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Sun-exposure is a key environmental variable in the study of human evolution . Several skin-pigmentation genes serve as classical examples of positive selection , suggesting that sun-exposure has significantly shaped worldwide genomic variation . Here we investigate the interaction between genetic variation and sun-exp...	Varying levels of sun-exposure across the world have significantly shaped human evolution . Previous analyses have found several skin pigmentation genes with evidence of strong evolutionary pressures throughout human history , manifesting as large differences in the frequency of genomic variants across populations . Bu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gene", "regulation", "variant", "genotypes", "population", "genetics", "sociology", "social", "sciences", "electromagnetic", "radiation", "genetic", "mapping", "molecular", "biology", "techniques", "evolutionary", "adaptation", "population", "biology", "research", "and", ...	2016	Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin
Worldwide , an estimated 30 to 100 million people are infected with Strongyloides stercoralis , a soil-transmitted helminth . Information on the parasite is scarce in most settings . In semi-rural Cambodia , we determined infection rates and risk factors; compared two diagnostic methods ( Koga agar plate [KAP] culture ...	The difficulty of diagnosing Strongyloides stercoralis infections is the reason why up to date , accurate information on its geographic distribution in endemic regions and the total global burden is lacking . We conducted a cross-sectional study among 458 schoolchildren , with the purpose of comparing two methods for d...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "strongyloidiasis", "neglected", "tropical", "diseases", "parasitic", "diseases", "helminth", "infection" ]	2013	Diagnosis, Treatment and Risk Factors of Strongyloides stercoralis in Schoolchildren in Cambodia
Protein-protein interactions ( PPIs ) may represent one of the next major classes of therapeutic targets . So far , only a minute fraction of the estimated 650 , 000 PPIs that comprise the human interactome are known with a tiny number of complexes being drugged . Such intricate biological systems cannot be cost-effici...	Protein-protein interactions ( PPIs ) are essential to life and various diseases states are associated with aberrant PPIs . Therefore significant efforts are dedicated to this new class of therapeutic targets . Even though it might not be possible to modulate the estimated 650 , 000 PPIs that regulate human life with d...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biochemistry/small", "molecule", "chemistry", "biochemistry/bioinformatics", "biochemistry/drug", "discovery", "chemical", "biology/small", "molecule", "chemistry" ]	2010	Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
Diabetes impacts approximately 200 million people worldwide , of whom approximately 10% are affected by type 1 diabetes ( T1D ) . The application of genome-wide association studies ( GWAS ) has robustly revealed dozens of genetic contributors to the pathogenesis of T1D , with the most recent meta-analysis identifying i...	Despite the fact that there is clearly a large genetic component to type 1 diabetes ( T1D ) , uncovering the genes contributing to this disease has proven challenging . However , in the past three years there has been relatively major progress in this regard , with advances in genetic screening technologies allowing in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetics", "biology", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2011	A Genome-Wide Meta-Analysis of Six Type 1 Diabetes Cohorts Identifies Multiple Associated Loci
Research on the biology of parasites requires a sophisticated and integrated computational platform to query and analyze large volumes of data , representing both unpublished ( internal ) and public ( external ) data sources . Effective analysis of an integrated data resource using knowledge discovery tools would signi...	Effective research in parasite biology requires analyzing experimental lab data in the context of constantly expanding public data resources . Integrating lab data with public resources is particularly difficult for biologists who may not possess significant computational skills to acquire and process heterogeneous dat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computer", "science", "biology", "computational", "biology", "microbiology", "information", "technology" ]	2012	A Semantic Problem Solving Environment for Integrative Parasite Research: Identification of Intervention Targets for Trypanosoma cruzi
While wild type polio has been nearly eradicated there will be a need to continue immunisation programmes for some time because of the possibility of re-emergence and the existence of long term excreters of poliovirus . All vaccines in current use depend on growth of virus and most of the non-replicating ( inactivated ...	There is a need for safe production of polio vaccines as eradication is approached . Empty capsids in a native conformation are produced by poliovirus and other picornaviruses seemingly as a necessary part of the assembly process , possibly to provide a reservoir of subunits in a form that is resistant to cellular path...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "insertion", "mutation", "pathogens", "immunology", "microbiology", "viral", "structure", "viruses", "v...	2017	Genetically Thermo-Stabilised, Immunogenic Poliovirus Empty Capsids; a Strategy for Non-replicating Vaccines
Impaired immune responses in the elderly lead to reduced vaccine efficacy and increased susceptibility to viral infections . Although several groups have documented age-dependent defects in adaptive immune priming , the deficits that occur prior to antigen encounter remain largely unexplored . Herein , we identify nove...	While West Nile virus ( WNV ) infection preferentially causes severe neuroinvasive disease in elderly humans , the basis for this epidemiological linkage has remained uncertain . Here , we studied the impact of aging on WNV pathogenesis and immune responses using a mouse model of infection . Old mice showed increased l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Age-Dependent Cell Trafficking Defects in Draining Lymph Nodes Impair Adaptive Immunity and Control of West Nile Virus Infection
Refolding of viral class-1 membrane fusion proteins from a native state to a trimer-of-hairpins structure promotes entry of viruses into cells . Here we present the structure of the bovine leukaemia virus transmembrane glycoprotein ( TM ) and identify a group of asparagine residues at the membrane-distal end of the tri...	Human T-cell leukaemia virus types-1 ( HTLV-1 ) and bovine leukaemia virus ( BLV ) are divergent blood borne viruses that cause hematological malignancies in humans and cattle respectively . In common with other enveloped viruses , infection of cells by HTLV-1 and BLV is dependent on the membrane fusion properties of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry", "biochemistry/protein", "chemistry", "virology" ]	2011	Charge-Surrounded Pockets and Electrostatic Interactions with Small Ions Modulate the Activity of Retroviral Fusion Proteins
The nuclear lamina lines the inner nuclear membrane providing a structural framework for the nucleus . Cellular processes , such as nuclear envelope breakdown during mitosis or nuclear export of large ribonucleoprotein complexes , are functionally linked to the disassembly of the nuclear lamina . In general , lamina di...	Viruses often adopt preexisting cellular pathways to promote their own replication . In this regard , the recently discovered alternative mechanism for the nuclear export of large messenger ribonucleoprotein ( mRNP ) complexes is particularly noteworthy . This process is mechanistically similar to the nuclear egress of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hela", "cells", "enzymes", "pathogens", "biological", "cultures", "microbiology", "enzymology", "green", "fluorescent", "protein", "viruses", "luminescent", "protein...	2016	The Prolyl Isomerase Pin1 Promotes the Herpesvirus-Induced Phosphorylation-Dependent Disassembly of the Nuclear Lamina Required for Nucleocytoplasmic Egress
Receptor tyrosine kinase KIT controls many signal transduction pathways and represents a typical allosterically regulated protein . The mutation-induced deregulation of KIT activity impairs cellular physiological functions and causes serious human diseases . The impact of hotspots mutations ( D816H/Y/N/V and V560G/D ) ...	Receptor tyrosine kinase KIT plays a crucial role in the regulation of cell signaling . This allosterically controlled activity may be affected by gain-of-function mutations that promote the development of several cancers . Identification of the molecular basis of KIT constitutive activation and allosteric regulation h...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "oncology", "physics", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology", "biophysics" ]	2014	Hotspot Mutations in KIT Receptor Differentially Modulate Its Allosterically Coupled Conformational Dynamics: Impact on Activation and Drug Sensitivity
Obesity-associated metabolic complications are generally considered to emerge from abnormalities in carbohydrate and lipid metabolism , whereas the status of protein metabolism is not well studied . Here , we performed comparative polysome and associated transcriptional profiling analyses to study the dynamics and func...	Chronic diseases including obesity and associated metabolic abnormalities have become the greatest threat to human health worldwide . How metabolic organs and organelles adapt to nutritional fluctuations , or fail to do so , remains incompletely understood . To explore these issues , we developed a new platform to expl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "systems", "biology", "biochemistry", "medicine", "public", "health", "and", "epidemiology", "model", "organisms", "nutrition", "global", "health", "endocrinology", "genetics", "and", "genomics", "biology", "diabetes", "and", "endocrinology", "molecular",...	2012	Polysome Profiling in Liver Identifies Dynamic Regulation of Endoplasmic Reticulum Translatome by Obesity and Fasting
Long interspersed nuclear element-1s ( LINE-1s , or L1s ) are an active family of retrotransposable elements that continue to mutate mammalian genomes . Despite the large contribution of L1 to mammalian genome evolution , we do not know where active L1 particles ( particles in the process of retrotransposition ) are lo...	Long interspersed nuclear elements ( LINEs ) are a class of retrotransposable elements that mutate mammalian genomes . LINEs have been highly successful in the human genome , multiplying to over 800 , 000 copies . The LINE-encoded replication machinery is also used by other retrotransposons , and in total , has been re...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "hela", "cells", "gene", "regulation", "biological", "cultures", "cloning", "immunoprecipitation", "forms", "of", "dna", "cell", "cultures", "dna", "molecular", "biology", "techniques", "cell", "nucleus", "cellular", "structures", "and", "organelles", "research", "and...	2017	A conserved role for the ESCRT membrane budding complex in LINE retrotransposition
Organismal size depends on the interplay between genetic and environmental factors . Genome-wide association ( GWA ) analyses in humans have implied many genes in the control of height but suffer from the inability to control the environment . Genetic analyses in Drosophila have identified conserved signaling pathways ...	Genetic studies in Drosophila have elucidated conserved signaling pathways and environmental factors that together control organismal size . In humans , hundreds of genes are associated with height variation , but these associations have not been performed in a controlled environment . As a result we are still lacking ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Genome-Wide Analysis Reveals Novel Regulators of Growth in Drosophila melanogaster
