Split (3)

train · 24.8k rows

Search is not available for this dataset

article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Mosquito-borne flaviviruses are among the most significant arboviral pathogens worldwide . Vaccinations and mosquito population control programs remain the most reliable means for flavivirus disease prevention , and live attenuated viruses remain one of the most attractive flavivirus vaccine platforms . Some live atten...	Despite advances in developing flavivirus live attenuated vaccine ( LAV ) candidates , a concern exists that they might not be safe in the environment due to their intrinsic genetic instability leading to potential reversion back to wild-type that could be associated with possible dissemination of these mutated viruses...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dual miRNA Targeting Restricts Host Range and Attenuates Neurovirulence of Flaviviruses
CD200 receptor ( CD200R ) negatively regulates peripheral and mucosal innate immune responses . Viruses , including herpesviruses , have acquired functional CD200 orthologs , implying that viral exploitation of this pathway is evolutionary advantageous . However , the role that CD200R signaling plays during herpesvirus...	Immune inhibitory receptors , including CD200 receptor ( CD200R ) , can limit immune responses in the mucosa to restrict reactivity to the plethora of harmless antigens that mucosal surfaces are continually exposed to . However , viruses may exploit these suppressive mechanisms to enable their persistence and spread . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	CD200 Receptor Restriction of Myeloid Cell Responses Antagonizes Antiviral Immunity and Facilitates Cytomegalovirus Persistence within Mucosal Tissue
Retina is a paradigmatic system for studying sensory encoding: the transformation of light into spiking activity of ganglion cells . The inverse problem , where stimulus is reconstructed from spikes , has received less attention , especially for complex stimuli that should be reconstructed “pixel-by-pixel” . We recorde...	Neurons in the retina transform patterns of incoming light into sequences of neural spikes . We recorded from ∼100 neurons in the rat retina while it was stimulated with a complex movie . Using machine learning regression methods , we fit decoders to reconstruct the movie shown from the retinal output . We demonstrated...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "electronics", "membrane", "potential", "ocular", "anatomy", "electrophysiology", "light", "neuroscience", "electromagnetic", "radiation", "luminance",...	2018	Nonlinear decoding of a complex movie from the mammalian retina
A complex disease has , by definition , multiple genetic causes . In theory , these causes could be identified individually , but their identification will likely benefit from informed use of anticipated interactions between causes . In addition , characterizing and understanding interactions must be considered key to ...	Interaction between organic molecules forms the basis of all biological systems . The availability of high-throughput genotyping and sequencing platforms enables us to cost-effectively genotype a large number of individuals . For sufficiently large datasets it is possible to reconstruct the genetic dependencies that un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "variant", "genotypes", "random", "variables", "covariance", "alleles", "genetic", "mapping", "probability", "distribution", "mathematics", "coronary", "heart", "disease", "statistics", "(ma...	2017	Fast and general tests of genetic interaction for genome-wide association studies
Epstein-Barr virus ( EBV ) is a human cancer-related virus closely associated with lymphoid and epithelial malignancies , and EBV glycoprotein B ( gB ) plays an essential role in viral entry into both B cells and epithelial cells by promoting cell-cell fusion . EBV gB is exclusively modified with high-mannose-linked N-...	EBV envelope glycoprotein B ( gB ) is a core component of the fusion machinery and plays an essential role in viral entry . EBV gB has been characterized as a high-mannose-containing glycoprotein , but the significance of this sugar type is unknown . In this work , we report the identification of FBXO2 , a glycosylatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "nasopharyngeal", "carcinoma", "carcinomas", "immunology", "microbiology", "cancers", "and", "neoplasms", "epit...	2018	Epstein-Barr virus activates F-box protein FBXO2 to limit viral infectivity by targeting glycoprotein B for degradation
Transposable elements in crop plants are the powerful drivers of phenotypic variation that has been selected during domestication and breeding programs . In tomato , transpositions of the LTR ( long terminal repeat ) retrotransposon family Rider have contributed to various phenotypes of agronomical interest , such as f...	Transposons are major constituents of plant genomes and represent a powerful source of internal genetic and epigenetic variation . For example , domestication of maize has been facilitated by a dramatic change in plant architecture , the consequence of a transposition event . Insertion of transposons near genes often c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "retrotransposons", "engineering", "and", "technology", "gene", "regulation", "plant", "science", "genetic", "elements", "plant", "genomics", "sequence", "motif", "analysis", "epigenetics", "dna", "plants", "chromatin", "dna", "methylation", "research", ...	2019	Environmental and epigenetic regulation of Rider retrotransposons in tomato
