HEN1 Ortholog, HENN-1, Methylates and Stabilizes Select Subclasses of Germline Small RNAs
Hemoglobin is the prototypic allosteric protein . Still , its molecular allosteric mechanism is not fully understood . To elucidate the mechanism of cooperativity on an atomistic level , we developed a novel computational technique to analyse the coupling of tertiary and quaternary motions . From Molecular Dynamics sim...	Hemoglobin transports oxygen from our lungs to other tissues . Its effectiveness in binding and unbinding of oxygen is based on a type of regulation called allostery . Thereby , already bound oxygen molecules in either of the four binding sites of hemoglobin increase the likelihood of oxygen binding in the other sites;...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Collective Dynamics Underlying Allosteric Transitions in Hemoglobin
Visceral leishmaniasis ( VL ) is hypoendemic in the Mediterranean region , where it is caused by the protozoan Leishmania infantum . An effective vaccine for humans is not yet available and the severe side-effects of the drugs in clinical use , linked to the parenteral administration route of most of them , are signifi...	Visceral leishmaniasis ( VL ) , caused by Leishmania infantum or L . donovani , is still one of the most threatening diseases affecting poor people in developing countries , with a fatality rate as high as 100% in two years in infected and untreated people . With no vaccine available and ineffective and toxic chemother...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Infrared Fluorescent Imaging as a Potent Tool for In Vitro, Ex Vivo and In Vivo Models of Visceral Leishmaniasis
Selection acting on genomic functional elements can be detected by its indirect effects on population diversity at linked neutral sites . To illuminate the selective forces that shaped hominid evolution , we analyzed the genomic distributions of human polymorphisms and sequence differences among five primate species re...	Comparisons of the human and chimpanzee genomes have revealed that the frequency of sequence differences between these species varies dramatically across the genome . Previously proposed explanations for this variation include a large ancestral population , variable mutation rates , or a complex speciation scenario in ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "evolutionary", "biology/human", "evolution", "computational", "biology/comparative", "sequence", "a...	2009	Widespread Genomic Signatures of Natural Selection in Hominid Evolution
ATP-dependent nucleosome-remodeling enzymes and covalent modifiers of chromatin set the functional state of chromatin . However , how these enzymatic activities are coordinated in the nucleus is largely unknown . We found that the evolutionary conserved nucleosome-remodeling ATPase ISWI and the poly-ADP-ribose polymera...	The ISWI protein is a highly conserved nucleosome remodeler that plays essential roles in regulating chromosome structure , DNA replication , and gene expression . The variety of functions associated with ISWI activity are probably connected to the ability of other cellular factors to regulate its ATP-dependent nucleos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "genetics", "and", "genomics" ]	2008	The Nucleosome-Remodeling ATPase ISWI Is Regulated by Poly-ADP-Ribosylation
Both for understanding mechanisms of disease and for the design of transgenes , it is important to understand the determinants of ribosome velocity , as changes in the rate of translation are important for protein folding , error attenuation , and localization . While there is great variation in ribosomal occupancy alo...	Ribosomes do not synthesize protein at a constant rate along transcripts , and changes in translation speed can have knock-on consequences for the expression of that protein , even altering its folding or subcellular localization . It has long been thought that RNA-level features modulate translation rates , whether by...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence", "analysis", "systems", "biology", "genome", "expression", "analysis", "genomics", "functional", "genomics", "gene", "expression", "genetics", "molecular", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2013	Positively Charged Residues Are the Major Determinants of Ribosomal Velocity
Pheromones form an essential chemical language of intraspecific communication in many animals . How olfactory systems recognize pheromonal signals with both sensitivity and specificity is not well understood . An important in vivo paradigm for this process is the detection mechanism of the sex pheromone ( Z ) -11-octad...	Animals produce chemical signals , called pheromones , to communicate with other members of the same species to regulate social behaviors . How pheromones are detected is a fundamental question . One important model system for pheromone recognition is in Drosophila , where the sex pheromone cis-vaccenyl acetate ( cVA )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "cellular", "neuroscience", "model", "organisms", "sensory", "systems", "biology", "sensory", "perception", "molecular", "cell", "biology", "neuroscience" ]	2013	Ligands for Pheromone-Sensing Neurons Are Not Conformationally Activated Odorant Binding Proteins
We demonstrate for the first time in vertebrates , that alternative splicing of interferon ( IFN ) genes can lead to a functional intracellular IFN ( iIFN ) . Fish IFN genes possess introns and in rainbow trout three alternatively spliced transcripts of the IFN1 gene exist . Two of the encoded IFNs are predicted to lac...	The type I interferon ( IFN ) family consists of multiple members which are encoded by intronless genes in reptiles , birds and mammals but intron-containing genes in amphibians and fish . They coordinate antiviral defence by binding to cell surface receptors . Here , we demonstrate for the first time in vertebrates , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Intracellular Interferons in Fish: A Unique Means to Combat Viral Infection
Lipopolysaccharide ( LPS ) is one of the most important virulence and antigenic components of Burkholderia pseudomallei , the causative agent of melioidosis . LPS diversity in B . pseudomallei has been described as typical , atypical or rough , based upon banding patterns on SDS-PAGE . Here , we studied the genetic and...	Burkholderia pseudomallei is an environmental Gram-negative bacterium and the cause of melioidosis , an often life-threatening disease affecting people in Southeast Asia and northern Australia . Melioidosis is usually contracted by bacterial inoculation , ingestion or inhalation . Effective vaccines for melioidosis are...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "genetics", "immunology", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2012	The Genetic and Molecular Basis of O-Antigenic Diversity in Burkholderia pseudomallei Lipopolysaccharide

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