Iron is an essential nutrient for bacterial pathogenesis , but in the host , iron is tightly sequestered , limiting its availability for bacterial growth . Although this is an important arm of host immunity , most studies examine how bacteria respond to iron restriction in laboratory rather than host settings , where t...	One of the most well-studied phenomena in microbiology is nutritional immunity , or how the host withholds nutrients such as iron to combat infection . As part of this , researchers have characterized how many pathogens respond to iron restriction . However , these studies are often conducted in laboratory media rather...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biofilms", "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "microbiology", "regulator", "genes", "signs", "and", "symptoms", "gene", "types", "sequence", "motif", "analysis", "mo...	2016	Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection
With the improvements in diagnostic techniques , Bartonella henselae ( B . henselae ) infection has recently been recognized to cause a widening spectrum of diseases . Cats are the natural reservoir hosts of B . henselae . The current study aims to investigate the prevalence of B . henselae infection in the cat populat...	Bartonella infection ( Bartonella henselae in paticular ) is responsible for a widening spectrum of human diseases . Cats are thought as the major source of human infections . In most of the developing countries , however , this infection lacks recognition especially in clinicians . Some well known bartonelloses , like...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "microbiology", "parasitic", "diseases", "babesiosis", "bartonellosis", "bacterial", "diseases", "neglected", "tropical", "diseases", "trench", "fever", "cat", "scratch", "dise...	2011	Bacteriological and Molecular Identification of Bartonella Species in Cats from Different Regions of China
Non-genetic phenotypic variations play a critical role in the adaption to environmental changes in microbial organisms . Candida albicans , a major human fungal pathogen , can switch between several morphological phenotypes . This ability is critical for its commensal lifestyle and for its ability to cause infections ....	The capacity of the yeast Candida albicans to grow in several cellular forms—a phenomenon known as phenotypic plasticity—is critical for its survival and for its ability to thrive and cause infection in the human host . In this study , we report a novel form of C . albicans , the “gray” phenotype , which may enhance fi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "pathogenesis" ]	2014	Discovery of a “White-Gray-Opaque” Tristable Phenotypic Switching System in Candida albicans: Roles of Non-genetic Diversity in Host Adaptation
Human APOBEC3 cytidine deaminases are intrinsic resistance factors to HIV-1 . However , HIV-1 encodes a viral infectivity factor ( Vif ) that degrades APOBEC3 proteins . In vitro APOBEC3F ( A3F ) anti-HIV-1 activity is weaker than A3G but is partially resistant to Vif degradation unlike A3G . It is unknown whether A3F ...	Cytidine deaminases of the human APOBEC3 ( A3 ) gene family serve as intrinsic resistance factors to HIV-1 and other retroviruses . HIV-1 encodes the viral infectivity factor ( Vif ) protein that degrades APOBEC3 proteins via the ubiquitination-proteosomal pathway . APOBEC3F ( A3F ) , unlike APOBEC3G ( A3G ) , is parti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pneumocystis", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "viral", "transmission", "and", "infection", "pathogens", "population", "genetics", "african", "americans", "microbiology", "retroviruses", "v...	2016	Role of APOBEC3F Gene Variation in HIV-1 Disease Progression and Pneumocystis Pneumonia
Amyloidogenic proteins associated with a variety of unrelated diseases are typically capable of forming several distinct self-templating conformers . In prion diseases , these different structures , called prion strains ( or variants ) , confer dramatic variation in disease pathology and transmission . Aggregate stabil...	Protein conformational disorders , including many neurodegenerative diseases , result when a protein misfolds and undergoes a conformational change to form self-templating aggregates , called amyloid . Interestingly , the proteins that misfold in these diseases tend to form a wide variety of distinct aggregate structur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "interactions", "mutation", "fungi", "model", "organisms", "protein", "folding", "chaperone", "proteins", "protein", "structure", "research", "and", "analysis", "methods", "saccharomyces", "proteins", "yeast", "biochemistry", "cell", "biology", "genetics", "b...	2014	Extensive Diversity of Prion Strains Is Defined by Differential Chaperone Interactions and Distinct Amyloidogenic Regions
Filtration usually eliminates water-living bacteria . Here , we report on the complete genome sequence of Minibacterium massiliensis , a β-proteobacteria that was recovered from 0 . 22-μm filtered water used for patients in the hospital . The unexpectedly large 4 , 110 , 251-nucleotide genome sequence of M . massiliens...	Microorganisms are ubiquitous , found in environments including humans and animals , air , soil , and water , even in extreme conditions . Indeed , we isolated an emerging small bacterium M . massiliensis in hemodialysis water despite microbiological control by filtration and chemicals . Its very small size allowed thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "none", "ecology", "computational", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	Genome Analysis of Minibacterium massiliensis Highlights the Convergent Evolution of Water-Living Bacteria
Virus assembly and interaction with host-cell proteins occur at length scales below the diffraction limit of visible light . Novel super-resolution microscopy techniques achieve nanometer resolution of fluorescently labeled molecules . The cellular restriction factor tetherin ( also known as CD317 , BST-2 or HM1 . 24 )...	Human immunodeficiency virus 1 ( HIV-1 ) assembles and interacts with cellular proteins at the plasma membrane of infected cells . Here , we analyzed individual HIV-1 virions , viral assembly sites and the mechanism of tetherin restriction by multicolor super-resolution microscopy using fully functional fluorescently l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "host-pathogen", "interaction", "viral", "structure", "immunodeficiency", "viruses", "viral", "core", "membranes", "and", "sorting", "biology", "viral", "packaging", "viral", "replication", "viral", "envelope", "cell", "biology", "virology", "molecular", ...	2011	Quantitative Multicolor Super-Resolution Microscopy Reveals Tetherin HIV-1 Interaction
Intracellular pathogens such as Mycobacterium tuberculosis have evolved strategies for coping with the pressures encountered inside host cells . The ability to coordinate global gene expression in response to environmental and internal cues is one key to their success . Prolonged survival and replication within macroph...	The impact of Mycobacterium tuberculosis on global health is undeniable , with ∼2 million deaths and ∼9 million new cases of tuberculosis each year . A key to the success of M . tuberculosis as a persistent , intracellular pathogen is its ability to survive for extended periods within professional phagocytes . Sustaine...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genome", "expression", "analysis", "infectious", "diseases", "bacterial", "diseases", "mycobacterium", "biology", "genomics", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "pathogenesis" ]	2012	Linking the Transcriptional Profiles and the Physiological States of Mycobacterium tuberculosis during an Extended Intracellular Infection
The current antibody tests used for monitoring in lymphatic filariasis ( LF ) elimination programs suffer from poor specificity because of the considerable geographical overlap with other filarial infections such as Loa loa ( Ll ) , Onchocerca volvulus ( Ov ) , and Mansonella perstans ( Mp ) . Using bioinformatics to a...	To address an unmet need for a surveillance tool to detect transmission of Wuchereria bancrofti ( Wb ) , a causative agent of lymphatic filariasis , following mass drug administration ( MDA ) control measures , we used a novel bioinformatic approach to identify Wb-specific antigens expressed primarily by the infective ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunoassays", "neglected", "tropical", "diseases", "immunology", "immunologic", "techniques", "lymphatic", "filariasis" ]	2012	Identification of Wb123 as an Early and Specific Marker of Wuchereria bancrofti Infection
Topoisomerase 1 ( Top1 ) , a Type IB topoisomerase , functions to relieve transcription- and replication-associated torsional stress in DNA . We investigated the effects of Top1 on genome stability in Saccharomyces cerevisiae using two different assays . First , a sectoring assay that detects loss of heterozygosity ( L...	Topoisomerase I ( Top1 ) nicks one strand of DNA to relieve torsional stress associated with replication , transcription and chromatin remodeling . The enzyme forms a transient , covalent intermediate with the nicked DNA and stabilization of the cleavage complex ( Top1cc ) leads to genetic instability . We examined the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Destabilizing Effects Associated with Top1 Loss or Accumulation of Top1 Cleavage Complexes in Yeast
Vibrio cholerae expresses two primary virulence factors , cholera toxin ( CT ) and the toxin-coregulated pilus ( TCP ) . CT causes profuse watery diarrhea , and TCP ( composed of repeating copies of the major pilin TcpA ) is required for intestinal colonization by V . cholerae . Antibodies to CT or TcpA can protect aga...	Vibrio cholerae is the bacterium that causes cholera , a pandemic diarrheal disease transmitted by ingestion of contaminated food or water . We developed a novel vaccine containing two protective antigens of V . cholerae , TcpA and CTB , incorporated into a defined oligomeric protein chimera . CTB is the non-toxic bind...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "gastroenterology", "and", "hepatology", "global", "health", "neglected", "tropical", "diseases", "infectious", "disease", "contr...	2014	Immunizing Adult Female Mice with a TcpA-A2-CTB Chimera Provides a High Level of Protection for Their Pups in the Infant Mouse Model of Cholera
Burkholderia pseudomallei is a category B agent that causes Melioidosis , an acute and chronic disease with septicemia . The current treatment regimen is a heavy dose of antibiotics such as ceftazidime ( CAZ ) ; however , the risk of a relapse is possible . Peptide antibiotics are an alternative to classical antibiotic...	Burkholderia pseudomallei is a category B agent that causes Melioidosis , an acute and chronic disease with septicemia . The current treatment regimen is a heavy dose of antibiotics such as ceftazidime ( CAZ ) , however , the risk of a relapse is possible . In this study we demonstrate that bactenecin , CA-MA , RTA3 an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "infectious", "diseases", "biology" ]	2013	Antimicrobial Action of the Cyclic Peptide Bactenecin on Burkholderia pseudomallei Correlates with Efficient Membrane Permeabilization
During recent West Nile virus ( WNV ) outbreaks in the US , half of the reported cases were classified as neuroinvasive disease . WNV neuroinvasion is proposed to follow two major routes: hematogenous and/or axonal transport along the peripheral nerves . How virus spreads once within the central nervous system ( CNS ) ...	West Nile virus ( WNV ) is a mosquito-borne neurotropic flavivirus that has emerged as a human pathogen of global scale . During recent WNV outbreaks in the US , half of the reported human cases were classified as neuroinvasive disease . Although much research has been done , there are still gaps in our understanding o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "nervous", "system", "pathogens", "microbiology", "brain", "viral", "structure", "neuroscience", "motor", "neurons", "viruses", "rna", "viruses", "spinal", "cord", "animal", "cells"...	2016	West Nile Virus Spreads Transsynaptically within the Pathways of Motor Control: Anatomical and Ultrastructural Mapping of Neuronal Virus Infection in the Primate Central Nervous System