Malaria transmission requires that Anopheles mosquitoes ingest Plasmodium gametocyte stages circulating in the human bloodstream . In the context of malaria elimination , understanding the epidemiology of gametocytes relative to all Plasmodium infections and the contribution of asymptomatic and sub-microscopic parasite...	Malaria elimination , i . e . the complete interruption of parasite transmission in a region , is in the agenda of health authorities in countries that achieved substantial reduction of the disease burden in the past decade . However , our understanding of transmission epidemiology for low transmission areas where Plas...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "gametocytes", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animals", "parasitology", "germ", "cells", "apicomplexa", "protozoan...	2017	Predominance of asymptomatic and sub-microscopic infections characterizes the Plasmodium gametocyte reservoir in the Peruvian Amazon
Replication of many RNA viruses is accompanied by extensive remodeling of intracellular membranes . In poliovirus-infected cells , ER and Golgi stacks disappear , while new clusters of vesicle-like structures form sites for viral RNA synthesis . Virus replication is inhibited by brefeldin A ( BFA ) , implicating some c...	All positive strand RNA viruses replicate their genomes in association with membranous structures that are formed after infection by remodeling pre-existing cellular organelles . The role of membranes and the mechanisms exploited by viral proteins to orchestrate the formation and functioning of viral membranous replica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation" ]	2008	A Critical Role of a Cellular Membrane Traffic Protein in Poliovirus RNA Replication
Human defensins are at the forefront of the host responses to HIV and other pathogens in mucosal tissues . However , their ability to inactivate HIV in the bloodstream has been questioned due to the antagonistic effect of serum . In this study , we have examined the effect of sub-inhibitory concentrations of human α-de...	Human neutrophil peptide 1 ( HNP-1 ) is a small cationic peptide that can directly block HIV-1 entry in the absence of serum . However , since serum attenuates the anti-HIV activity of this peptide , HNP-1 is unlikely to inhibit infection in the bloodstream . Here , we demonstrate that sub-inhibitory doses of HNP-1 in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biology", "microbiology" ]	2013	Sub-Inhibitory Concentrations of Human α-defensin Potentiate Neutralizing Antibodies against HIV-1 gp41 Pre-Hairpin Intermediates in the Presence of Serum
The primitive face is composed of neural crest cell ( NCC ) derived prominences . The medial nasal processes ( MNP ) give rise to the upper lip and vomeronasal organ , and are essential for normal craniofacial development , but the mechanism of MNP development remains largely unknown . PDGFRα signaling is known to be c...	Craniofacial anomalies , including cleft lip and palate , are frequent birth defects . Although these are often associated with defects in neural crest development , the more severe phenotypic manifestations of midline defects is facial clefting , which is poorly understood . In this work , we show that the facial clef...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Critical Role for PDGFRα Signaling in Medial Nasal Process Development
Phagocytosis requires locally coordinated cytoskeletal rearrangements driven by actin polymerization and myosin motor activity . How this actomyosin dynamics is dependent upon systems that provide access to ATP at phagosome microdomains has not been determined . We analyzed the role of brain-type creatine kinase ( CK-B...	To do work , cells need energy in the form of ATP . High and sudden energy demand is seen during cell-shape change , a process in which ATP fuels the cytoskeletal machinery that drives cell-morphology alteration . How a cell organizes high-energy surges without disrupting global ATP homeostasis remains an important res...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "physiology", "immunology" ]	2008	Creatine Kinase–Mediated ATP Supply Fuels Actin-Based Events in Phagocytosis
The Kaposi’s sarcoma associated herpesvirus ( KSHV ) is an oncogenic virus that causes Kaposi’s sarcoma , primary effusion lymphoma ( PEL ) , and some forms of multicentric Castleman’s disease . The KSHV ORF57 protein is a conserved posttranscriptional regulator of gene expression that is essential for virus replicatio...	During viral replication , the oncogenic Kaposi’s sarcoma-associated herpesvirus ( KSHV ) modulates both host and viral gene expression . KSHV ORF57 is a multifunctional posttranscriptional regulator that is essential for viral replication and stabilizes viral RNAs . Previous studies demonstrated that ORF57 RNA-binding...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	HITS-CLIP Analysis Uncovers a Link between the Kaposi’s Sarcoma-Associated Herpesvirus ORF57 Protein and Host Pre-mRNA Metabolism