Replication Protein A ( RPA ) is a heterotrimeric , single-stranded DNA ( ssDNA ) –binding complex required for DNA replication and repair , homologous recombination , DNA damage checkpoint signaling , and telomere maintenance . Whilst the larger RPA subunits , Rpa1 and Rpa2 , have essential interactions with ssDNA , t...	Proteins that bind single-stranded DNA ( ssDNA ) are essential for DNA replication , most types of DNA repair including homologous recombination , DNA damage signaling , and maintenance of telomeres . In eukaryotes , the most ubiquitous and abundant ssDNA binding protein is Replication Protein A ( RPA ) , a 3-subunit p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "molecular", "biology/recombination", "molecular", "biology/dna", "repair" ]	2010	Critical Functions of Rpa3/Ssb3 in S-Phase DNA Damage Responses in Fission Yeast
Pathologies caused by mutations in extracellular matrix proteins are generally considered to result from the synthesis of extracellular matrices that are defective . Mutations in type X collagen cause metaphyseal chondrodysplasia type Schmid ( MCDS ) , a disorder characterised by dwarfism and an expanded growth plate h...	Mutations in genes for extracellular matrix proteins are generally thought to exert their pathogenic effects because of resulting defects in extracellular matrix . However , it is becoming increasingly clear that such mutations can also have significant effects inside the cell due to the induction of ER stress . Mutati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "biochemistry", "rheumatology/connective", "tissue", "disease", "rheumatology/cartilage", "biology", "and", "osteoarthritis" ]	2009	Targeted Induction of Endoplasmic Reticulum Stress Induces Cartilage Pathology
The human malaria parasite , Plasmodium vivax , is proving more difficult to control and eliminate than Plasmodium falciparum in areas of co-transmission . Comparisons of the genetic structure of sympatric parasite populations may provide insight into the mechanisms underlying the resilience of P . vivax and can help g...	The neglected human malaria parasite Plasmodium vivax is responsible for a large proportion of the global malaria burden . Efforts to control malaria have revealed that P . vivax is more resilient than the other major human malaria parasite , Plasmodium falciparum . This study utilised population genetics to compare pa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Plasmodium vivax Populations Are More Genetically Diverse and Less Structured than Sympatric Plasmodium falciparum Populations
Epstein-Barr virus ( EBV ) is associated with roughly 10% of gastric carcinomas worldwide ( EBVaGC ) . Although previous investigations provide a strong link between EBV and gastric carcinomas , these studies were performed using selected EBV gene probes . Using a cohort of gastric carcinoma RNA-seq data sets from The ...	Epstein-Barr virus ( EBV ) is detected in roughly 10% of gastric carcinoma ( GC ) cases worldwide . Despite a strong link between EBV and gastric carcinoma , the contribution of EBV to the tumor environment in EBV associated gastric carcinoma is unclear . We performed a global assessment of EBV and host cell gene expre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequence", "analysis", "mechanisms", "of", "resistance", "and", "susceptibility", "viral", "immune", "evasion", "immunity", "virology", "viruses", "and", "cancer", "immune", "activation", "immune", "tolerance", "biology", "computational", "biology", "microbiology", "im...	2013	Differences in Gastric Carcinoma Microenvironment Stratify According to EBV Infection Intensity: Implications for Possible Immune Adjuvant Therapy
Scabies is a skin infestation with the mite Sarcoptes scabiei causing itch and rash and is a major risk factor for bacterial skin infections and severe complications . Here , we evaluated the treatment outcome of 2866 asylum seekers who received ( preventive ) scabies treatment before and during a scabies intervention ...	The high number of asylum seekers arriving in Europe between 2014 and 2016 emphasized the importance to expand knowledge on best practice regarding health care provision and control of infectious diseases that may come with migration . Adequate control of scabies is important to prevent severe forms of scabies and prev...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "european", "union", "pathology", "and", "laboratory", "medicine", "medical", "personnel", "tropical", "diseases", "geographical", "locations", "eritrea", "parasitic", "diseases", "animals", "health", "care", "he...	2018	Efficacy of ivermectin mass-drug administration to control scabies in asylum seekers in the Netherlands: A retrospective cohort study between January 2014 – March 2016
The cellular invasion machinery of the enteric pathogen Salmonella consists of a type III secretion system ( T3SS ) with injectable virulence factors that induce uptake by macropinocytosis . Salmonella invasion at the apical surface of intestinal epithelial cells is inefficient , presumably because of a glycosylated ba...	The bacterial pathogen Salmonella enterica is one of the most common causes of human foodborne infection affecting millions of people worldwide each year . To establish infection , Salmonella needs to cross the mucus layer and invade intestinal epithelial cells from the apical surface . However , the apical surface of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "light", "microscopy", "epithelial", "cells", "bacterial", "diseases", "microscopy", "enterobacteriaceae", "confocal", "microscopy", "bacteria...	2019	MUC1 is a receptor for the Salmonella SiiE adhesin that enables apical invasion into enterocytes
The crab Cancer borealis undergoes large daily fluctuations in environmental temperature ( 8–24°C ) and must maintain appropriate neural function in the face of this perturbation . In the pyloric circuit of the crab stomatogastric ganglion , we pharmacologically isolated the pacemaker kernel ( the AB and PD neurons ) a...	The nervous systems of cold-blooded animals must maintain essential function despite fluctuations in environmental temperature . We studied the pyloric rhythm of the crab , Cancer borealis . The pyloric rhythm is important for the animal's feeding behavior , and previous work has shown that relative timing , or phase ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "cellular", "neuroscience", "ion", "channels", "computational", "neuroscience", "single", "neuron", "function", "biology", "neuroscience" ]	2013	The Effects of Temperature on the Stability of a Neuronal Oscillator
SUMOylation participates in ecdysteroid biosynthesis at the onset of metamorphosis in Drosophila melanogaster . Silencing the Drosophila SUMO homologue smt3 in the prothoracic gland leads to reduced lipid content , low ecdysone titers , and a block in the larval–pupal transition . Here we show that the SR-BI family of ...	Steroid hormones are cholesterol derivates that control many aspects of animal physiology , including development of the adult organisms , growth , energy storage , and reproduction . In insects , pulses of the steroid hormone ecdysone precede molting and metamorphosis , the regulation of hormonal synthesis being a cru...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "growth", "control", "animal", "genetics", "endocrine-related", "substances", "rna", "interference", "anatomy", "and", "physiology", "hormones", "gene", "function", "endocrine", "physiology", "animal", "models", "developmental", "biology", "drosophila", "melan...	2013	Scavenger Receptors Mediate the Role of SUMO and Ftz-f1 in Drosophila Steroidogenesis
The histiocytoses are a heterogeneous group of disorders characterised by an excessive number of histiocytes . In most cases the pathophysiology is unclear and treatment is nonspecific . Faisalabad histiocytosis ( FHC ) ( MIM 602782 ) has been classed as an autosomal recessively inherited form of histiocytosis with sim...	The histiocytoses are a group of systemic disorders usually confined to childhood and are caused by an excessive number of histiocytes which phagocytose other cells and process antigens . Although nearly a century has passed since histiocytic disorders were recognised , their pathophysiology remains largely unclear , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "discovery" ]	2010	Mutations in SLC29A3, Encoding an Equilibrative Nucleoside Transporter ENT3, Cause a Familial Histiocytosis Syndrome (Faisalabad Histiocytosis) and Familial Rosai-Dorfman Disease
While most chemokine receptors fail to cross the chemokine class boundary with respect to the ligands that they bind , the human cytomegalovirus ( HCMV ) -encoded chemokine receptor US28 binds multiple CC-chemokines and the CX3C-chemokine Fractalkine . US28 binding to CC-chemokines is both necessary and sufficient to i...	Chemokines are small cytokines that are critical for recruiting and activating the cells of the immune system during viral infections . A number of viruses , including the large herpes virus human cytomegalovirus ( HCMV ) , encode mechanisms to impede the effects of chemokines or have gained the ability to use these mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "cell", "biology/cell", "signaling", "cardiovascular", "disorders/cardiac", "surgery", "and", "transplantations", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "cell", "biology/cytoskeleton" ]	2009	Differential Ligand Binding to a Human Cytomegalovirus Chemokine Receptor Determines Cell Type–Specific Motility
Cancer genomes contain vast amounts of somatic mutations , many of which are passenger mutations not involved in oncogenesis . Whereas driver mutations in protein-coding genes can be distinguished from passenger mutations based on their recurrence , non-coding mutations are usually not recurrent at the same position . ...	Precise regulation of gene expression is controlled by cis-regulatory modules ( CRM ) containing binding sites for transcription factors ( TF ) . The genome-wide location of all TF binding sites can often be obtained by ChIP-seq ( chromatin immunoprecipitation followed by deep sequencing ) , yet in most cases only a mi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models
Angiostrongylus cantonensis is of increasing public health importance as the main zoonotic pathogen causing eosinophilic meningitis or meningoencephalitis , which has been documented all over the world . However , there are very limited studies about its phylogeography and spread pattern . In the present study , the ph...	Since it was described in 1935 , more than 2800 cases of the disease have reportedly been caused by A . cantonensis worldwide , primarily in tropical and subtropical regions . Despite a relevant body of research on pathology , diagnosis and treatment , little is known about the phylogeography of A . cantonensis . Since...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Data", "analyses", "Results", "Discussion", "Conclusion" ]	[ "biogeography", "taxonomy", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "china", "population", "genetics", "geographical", "locations", "genetic", "mapping", "phylogenetics", "data",...	2017	Phylogeography of Angiostrongylus cantonensis (Nematoda: Angiostrongylidae) in southern China and some surrounding areas
Sand fly species able to support the survival of the protozoan parasite Leishmania have been classified as permissive or specific , based upon their ability to support a wide or limited range of strains and/or species . Studies of a limited number of fly/parasite species combinations have implicated parasite surface mo...	Phlebotomine sand flies are small blood-feeding insects , medically important as vectors of protozoan parasites of the genus Leishmania . Sand flies species can be divided roughly into two groups , termed specific or permissive , depending on their ability to support development of one or a few strains vs . a broad spe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/parasitology" ]	2010	Leishmania major Glycosylation Mutants Require Phosphoglycans (lpg2−) but Not Lipophosphoglycan (lpg1−) for Survival in Permissive Sand Fly Vectors
Trypanosoma rangeli is a hemoflagellate protozoan parasite infecting humans and other wild and domestic mammals across Central and South America . It does not cause human disease , but it can be mistaken for the etiologic agent of Chagas disease , Trypanosoma cruzi . We have sequenced the T . rangeli genome to provide ...	Comparative genomics is a powerful tool that affords detailed study of the genetic and evolutionary basis for aspects of lifecycles and pathologies caused by phylogenetically related pathogens . The reference genome sequences of three trypanosomatids , T . brucei , T . cruzi and L . major , and subsequent addition of m...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "functional", "genomics", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "genome", "sequencing", "genomic", "databases", "protozoans", "genome", "analysis", "dna", "m...	2014	Genome of the Avirulent Human-Infective Trypanosome—Trypanosoma rangeli
In vivo , cortical pyramidal cells are bombarded by asynchronous synaptic input arising from ongoing network activity . However , little is known about how such ‘background’ synaptic input interacts with nonlinear dendritic mechanisms . We have modified an existing model of a layer 5 ( L5 ) pyramidal cell to explore ho...	In the brains of awake animals , networks are active even when there is no input from the outside world . Neurons embedded within cortical networks experience this intrinsic ongoing firing as ‘background’ synaptic input . While the effect of this background input on the integration properties of neurons has been studie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "glutamate", "biochemistry", "neurochemistry", "computational", "neuroscience", "single", "neuron", "function", "biology", "and", "life", "sciences", "neurotransmitters", "computational", "biology", "neuroscience" ]	2014	Glutamate-Bound NMDARs Arising from In Vivo-like Network Activity Extend Spatio-temporal Integration in a L5 Cortical Pyramidal Cell Model
The attenuation of myxoma virus ( MYXV ) following its introduction as a biological control into the European rabbit populations of Australia and Europe is the canonical study of the evolution of virulence . However , the evolutionary genetics of this profound change in host-pathogen relationship is unknown . We descri...	The text-book example of the evolution of virulence is the attenuation of myxoma virus ( MYXV ) following its introduction as a biological control into the European rabbit populations of Australia and Europe in the 1950s . However , the key work on this topic , most notably by Frank Fenner and his colleagues , occurred...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "ecology", "genomic", "evolution", "microbial", "evolution", "virology", "biology", "evolutionary", "biology", "comparative", "genomics", "microbiology", "evolutionary", "genetics" ]	2012	Evolutionary History and Attenuation of Myxoma Virus on Two Continents
Infection of the vascular system by Pseudomonas aeruginosa ( Pa ) occurs during bacterial dissemination in the body or in blood-borne infections . Type 3 secretion system ( T3SS ) toxins from Pa induce a massive retraction when injected into endothelial cells . Here , we addressed the role of type 2 secretion system ( ...	Pseudomonas aeruginosa ( Pa ) is a leading agent of nosocomial infections in humans , and clinical isolates are often multiresistant to antibiotics . As with most Gram-negative bacteria , Pa possesses a type III secretion system which consists of an injectisome through which the bacterium injects exotoxins inducing cyt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "model", "organisms", "molecular", "cell", "biology", "cell", "adhesion", "host-pathogen", "interaction", "biology", "microbiology", "pathogenesis", "bacterial", "pathogens" ]	2014	VE-Cadherin Cleavage by LasB Protease from Pseudomonas aeruginosa Facilitates Type III Secretion System Toxicity in Endothelial Cells
Receptor Tyrosine Kinase ( RTK ) signaling pathways induce multiple biological responses , often by regulating the expression of downstream genes . The HMG-box protein Capicua ( Cic ) is a transcriptional repressor that is downregulated in response to RTK signaling , thereby enabling RTK-dependent induction of Cic targ...	Understanding the evolution of developmental regulatory mechanisms is a central challenge of biology . Here we uncover a newly evolved mechanism of transcriptional repression by Capicua ( Cic ) , a conserved sensor of Receptor Tyrosine Kinase ( RTK ) signaling . In Drosophila , Cic patterns the central regions of the e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "network", "analysis", "molecular", "biology", "techniques", "embryos", "research", "and", "analysis", "methods", "protein", "kinase", "signalin...	2015	Origins of Context-Dependent Gene Repression by Capicua
Post-transcriptional control of protein abundance is a highly important , underexplored regulatory process by which organisms respond to their environments . Here we describe an important and previously unidentified regulatory pathway involving the ribosomal modification protein RimK , its regulator proteins RimA and R...	Post-transcriptional control of protein abundance is a significant and underexplored regulatory process by which organisms respond to environmental change . We have discovered an important new mechanism for this control in bacteria , based on the covalent modification of a small ribosomal protein by the widespread enzy...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "neurochemistry", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "neuroscience", "pseudomonas", "aeruginosa", "membrane", "proteins", "plant", "science", "n...	2016	Adaptive Remodeling of the Bacterial Proteome by Specific Ribosomal Modification Regulates Pseudomonas Infection and Niche Colonisation
To date schistosomiasis control programmes based on chemotherapy have largely aimed at controlling morbidity in treated individuals rather than at suppressing transmission . In this study , a mathematical modelling approach was used to estimate reductions in the rate of Schistosoma mansoni reinfection following annual ...	Schistosomiasis is a parasitic disease of enormous public health importance , infecting over 200 million people worldwide , of which the large majority live in sub-Saharan Africa . Control programmes based on the mass treatment of individuals in infected areas with the drug praziquantel have been shown to be successful...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/health", "policy", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious",...	2010	Observed Reductions in Schistosoma mansoni Transmission from Large-Scale Administration of Praziquantel in Uganda: A Mathematical Modelling Study
Scabies and impetigo are common and important skin conditions which are often neglected in developing countries . Limited data have been published on the prevalence of scabies and impetigo in Timor-Leste . Sequelae including cellulitis , bacteraemia , nephritis , acute rheumatic fever and rheumatic heart disease contri...	Scabies and impetigo are common and important skin conditions which are often neglected in developing countries . Scabies affects more than 200 million people globally . There are limited data on the prevalence of these conditions in Timor-Leste . Scabies is a parasitic infection which causes an intensely itchy rash in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "group", "a", "streptococcal", "infection", "parasitic", "diseases", ...	2018	Scabies and impetigo in Timor-Leste: A school screening study in two districts
Mycobacterium tuberculosis requires the enzyme isocitrate lyase ( ICL ) for growth and virulence in vivo . The demonstration that M . tuberculosis also requires ICL for survival during nutrient starvation and has a role during steady state growth in a glycerol limited chemostat indicates a function for this enzyme whic...	The role of the enzyme isocitrate lyase ( ICL ) in the metabolism of Mycobacterium tuberculosis has been intensively studied since the demonstration that both of the isocitrate lyase genes encoded by this pathogen , icl1 and icl2 ( although some strains only have icl1 ) are essential for the survival of this pathogen i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	13C Metabolic Flux Analysis Identifies an Unusual Route for Pyruvate Dissimilation in Mycobacteria which Requires Isocitrate Lyase and Carbon Dioxide Fixation
Many biological studies involve either ( i ) manipulating some aspect of a cell or its environment and then simultaneously measuring the effect on thousands of genes , or ( ii ) systematically manipulating each gene and then measuring the effect on some response of interest . A common challenge that arises in these stu...	There is a multitude of publicly available databases that contain information about biological entities ( i . e . , genes , proteins , and other small molecules ) as well as information about how these entities interact together . However , these databases are often incomplete . There is a wealth of information present...	[ "Abstract", "Introduction", "Methods", "Results/discussion" ]	[ "medicine", "and", "health", "sciences", "genetic", "networks", "rna", "interference", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "pathogens", "protein", "interaction", "networks", "microbiology", "retroviruses", "viruses", "immunodeficiency", ...	2019	Augmenting subnetwork inference with information extracted from the scientific literature
Bacterial RNA polymerases must associate with a σ factor to bind promoter DNA and initiate transcription . There are two families of σ factor: the σ70 family and the σ54 family . Members of the σ54 family are distinct in their ability to bind promoter DNA sequences , in the context of RNA polymerase holoenzyme , in a t...	Bacterial RNA polymerases must associate with a σ factor to bind to promoter DNA sequences upstream of genes and initiate transcription . There are two families of σ factor: σ70 and σ54 . Members of the σ54 family are distinct from members of the σ70 family in their ability to bind promoter DNA sequences , in associati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Scale Mapping of Escherichia coli σ54 Reveals Widespread, Conserved Intragenic Binding
Hepatitis C virus ( HCV ) is among the most relevant causes of liver cirrhosis and hepatocellular carcinoma . Research is complicated by a lack of accessible small animal models . The systematic investigation of viruses of small mammals could guide efforts to establish such models , while providing insight into viral e...	The hepatitis C virus ( HCV ) is one of the most relevant causes of liver disease and cancer in humans . The lack of a small animal models represents an important hurdle on our way to understanding , treating , and preventing hepatitis C . The investigation of small mammals could identify virus infections similar to he...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "model", "organisms", "veterinary", "microbiology", "gastroenterology", "and", "hepatology", "biology", "microbiology", "evolutionary", "biology", "veterinary", "science" ]	2013	Evidence for Novel Hepaciviruses in Rodents
Reconstructing regulatory and signaling response networks is one of the major goals of systems biology . While several successful methods have been suggested for this task , some integrating large and diverse datasets , these methods have so far been applied to reconstruct a single response network at a time , even whe...	To understand why some flu strains are more virulent than others , researchers attempt to profile and model the molecular human response to these strains and identify similarities and differences between the resulting models . So far , the modeling and analysis part has been done independently for each strain and the r...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "medicine", "and", "health", "sciences", "genetic", "networks", "transcription", "activators", "rna", "interference", "genome", "scans", "gene", "regulation", "influenza", "protein", "interaction", "networks", "immunology", "dna-binding...	2014	Multitask Learning of Signaling and Regulatory Networks with Application to Studying Human Response to Flu
The evolution of insecticide resistance is a global constraint to agricultural production . Spinosad is a new , low-environmental-risk insecticide that primarily targets nicotinic acetylcholine receptors ( nAChR ) and is effective against a wide range of pest species . However , after only a few years of application , ...	Evolving resistance to control agents , such as antibiotics or insecticides , can have major costs to human health or agricultural food production . Once a genetic mechanism for resistance to a particular compound has been identified , other resistant species can be rapidly assessed to search for a parallel mechanism ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/rna", "splicing", "evolutionary", "biology/genomics" ]	2010	Mis-Spliced Transcripts of Nicotinic Acetylcholine Receptor α6 Are Associated with Field Evolved Spinosad Resistance in Plutella xylostella (L.)
Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses , such as SARS-CoV and MERS-CoV . They are known to efficiently evade early innate immune responses , manifesting in almost negligible expression of type-I interferons ( IFN-I ) . This evasion strategy suggests an evol...	Coronaviruses are long known to be particularly successful in evading host innate immune responses . This manifests in barely detectable interferon responses during the first hours of infection and greatly facilitates establishment of robust virus replication . This phenotype of early innate immune evasion is common to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "coronaviruses", "nucleic", "acid", "synthesis", "immune", "cells", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "nucleases", "enzymes", "pathogens", "immunology", ...	2017	Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication
A major goal of human genetics is to elucidate the genetic architecture of human disease , with the goal of fueling improvements in diagnosis and the understanding of disease pathogenesis . The degree to which epistasis , or non-additive effects of risk alleles at different loci , accounts for common disease traits is ...	The contribution of epistasis , or non-additive effects of risk alleles at different loci , to complex traits is much debated among human geneticists . In this study we use modeling and simulation to identify when evolutionary forces should drive epistasis to become a major part of the explanation for such traits . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "epistasis", "evolutionary", "genetics", "developmental", "biology", "fitness", "epistasis", "phenotypes", "natural", "selection", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "population", "biology", "evolutionary", "biology", "...	2016	Survival of the Curviest: Noise-Driven Selection for Synergistic Epistasis
During acute infection in human and animal hosts , the obligate intracellular protozoan Toxoplasma gondii infects a variety of cell types , including leukocytes . Poised to respond to invading pathogens , dendritic cells ( DC ) may also be exploited by T . gondii for spread in the infected host . Here , we report that ...	Toxoplasma gondii is an obligate intracellular protozoan parasite and an important food- and water-borne human and veterinary pathogen . Toxoplasmosis is normally self-limiting but severe manifestations occur upon congenital transmission to the developing fetus or during infection in immune-compromised individuals . To...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "model", "organisms", "parasitic", "diseases", "neurological", "disorders", "neurology", "immunology", "biology", "microbiology", "infectious", "disease", "modeling", "neuros...	2012	GABAergic Signaling Is Linked to a Hypermigratory Phenotype in Dendritic Cells Infected by Toxoplasma gondii
Protocell multilevel selection models have been proposed to study the evolutionary dynamics of vesicles encapsulating a set of replicating , competing and mutating sequences . The frequency of the different sequence types determines protocell survival through a fitness function . One of the defining features of these m...	The protocell hypothesis conjectures the existence of a vesicle containing catalytic and replicating sequences as the primordial cellular organization during the early stages of the evolution of life . Mathematical models of protocells traditionally consider RNA sequences being encapsulated and having both an informati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "vesicles", "population", "genetics", "ploidy", "metabolic", "networks", "vertebrates", "enzymology", "animals", "mammals", "network", "analysis", "enzyme", "metabolism", "sequence", "motif", "analysis", "population", "biology", "cellular", "structures", "and", "organelle...	2018	The evolutionary dynamics of metabolic protocells
T-Cell antigen Receptor ( TR ) repertoire is generated through rearrangements of V and J genes encoding α and β chains . The quantification and frequency for every V-J combination during ontogeny and development of the immune system remain to be precisely established . We have addressed this issue by building a model a...	Lymphocytes of the immune system ensure the body defense by the expression of receptors which are specific of targets , termed antigens . Each lymphocyte , deriving from the same original clone , expresses the same unique receptor . To achieve the production of receptors covering the wide variety of antigens , lymphocy...	[ "Abstract", "Introduction", "Results", "Materials", "and", "Methods" ]	[ "immunology/genetics", "of", "the", "immune", "system", "computational", "biology/molecular", "genetics", "immunology/immune", "response", "computational", "biology/systems", "biology" ]	2010	Numerical Modelling Of The V-J Combinations Of The T Cell Receptor TRA/TRD Locus
Human Cytomegalovirus ( HCMV ) is a major cause of morbidity and mortality in transplant patients and in fetuses following congenital infection . The glycoprotein complexes gH/gL/gO and gH/gL/UL128/UL130/UL131A ( Pentamer ) are required for HCMV entry in fibroblasts and endothelial/epithelial cells , respectively , and...	Human Cytomegalovirus ( HCMV ) is a double stranded DNA , enveloped virus infecting >60% of the population worldwide . Typically asymptomatic in healthy adults , HCMV infection causes morbidity and mortality in immunocompromised patients and is the most common viral cause of birth defects in industrialized countries . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Antigenic Characterization of the HCMV gH/gL/gO and Pentamer Cell Entry Complexes Reveals Binding Sites for Potently Neutralizing Human Antibodies
Traveling waves of neuronal oscillations have been observed in many cortical regions , including the motor and sensory cortex . Such waves are often modulated in a task-dependent fashion although their precise functional role remains a matter of debate . Here we conjecture that the cortex can utilize the direction and ...	Physiological studies in humans and monkeys have revealed spatially organized waves of neuronal activity that propagate across the cortex during sensory or behavioral tasks . However the functional role of such waves remains elusive . In the present study , we use numerical simulation to investigate whether wave patter...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	A Dendritic Mechanism for Decoding Traveling Waves: Principles and Applications to Motor Cortex
Cytomegaloviruses express large amounts of viral miRNAs during lytic infection , yet , they only modestly alter the cellular miRNA profile . The most prominent alteration upon lytic murine cytomegalovirus ( MCMV ) infection is the rapid degradation of the cellular miR-27a and miR-27b . Here , we report that this regula...	MicroRNAs are small , non-coding RNAs which shape and fine-tune gene expression of at least a third of our genes . During millions of years of coevolution with their hosts , herpesviruses have both usurped the host cell miRNA machinery by expressing their own sets of miRNAs , and learned to modify host miRNA expression...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "infectious", "diseases", "model", "organisms", "biology", "microbiology", "viral", "diseases" ]	2012	Degradation of Cellular miR-27 by a Novel, Highly Abundant Viral Transcript Is Important for Efficient Virus Replication In Vivo
ATP-dependent chromatin remodelers are molecular machines that control genome organization by repositioning , ejecting , or editing nucleosomes , activities that confer them essential regulatory roles on gene expression and DNA replication . Here , we investigate the molecular mechanism of active nucleosome sliding by ...	Nucleosomes are the protein-DNA complexes underlying Eukaryotic genome organization , and serve as regulators of gene expression by occluding DNA to other proteins . This regulation requires the precise positioning of nucleosomes along DNA . Chromatin remodelers are the molecular machines that consume ATP to slide nucl...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "electricity", "dna-binding", "proteins", "electrostatics", "sequence", "motif", "analysis", "epigenetics", "thermodynamics", "chromatin", "research", "and", "analysis", "methods", "sequence", "analysis", "chromosome", "biology", "proteins", "bioinformatics", "gene", "expre...	2018	Chromatin remodelers couple inchworm motion with twist-defect formation to slide nucleosomal DNA
The structure of immature and mature HIV-1 particles has been analyzed in detail by cryo electron microscopy , while no such studies have been reported for cellular HIV-1 budding sites . Here , we established a system for studying HIV-1 virus-like particle assembly and release by cryo electron tomography of intact huma...	The production of new HIV-1 particles is initiated at the plasma membrane where the viral polyprotein Gag assembles into a budding site , and proceeds through release of an immature virion which is subsequently transformed to the infectious virion by proteolytic cleavage of Gag . Here , we established experimental syst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/immunodeficiency", "viruses", "biophysics/macromolecular", "assemblies", "and", "machines" ]	2010	Cryo Electron Tomography of Native HIV-1 Budding Sites
Many DNA hypermethylated and epigenetically silenced genes in adult cancers are Polycomb group ( PcG ) marked in embryonic stem ( ES ) cells . We show that a large region upstream ( ∼30 kb ) of and extending ∼60 kb around one such gene , GATA-4 , is organized—in Tera-2 undifferentiated embryonic carcinoma ( EC ) cells—...	Polycomb group ( PcG ) proteins and DNA methylation are fundamental epigenetic regulators of gene expression . The mechanisms underlying such regulation , the crosstalk between these mechanisms , and the role of higher order chromatin folding in mediating transcriptional control of involved genes remains unclear . Abno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "molecular", "biology", "genetics", "and", "genomics" ]	2008	PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping
While HSV-2 typically causes genital lesions , HSV-1 is increasingly the cause of genital herpes . In addition , neonatal HSV infections are associated with a high rate of mortality and HSV-2 may increase the risk for HIV or Zika infections , reinforcing the need to develop an effective vaccine . In the GSK Herpevac tr...	Understanding the complex steps of herpes simplex virus ( HSV ) entry into susceptible cells is key for developing an effective vaccine to prevent clinical disease and control recurrences of this important human pathogen . For either serotype ( HSV-1 or HSV-2 ) , it is the interaction of glycoprotein D ( gD ) with rece...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "herpes", "simplex", "virus", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "condensed", "matter", "physics", "microbiology"...	2017	Global sensing of the antigenic structure of herpes simplex virus gD using high-throughput array-based SPR imaging