The control and elimination of Plasmodium vivax will require a better understanding of its transmission dynamics , through the application of genotyping and population genetics analyses . This paper describes VivaxGEN ( http://vivaxgen . menzies . edu . au ) , a web-based platform that has been developed to support P ....	The Plasmodium vivax malaria parasite inflicts significant morbidity in endemic populations across the globe , but has been overshadowed by the more fatal P . falciparum parasite . In malaria-endemic regions outside of Africa , the declining prevalence of P . falciparum is coupled with a proportionate rise in P . vivax...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion", "Conclusions" ]	[ "computer", "applications", "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "population", "genetics", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protoz...	2017	VivaxGEN: An open access platform for comparative analysis of short tandem repeat genotyping data in Plasmodium vivax populations
Mechanical coherence of cell layers is essential for epithelia to function as tissue barriers and to control active tissue dynamics during morphogenesis . RhoA signaling at adherens junctions plays a key role in this process by coupling cadherin-based cell-cell adhesion together with actomyosin contractility . Here we ...	Mathematical models play a key role in uncovering mechanisms responsible for the formation of patterns in cells and tissues . The well known Turing mechanism based on nonlinear reaction kinetics and differential diffusion explains the formation of static patterns , while positive feedback interactions can generate dyna...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "fluid", "mechanics", "mathematical", "models", "epithelial", "cells", "guanine", "nucleotide", "exchange", "factors", "molecular", "motors", "actin", "motors", "gtpase", "signaling", "reaction", "dynami...	2017	Bistable front dynamics in a contractile medium: Travelling wave fronts and cortical advection define stable zones of RhoA signaling at epithelial adherens junctions
Chronic infections are characterized by the inability to eliminate the persisting pathogen and often associated with functional impairment of virus-specific T-cell responses . Costimulation through Glucocorticoid-induced TNFR-related protein ( GITR ) can increase survival and function of effector T cells . Here , we re...	The ability of the immune system to rapidly respond to a viral infection is a prerequisite for the survival of an individual . The immediate reaction of innate immune cells and the subsequent response of antigen-specific lymphocytes is usually effective for rapid neutralization and removal of the invading virus . Yet ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Enhanced CD8 T Cell Responses through GITR-Mediated Costimulation Resolve Chronic Viral Infection
Spatial modelling of STH and schistosomiasis epidemiology is now commonplace . Spatial epidemiological studies help inform decisions regarding the number of people at risk as well as the geographic areas that need to be targeted with mass drug administration; however , limited attention has been given to propagated unc...	In recent years spatial modelling studies of schistosome and soil-transmitted helminth infections have become commonplace; however there is no standard framework for uncertainty evaluation and reporting . In this study we aim to identify faults in existing studies and propose a framework for evaluation and reporting . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "parasitic", "diseases", "animals", "health", "care", "mathematics", "forecasting", "statistics", "(mathematics)", "neglected", "tropical", "diseases", "infectious"...	2016	Mapping Soil Transmitted Helminths and Schistosomiasis under Uncertainty: A Systematic Review and Critical Appraisal of Evidence
Overexpression of miRNA , miR-24 , in mouse hematopoietic progenitors increases monocytic/ granulocytic differentiation and inhibits B cell development . To determine if endogenous miR-24 is required for hematopoiesis , we antagonized miR-24 in mouse embryonic stem cells ( ESCs ) and performed in vitro differentiations...	Studies of mouse embryos and embryonic stem cells ( ESCs ) have defined the ontogeny of mammalian embryonic hematopoietic cells . The ESC differentiation system has been valuable for dissecting the molecular regulation of the development of mesoderm into HPCs . Extracellular signals regulate a complex network of transc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	MiR-24 Is Required for Hematopoietic Differentiation of Mouse Embryonic Stem Cells
Somatic mutations in protein-coding regions can generate ‘neoantigens’ causing developing cancers to be eliminated by the immune system . Quantitative estimates of the strength of this counterselection phenomenon have been lacking . We quantified the extent to which somatic mutations are depleted in peptides that are p...	Cancer immunotherapy and personalized cancer vaccines depend on clearance of cancer and pre-cancer cells by the immune system . However , little is known about the strength of this phenomenon as it acts on the cell populations which give rise to tumors . Here we provide an initial quantitative estimate of the fraction ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mhc", "class", "i", "genes", "medicine", "and", "health", "sciences", "immune", "physiology", "immunology", "alleles", "mutation", "protein", "expression", "clinical", "medicine", "gene", "types", "molecular", "biology", "techniques", "research", "and", "analysis", ...	2019	Quantifying immune-based counterselection of somatic mutations