Much of the observed wintertime increase of mortality in temperate regions is attributed to seasonal influenza . A recent reanalysis of laboratory experiments indicates that absolute humidity strongly modulates the airborne survival and transmission of the influenza virus . Here , we extend these findings to the human ...	The origin of seasonality in influenza transmission is both of palpable public health importance and basic scientific interest . Here , we present statistical analyses and a mathematical model of epidemic influenza transmission that provide strong epidemiological evidence for the hypothesis that absolute humidity ( AH ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2010	Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States
During meiosis , accurate chromosome segregation relies on the proper interaction between homologous chromosomes , including synapsis and recombination . The meiotic recombination checkpoint is a quality control mechanism that monitors those crucial events . In response to defects in synapsis and/or recombination , thi...	In sexually reproducing organisms , meiosis divides the number of chromosomes by half to generate gametes . Meiosis involves a series of interactions between maternal and paternal chromosomes leading to the exchange of genetic material by recombination . Completion of these processes is required for accurate distributi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	Dot1-Dependent Histone H3K79 Methylation Promotes Activation of the Mek1 Meiotic Checkpoint Effector Kinase by Regulating the Hop1 Adaptor
The brain blood vasculature consists of a highly ramified vessel network that is tailored to meet its physiological functions . How the brain vasculature is formed has long been fascinating biologists . Here we report that the developing vasculature in the zebrafish midbrain undergoes not only angiogenesis but also ext...	Although the brain comprises only 2% of body weight , it receives 15% of cardiac output and consumes 20% of total body oxygen delivered through its blood vasculature . The brain blood vasculature consists of a highly branched vessel network that is tailored to efficiently deliver oxygen and nutrients to each brain regi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "zebrafish", "model", "organisms", "organism", "development", "biology", "computational", "biology", "morphogenesis", "pattern", "formation" ]	2012	Haemodynamics-Driven Developmental Pruning of Brain Vasculature in Zebrafish
Dengue hemorrhagic fever ( DHF ) is observed in individuals that have pre-existing heterotypic dengue antibodies and is associated with increased viral load and high levels of pro-inflammatory cytokines early in infection . Interestingly , a recent study showed that dengue virus infection in the presence of antibodies ...	Dengue virus ( DENV ) infections cause a broad spectrum of clinical manifestations , ranging from self-limited fever to severe disease , such as dengue hemorrhagic fever ( DHF ) that can be fatal . The pathogenesis of severe dengue is associated with an inadequate immune response characterized by the over-production of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2013	Differential Expression of Toll-like Receptors in Dendritic Cells of Patients with Dengue during Early and Late Acute Phases of the Disease
Cystic hydatid disease is a zoonosis caused by the larval stage ( hydatid ) of Echinococcus granulosus ( Cestoda , Taeniidae ) . The hydatid develops in the viscera of intermediate host as a unilocular structure filled by the hydatid fluid , which contains parasitic excretory/secretory products . The lipoprotein Antige...	Antigen B ( AgB ) is an oligomeric lipoprotein highly abundant in Echinococcus granulosus hydatid fluid . AgB has already been characterized as an immunomodulatory protein , capable of inducing a permissive immune response to parasite development . Also , an important role in lipid acquisition is attributed to AgB , be...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "cestodes", "helminths", "drugs", "cell", "processes", "immunology", "light", "microscopy", "parasitic", "diseases", "animals", "microscopy", "chlorpromazine", "confocal", "mi...	2018	Antigen B from Echinococcus granulosus enters mammalian cells by endocytic pathways
The successive events that cells experience throughout development shape their intrinsic capacity to respond and integrate RTK inputs . Cellular responses to RTKs rely on different mechanisms of regulation that establish proper levels of RTK activation , define duration of RTK action , and exert quantitative/qualitativ...	The need to achieve precise control of RTK activation is highlighted by human pathologies such as congenital malformations and cancers caused by aberrant RTK signalling . Identifying strategies to restrain RTK activity in cancer and/or to reactivate RTKs for counteracting degenerative processes is the focus of intense ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Tissue-Specific Gain of RTK Signalling Uncovers Selective Cell Vulnerability during Embryogenesis
Tunga penetrans are fleas that cause tungiasis , a condition characterized by high transmission rate due to poor housing conditions , social neglect and inadequate health care in economically disadvantaged communities in developing countries . This study therefore aimed at characterizing jiggers antigens to identify im...	Tungiasis is the condition caused by jigger infestation . It is common in tropical countries where it has caused high morbidity among economically disadvantaged communities . It is a neglected tropical disease to an extent that enough research has not been done in this area . More over the infested hardly seek medical ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Characterization of Tunga penetrans Antigens in Selected Epidemic Areas in Murang’a County in Kenya
Memory CD8 T cells provide protection to immune hosts by eliminating pathogen-infected cells during re-infection . While parameters influencing the generation of primary ( 1° ) CD8 T cells are well established , the factors controlling the development of secondary ( 2° ) CD8 T cell responses remain largely unknown . He...	Since memory CD8 T cells afford hosts increased protection , extensive research has been devoted to understanding the parameters that affect the generation of these cells . Humans are typically infected with pathogens more than once , thus leading to re-stimulation of existing primary memory CD8 T cell populations . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Timing of Stimulation and IL-2 Signaling Regulate Secondary CD8 T Cell Responses
Reinforcement learning ( RL ) provides an influential characterization of the brain's mechanisms for learning to make advantageous choices . An important problem , though , is how complex tasks can be represented in a way that enables efficient learning . We consider this problem through the lens of spatial navigation ...	The central problem of learning is generalization: how to apply what was discovered in past experiences to future situations , which will inevitably be the same in some respects and different in others . Effective learning requires generalizing appropriately: to situations which are similar in relevant respects , thoug...	[ "Abstract", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology", "neuroscience" ]	2011	Grid Cells, Place Cells, and Geodesic Generalization for Spatial Reinforcement Learning
Mitochondria play a vital role in embryo development . They are the principal site of energy production and have various other critical cellular functions . Despite the importance of this organelle , little is known about the extent of variation in mitochondrial DNA ( mtDNA ) between individual human embryos prior to i...	Mitochondria are small membrane-enclosed structures and are found inside the cells of the body . Mitochondria actively participate in cellular life , and their main function is to generate energy which is used by the cell . For this reason mitochondria are considered as the powerhouses of cells . Unlike other cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Altered Levels of Mitochondrial DNA Are Associated with Female Age, Aneuploidy, and Provide an Independent Measure of Embryonic Implantation Potential
Berardinelli-Seip congenital generalized lipodystrophy is associated with increased bone mass suggesting that fat tissue regulates the skeleton . Because there is little mechanistic information regarding this issue , we generated "fat-free" ( FF ) mice completely lacking visible visceral , subcutaneous and brown fat . ...	Berardinelli-Seip congenital generalized lipodystrophy is a human disorder associated with increased bone mass suggesting that fat , per se , regulates the skeleton . To test this hypothesis we generated a murine model of congenital generalized lipodystrophy in which both brown and white adipose tissue are entirely dep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "immunology", "hormones", "animal", "models", "developmental", "biology", "adiponectin", "model", "organisms", "adipocytes", "organism", "development", "bone", "c...	2019	Congenital lipodystrophy induces severe osteosclerosis
One of the primary mechanisms through which a cell exerts control over its metabolic state is by modulating expression levels of its enzyme-coding genes . However , the changes at the level of enzyme expression allow only indirect control over metabolite levels , for two main reasons . First , at the level of individua...	Regulation of metabolic activity in response to environmental and genetic perturbations is fundamental to the growth and maintenance of all cells . A primary regulatory process used by cells to control the activity of their metabolic network is the alteration in the expression of enzyme-coding genes . How these alterat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "microbial", "metabolism", "fungi", "computer", "and", "information", "sciences", "model", "organisms", "microbial", "physiology", "research", "and", "analysis", "methods", "network", "analysis", "biology", "and", "life", "sciences", "metabolic", ...	2014	Contribution of Network Connectivity in Determining the Relationship between Gene Expression and Metabolite Concentration Changes
Epidermal growth factor receptor ( EGFR ) and platelet-derived growth factor receptor-α ( PDGFRα ) were reported to mediate entry of HCMV , including HCMV lab strain AD169 . AD169 cannot assemble gH/gL/UL128–131 , a glycoprotein complex that is essential for HCMV entry into biologically important epithelial cells , end...	Human cytomegalovirus ( HCMV ) causes substantial morbidity and mortality in immunocompromised patients and in developing infants . HCMV pathogenesis involves the capacity to infect many different cell types by multiple distinct entry pathways . Among the biologically important cell types infected in vivo are epithelia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "molecular", "cell", "biology" ]	2012	PDGF Receptor-α Does Not Promote HCMV Entry into Epithelial and Endothelial Cells but Increased Quantities Stimulate Entry by an Abnormal Pathway
Cellular antiviral programs encode molecules capable of targeting multiple steps in the virus lifecycle . Zinc-finger antiviral protein ( ZAP ) is a central and general regulator of antiviral activity that targets pathogen mRNA stability and translation . ZAP is diffusely cytoplasmic , but upon infection ZAP is targete...	Organisms encode immune programs , present in most somatic cells , to combat pathogens . The components of these antiviral programs are both constitutively expressed and highly upregulated upon pathogen recognition . Interestingly , a broadly acting antiviral factor is the zinc-finger antiviral protein ( ZAP ) . ZAP is...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cellular", "stress", "responses", "bhk", "cells", "diagnostic", "radiology", "chemical", "compounds", "aliphatic", "amino", "acids", "biological", "cultures", "cell", "processes", "microbiology", "viral", "structure", "organic",...	2019	ZAP’s stress granule localization is correlated with its antiviral activity and induced by virus replication
Cryptococcus neoformans is a human fungal pathogen with a defined sexual cycle . Nutrient-limiting conditions and pheromones induce a dimorphic transition from unicellular yeast to multicellular hyphae and the production of infectious spores . Sexual reproduction involves cells of either opposite ( bisexual ) or one ( ...	Sexual reproduction drives genetic diversity throughout the eukaryotic kingdom and also purges deleterious mutations . Sexual development usually occurs between partners of opposite sex or mating type; however , in the absence of a compatible partner , unisexual reproduction can occur involving cells of only one mating...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "mycology", "molecular", "cell", "biology", "cell", "division", "emerging", "infectious", "diseases", "genetics", "molecular", "genetics", "biology", "microbiology", "fungal", "reproduction" ]	2013	Genetic Circuits that Govern Bisexual and Unisexual Reproduction in Cryptococcus neoformans
Gene targeting in human somatic cells is of importance because it can be used to either delineate the loss-of-function phenotype of a gene or correct a mutated gene back to wild-type . Both of these outcomes require a form of DNA double-strand break ( DSB ) repair known as homologous recombination ( HR ) . The mechanis...	Gene targeting is important for basic research and clinical applications . In the laboratory , gene targeting is used to knockout genes so that loss-of-function phenotypes can be assessed . In the clinic , gene targeting is the gold standard to which most gene therapy approaches aspire . One of the most promising tools...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "and", "health", "sciences", "clinical", "genetics", "cell", "biology", "gene", "therapy", "genetics", "cancer", "treatment", "biology", "and", "life", "sciences", "molecular", "biology", "techniques", "genomics", "molecular", "cell", "biology"...	2014	The Mechanism of Gene Targeting in Human Somatic Cells
We analyse new genomic data ( 0 . 05–2 . 95x ) from 14 ancient individuals from Portugal distributed from the Middle Neolithic ( 4200–3500 BC ) to the Middle Bronze Age ( 1740–1430 BC ) and impute genomewide diploid genotypes in these together with published ancient Eurasians . While discontinuity is evident in the tra...	Recent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age . In Iberia , archaeological change at the level of material culture and funerary rituals has been reported during this p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biogeography", "geologic", "time", "ecology", "and", "environmental", "sciences", "population", "genetics", "variant", "genotypes", "social", "sciences", "genetic", "mapping", "neolithic", "period", "archaeology", "geology", "paleontology", "paleogenetics", "population", ...	2017	The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods
Human visceral leishmaniasis ( VL ) , a potentially fatal disease , has emerged as an important opportunistic condition in HIV infected patients . In immunocompromised patients , serological investigation is considered not an accurate diagnostic method for VL diagnosis and molecular techniques seem especially promising...	Human visceral leishmaniasis ( VL ) , a potentially fatal disease , has emerged as an important opportunistic condition in HIV infected patients . In immunocompromised patients , serological investigation is considered not an accurate diagnostic method for VL diagnosis and molecular techniques seem especially promising...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "diagnostic", "medicine", "sexually", "transmitted", "diseases", "aids", "leishmaniasis", "neglected", "tropical", "diseases" ]	2012	The Diagnostic Accuracy of Serologic and Molecular Methods for Detecting Visceral Leishmaniasis in HIV Infected Patients: Meta-Analysis
In eukaryotic cells , the unfolded protein response ( UPR ) pathway plays a crucial role in cellular homeostasis of the endoplasmic reticulum ( ER ) during exposure to diverse environmental conditions that cause ER stress . Here we report that the human fungal pathogen Cryptococcus neoformans has evolved a unique UPR p...	The unfolded protein response ( UPR ) is a widely conserved signaling pathway in eukaryotic cells and protects cells from the ER stress causing accumulation of toxic unfolded or misfolded proteins . Nevertheless , the UPR pathway has been poorly exploited as a therapeutic target for treatment of eukaryotic fungal patho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "pathogenesis" ]	2011	Unique Evolution of the UPR Pathway with a Novel bZIP Transcription Factor, Hxl1, for Controlling Pathogenicity of Cryptococcus neoformans
The sandfly Phlebotomus papatasi is the vector of Leishmania major , the main causative agent of Old World cutaneous leishmaniasis ( CL ) in Saudi Arabia . Sandflies inject saliva while feeding and the salivary protein PpSP32 was previously shown to be a biomarker for bite exposure . Here we used recombinant PpSP32 to ...	Leishmania is transmitted by the bite of infected female sandflies . When a sandfly bites a vertebrate host , it injects a cocktail of salivary proteins meant to facilitate blood feeding . The constant exposure to sandfly bites in endemic areas triggers a humoral response against the major antigenic components in the s...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Severity of Old World Cutaneous Leishmaniasis Is Influenced by Previous Exposure to Sandfly Bites in Saudi Arabia
The circadian oscillator is a molecular feedback circuit whose orchestration involves posttranslational control of the activity and protein levels of its components . Although controlled proteolysis of circadian proteins is critical for oscillator function , our understanding of the underlying mechanisms remains incomp...	In mammals , circadian rhythms are generated by a molecular oscillator in which the circadian locomotor output cycles protein kaput ( CLOCK ) –brain and muscle ARNT-like protein 1 ( BMAL1 ) transcription factors drive expression of the genes coding for their own repressors , the CRYPTOCHROME ( CRY ) and PERIOD ( PER ) ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "circadian", "oscillators", "muscle", "proteins", "transcription", "factors", "chronobiology", "small", "interfering", "rnas", "proteins", "gene", "expression", "biochemistry", "circadian", "rhythms"...	2018	JMJD5 links CRY1 function and proteasomal degradation
Ribosomal RNAs ( rRNAs ) are transcribed from two multicopy DNA arrays: the 5S ribosomal DNA ( rDNA ) array residing in a single human autosome and the 45S rDNA array residing in five human autosomes . The arrays are among the most variable segments of the genome , exhibit concerted copy number variation ( cCNV ) , enc...	The 45S and 5S ribosomal DNA ( rDNA ) arrays contain hundreds of rDNA copies , with substantial variability across individuals in human populations . Although physically unlinked , the arrays also exhibit joint variation across individual genotypes . However , whether this co-variation in copy number ( CN ) is universa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "population", "genetics", "ploidy", "cancers", "and", "neoplasms", "carcinomas", "oncology", "mutation", "non-coding", "rna", "adenocarcinomas", "population", "biology", "cellular", "structures", "and", "organelles", "genome", "c...	2017	Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation
There is now substantial evidence that compounds released during host stress directly activate the virulence of certain opportunistic pathogens . Here , we considered that endogenous opioids might function as such compounds , given that they are among the first signals to be released at multiple tissue sites during hos...	Precisely how bacterial pathogens such as Pseudomonas aeruginosa cause fatal infections in critically ill humans is unknown . Evidence suggests that a major source of infection may be the patient's own intestinal microflora , which is subjected to unusual environmental conditions during critical illness . Here , we sho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "pathology", "gastroenterology", "and", "hepatology", "caenorhabditis", "microbiology", "mus", "(mouse)", "eubacteria" ]	2007	Dynorphin Activates Quorum Sensing Quinolone Signaling in Pseudomonas aeruginosa
A face-to-face survey of 158 policymakers and other influential professionals was conducted in eight dengue-endemic countries in Asia ( India , Sri Lanka , Thailand , Vietnam ) and Latin America ( Brazil , Colombia , Mexico , Nicaragua ) to provide an indication of the potential demand for dengue vaccination in endemic...	Information gleaned from surveys of country-level policymakers and other opinion leaders can assist in planning the development , production and introduction of new or upcoming vaccines into public sector immunization programs . In the case of dengue vaccines , prevailing views among these leaders about the importance ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "viral", "vaccines", "social", "and", "behavioral", "sciences", "dengue", "microbiology", "immunology", "vaccines", "neglected", "tropical", "diseases", "vaccination", "infectious", "diseases", "dengue", "fever", "biology", "clinical", "immunology", "immunity"...	2013	Will Dengue Vaccines Be Used in the Public Sector and if so, How? Findings from an 8-country Survey of Policymakers and Opinion Leaders