Protein loops connect regular secondary structures and contain 4-residue beta turns which represent 63% of the residues in loops . The commonly used classification of beta turns ( Type I , I’ , II , II’ , VIa1 , VIa2 , VIb , and VIII ) was developed in the 1970s and 1980s from analysis of a small number of proteins of ...	Folded proteins consist of elements of regular secondary structure , such as alpha helices and beta sheets connected by irregular structures called loops . Loops have a varying length and typically contain U-shaped beta turns which abruptly change the direction of the chain . Beta turns are formed by four sequential am...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "bonding", "condensed", "matter", "physics", "geometry", "mathematics", "protein", "structure", "prediction", "protein", "structure", "hydrogen", "bonding", "physical", "chemistry", "protein", "structure", "determination", "proteins", "chemistry", "beta", "hel...	2019	A new clustering and nomenclature for beta turns derived from high-resolution protein structures
The spread of infectious diseases fundamentally depends on the pattern of contacts between individuals . Although studies of contact networks have shown that heterogeneity in the number of contacts and the duration of contacts can have far-reaching epidemiological consequences , models often assume that contacts are ch...	The transmission dynamics of infectious diseases are sensitive to the patterns of interactions among susceptible and infectious individuals . Human social contacts are known to be highly heterogeneous ( the number of social contacts ranges from few to very many ) and to be highly clustered ( the social contacts of a si...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "social", "and", "behavioral", "sciences", "population", "modeling", "social", "networks", "sociology", "biology", "computational", "biology", "infectious", "disease", "modeling" ]	2011	Effects of Heterogeneous and Clustered Contact Patterns on Infectious Disease Dynamics
Trachoma is the commonest infectious cause of blindness worldwide . Recurrent infection of the ocular surface by Chlamydia trachomatis , the causative agent , leads to inturning of the eyelashes ( trichiasis ) and blinding corneal opacification . Trachoma is endemic in more than 50 countries . It is currently estimated...	This review examines the various attempts to estimate the burden of disease from trachoma , the commonest infectious cause of blindness worldwide . Reports vary considerably because of differences in methodology and changing estimates of the number of people affected . Currently about 1 . 3 million are blind from trach...	[ "Abstract", "Introduction", "Pathogenesis", "and", "Clinical", "Features", "Epidemiology", "Global", "Prevalence", "of", "Trachoma", "Global", "Burden", "of", "Trachoma", "Economic", "Cost", "of", "Trachoma", "Trachoma", "Control", "and", "Its", "Cost-effectiveness", ...	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "review" ]	2009	The Global Burden of Trachoma: A Review
Although information theoretic approaches have been used extensively in the analysis of the neural code , they have yet to be used to describe how information is accumulated in time while sensory systems are categorizing dynamic sensory stimuli such as speech sounds or visual objects . Here , we present a novel method ...	Just as the recognition of faces requires neural representations that are invariant to scale and rotation , the recognition of behaviorally relevant auditory objects , such as spoken words , requires neural representations that are invariant to the speaker uttering the word and to his or her location . Here , we used i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "information", "entropy", "vocalization", "vertebrates", "social", "sciences", "neuroscience", "animals", "animal", "models", "probability", "distribution", "mathematics", "animal", "behavior", "experimental", "organism", "systems", "computational", "neuroscience", "zoology",...	2019	Invariant neural responses for sensory categories revealed by the time-varying information for communication calls
During experimental cerebral malaria ( ECM ) mice develop a lethal neuropathological syndrome associated with microcirculatory dysfunction and intravascular leukocyte sequestration . The precise spatio-temporal context in which the intravascular immune response unfolds is incompletely understood . We developed a 2-phot...	Cerebral malaria ( CM ) is a severe complication of Plasmodium falciparum infection that takes a significant toll on human life . Blockage of the brain blood vessels contributes to the clinical signs of CM , however we know little about the precise pathological events that lead to this disease . To this end , studies i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "parasite", "groups", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "parasitology", "global", "health", "immunoregulation", "public", "and", "occupational", "health", "infectious", "diseases", "whi...	2014	Real-Time Imaging Reveals the Dynamics of Leukocyte Behaviour during Experimental Cerebral Malaria Pathogenesis