Individuals vary extensively in the way they respond to disease but the genetic basis of this variation is not fully understood . We found substantial individual variation in resistance and tolerance to the fungal pathogen Metarhizium anisopliae Ma549 using the Drosophila melanogaster Genetic Reference Panel ( DGRP ) ....	We have shown that there is significant genetic variation for host defenses against the fungus M . anisopliae ( Ma549 ) in a set of 188 Drosophila lines derived from nature that have been completely sequenced . This manifested as differences between lines in mean survival times , how they balanced resistance and tolera...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "pathogens", "population", "genetics", "microbiology", "animals", "animal", "models", "drosophila", "mela...	2017	The genetic basis for variation in resistance to infection in the Drosophila melanogaster genetic reference panel
Microbial agents can aggravate inflammatory diseases , such as multiple sclerosis ( MS ) and its animal model , experimental autoimmune encephalomyelitis ( EAE ) . An example is pertussis toxin ( PTX ) , a bacterial virulence factor commonly used as an adjuvant to promote EAE , but whose mechanism of action is unclear ...	Microbial agents can aggravate inflammatory diseases , such as multiple sclerosis ( MS ) and its animal model , experimental autoimmune encephalomyelitis ( EAE ) . An example is pertussis toxin ( PTX ) , which is used to promote EAE by an obscure mechanism . We have reported that PTX triggers an IL-6-mediated signaling...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "immune", "cells", "cytokines", "immune", "activation", "immunology", "microbiology", "developmental", "biology", "molecular", "development", "white", "blood", "cells", "inflammation", "animal", "cells", "t", "cells", "i...	2014	The Inflammasome Pyrin Contributes to Pertussis Toxin-Induced IL-1β Synthesis, Neutrophil Intravascular Crawling and Autoimmune Encephalomyelitis
Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate , among other things , the construction of optimized search engines . To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construc...	The need for the construction of a dengue ontology arose through the fact that the incidence of dengue fever is on the rise across the world; the number of cases may be three to four times higher than the 100 million estimated by the WHO and a vaccine is still not available in spite of the significant efforts undertake...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[]	2015	Describing the Breakbone Fever: IDODEN, an Ontology for Dengue Fever
Polymyxins are the last line of defense against lethal infections caused by multidrug resistant Gram-negative pathogens . Very recently , the use of polymyxins has been greatly challenged by the emergence of the plasmid-borne mobile colistin resistance gene ( mcr-1 ) . However , the mechanistic aspects of the MCR-1 col...	Colistin is an ultimate line of refuge against fatal infections by multidrug-resistant Gram-negative pathogens . The plasmid-mediated transfer of the mobile colistin resistance gene ( mcr-1 ) represents a novel mechanism for antibacterial drug resistance , and also poses new threats to public health . However , the mec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "antimicrobials", "medicine", "and", "health", "sciences", "enzymes", "split-decomposition", "method", "drugs", "enzymology", "microbiology", "multiple", "alignment", "calculation", "antibiotics", "molecular", "biology", "techniques", "pharmacology...	2016	Dissemination and Mechanism for the MCR-1 Colistin Resistance
In order to guarantee the fulfillment of their complex lifecycle , adult filarial nematodes release millions of microfilariae ( MF ) , which are taken up by mosquito vectors . The current strategy to eliminate lymphatic filariasis as a public health problem focuses upon interrupting this transmission through annual mas...	The tropical helminth infection lymphatic filariasis affects more than 120 million people worldwide and is considered a major public health concern . Over 90% of infections are elicited by Wucheria bancrofti and adult worms reside in the lymphatic system releasing millions of microfilariae ( MF ) , which periodically c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "clinical", "immunology", "immunity", "global", "health", "immunology", "biology", "public", "health", "immune", "system" ]	2012	Elevated Adaptive Immune Responses Are Associated with Latent Infections of Wuchereria bancrofti
Trypanosoma cruzi is a protozoan parasite that causes severe disease in millions of habitants of developing countries . Currently there is no vaccine to prevent this disease and the available drugs have the consequences of side effects . Live vaccines are likely to be more effective in inducing protection than recombin...	Chagas disease is the clinical manifestation of the infection produced by the flagellate parasite Trypanosoma cruzi and currently there is no vaccine to prevent this disease . Therefore , different approaches or alternatives are urgently needed . Vaccination with live attenuated parasites has been used effectively in m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetic", "mutation", "immunology", "microbiology", "parastic", "protozoans", "immunizations", "microbial", "pathogens", "biology", "mutagenesis", "trypanosoma", "immunity", "genetics", "protozoology", "genetics", "and", "genomics" ]	2011	Knockout of the dhfr-ts Gene in Trypanosoma cruzi Generates Attenuated Parasites Able to Confer Protection against a Virulent Challenge
The structure of the physical world projects images onto our eyes . However , those images are often poorly representative of environmental structure: well-defined boundaries within the eye may correspond to irrelevant features of the physical world , while critical features of the physical world may be nearly invisibl...	Biological vision is designed to discover the structure of the environment around us . To do this , it relies on ambiguous and often misleading information from the eyes: the boundary of a critical object may be invisible against a background of similar appearance , and may be overlooked in favour of the sharp contour ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "signal", "processing", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "light", "neuroscience", "signal", "filtering", "electromagnetic", "radiation", "clinical", "medicin...	2017	Object segmentation controls image reconstruction from natural scenes
The actin cytoskeleton coordinates the organization of signaling microclusters at the immune synapse ( IS ) ; however , the mechanisms involved remain poorly understood . We show here that nitric oxide ( NO ) generated by endothelial nitric oxide synthase ( eNOS ) controls the coalescence of protein kinase C-θ ( PKC-θ ...	T cells are an essential arm of the immunity against the invasion of pathogenic agents in organisms . These specialized cells recognize foreign antigens displayed on the surface of antigen-presenting cells ( APC ) by means of the T cell receptor ( TCR ) . Early signaling takes place in these cells through the specific ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "neurochemistry", "immune", "cells", "antigen-presenting", "cells", "immunology", "cell", "processes", "light", "microscopy", "neuroscience", "microscopy", "research", "and", "analysis",...	2017	eNOS S-nitrosylates β-actin on Cys374 and regulates PKC-θ at the immune synapse by impairing actin binding to profilin-1
Yellow fever is endemic in some countries in Africa , and Aedes aegpyti is one of the most important vectors implicated in the outbreak . The mapping of the nation-wide distribution and the detection of insecticide resistance of vector mosquitoes will provide the beneficial information for forecasting of dengue and yel...	Aedes aegpyti is one of the most important vectors of yellow fever and dengue fever . Pyrethroid insecticides are emerging as the predominant insecticides for vector control , and resistance of vector mosquitoes to pyrethroid is a major problem for the vector control program . Several mutations in the voltage-gated sod...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "population", "genetics", "geographical", "locations", "animals", "mutation", "ddt", "phylogenetic", "analysis", "molecular", "biology", "techniques", "population", "biology", "insect", "vectors", "africa", "resear...	2016	Discovery of Point Mutations in the Voltage-Gated Sodium Channel from African Aedes aegypti Populations: Potential Phylogenetic Reasons for Gene Introgression
Non-self recognition is a common phenomenon among organisms; it often leads to innate immunity to prevent the invasion of parasites and maintain the genetic polymorphism of organisms . Fungal vegetative incompatibility is a type of non-self recognition which often induces programmed cell death ( PCD ) and restricts the...	Self/non-self recognition , as the most fundamental immune system , is an essential part in response to nonself host defense in fungi , plants and animals against pathogens or molecular parasites . Vegetative incompatibility as a conspecific nonself system in filamentous fungi results in PCD when cells of incompatible ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "fungal", "genetics", "microbiology", "parasitic", "diseases", "fungal", "structure", "fungi", "plant", "science", "mycelium", "plant", ...	2017	Virus-mediated suppression of host non-self recognition facilitates horizontal transmission of heterologous viruses
Chromosomal DNA must be in single-strand form for important transactions such as replication , transcription , and recombination to occur . The single-strand DNA ( ssDNA ) is more prone to damage than double-strand DNA ( dsDNA ) , due to greater exposure of chemically reactive moieties in the nitrogenous bases . Thus ,...	A cell's genome is encoded within double-strand DNA . Yet DNA must exist transiently in single-strand form to template transcription , replication , and repair . As DNA is more prone to damage in single-strand ( ssDNA ) than double-strand ( dsDNA ) form , there can be agents that mutate ssDNA , but not dsDNA . Since ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "genetic", "mutation", "microbiology", "mutational", "hypotheses", "toxicology", "model", "organisms", "mutation", "types", "dna", "genetics", "and", "genomics", "biology", "public", "health", "molecular", "biology"...	2012	Base Damage within Single-Strand DNA Underlies In Vivo Hypermutability Induced by a Ubiquitous Environmental Agent

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