Phlebotomus tobbi is a vector of Leishmania infantum , and P . sergenti is a vector of Leishmania tropica . Le . infantum and Le . tropica typically cause visceral or cutaneous leishmaniasis , respectively , but Le . infantum strains transmitted by P . tobbi can cause cutaneous disease . To better understand the compon...	Phlebotomine female sand flies require a blood meal for egg development , and it is during the blood feeding that pathogens can be transmitted to a host . Leishmania parasites are among these pathogens and can cause disfiguring cutaneous or even possibly fatal visceral disease . The Leishmania parasites are deposited i...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "functional", "genomics", "immunology", "parasitic", "diseases", "neglected", "tropical", "diseases", "glycoproteins", "veterinary", "science", "infectious", "diseases", "veterinary", "diseases", "zoonoses", "veterinary", "parasitology", "comparative", "genomics",...	2012	Salivary Gland Transcriptomes and Proteomes of Phlebotomus tobbi and Phlebotomus sergenti, Vectors of Leishmaniasis
Chikungunya virus ( CHIKV ) is a mosquito-transmitted RNA alphavirus causing major outbreaks of infectious chronic inflammatory rheumatisms ( CIR ) . Recently , methotrexate ( MTX ) , a disease modifying anti-rheumatic drug has been used successfully to treat patients suffering from rheumatoid-like arthritis post-CHIK ...	Chikungunya is a mosquito-borne virus ( CHIKV ) and has been incriminated in the development of arthralgia ( pain of the joint ) and arthritis particularly in elderly patients . Methotrexate ( MTX ) has been used widely to effectively treat these chronic rheumatic symptoms . Using a model of primary human joint fibrobl...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "m...	2018	Immunomodulatory drug methotrexate used to treat patients with chronic inflammatory rheumatisms post-chikungunya does not impair the synovial antiviral and bone repair responses
Diagnosis of intestinal schistosomiasis in low endemic areas is a problem because often control measures have reduced egg burdens in feces to below the detection limits of classical coproparasitological methods . Evaluation of molecular methods is hindered by the absence of an established standard with maximum sensitiv...	Schistosomiasis mansoni is a parasitic infection that affects approximately 200 million people , mainly in the tropics . The worms live inside the veins of intestines and liver and produce eggs that are eliminated within feces . If the eggs reach water , a ciliated larva is released and enters snails to develop into a ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "microbiology/parasitology", "infectious", "diseases/epidemiology", "and", "control", "of", "...	2007	Detection of Schistosoma mansoni Eggs in Feces through their Interaction with Paramagnetic Beads in a Magnetic Field
Effective immune responses require the directed migration of leukocytes from the vasculature to the site of injury or infection . How immune cells “find” their site of extravasation remains largely obscure . Here , we identified a previously unrecognized role of platelets as pathfinders guiding leukocytes to their exit...	White blood cells ( leukocytes ) are the effector cells of the immune system . The movement ( extravasation ) of leukocytes from the bloodstream to the surrounding tissue is a prerequisite for proper host defense . Platelets are anucleate cell particles that circulate in the blood and play a fundamental role in hemosta...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "cardiovascular", "anatomy", "endothelial", "cells", "immunology", "cloning", "epithelial", "cells", "integrins", "signs", "an...	2016	Platelets Guide Leukocytes to Their Sites of Extravasation
Human cyclophilin A , or CypA , encoded by the gene peptidyl prolyl isomerase A ( PPIA ) , is incorporated into the HIV type 1 ( HIV-1 ) virion and promotes HIV-1 infectivity by facilitating virus uncoating . We examined the effect of single nucleotide polymorphisms ( SNPs ) and haplotypes within the PPIA gene on HIV-1...	Individual risk of acquiring HIV type 1 ( HIV-1 ) infection and developing AIDS is not equal; some people are more prone to HIV/AIDS than others . Susceptibility to HIV-1/AIDS is likely determined by a combination of environmental , viral , and host genetic factors . Genetic variations in host cellular factors involved...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "genetics", "and", "genomics", "homo", "(human)", "virology" ]	2007	Regulatory Polymorphisms in the Cyclophilin A Gene, PPIA, Accelerate Progression to AIDS
Experimental studies on enzyme evolution show that only a small fraction of all possible mutation trajectories are accessible to evolution . However , these experiments deal with individual enzymes and explore a tiny part of the fitness landscape . We report an exhaustive analysis of fitness landscapes constructed with...	Is evolution deterministic , hence predictable , or stochastic , that is unpredictable ? What would happen if one could “replay the tape of evolution”: will the outcomes of evolution be completely different or is evolution so constrained that history will be repeated ? Arguably , these questions are among the most intr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "computational", "biology", "evolutionary", "biology" ]	2011	Predictability of Evolutionary Trajectories in Fitness Landscapes
Taenia solium is a neglected zoonotic parasite endemic throughout many low-income countries worldwide , including Zambia , where it causes human and pig diseases with high health and socioeconomic burdens . Lack of knowledge is a recognized risk factor , and consequently targeted health educational programs can decreas...	The zoonotic parasite Taenia solium , commonly known as the pork tapeworm , causes substantial public health and economic losses worldwide . It is commonly found in low-income countries where pigs are raised in areas of poor sanitation , including Zambia . The links between the parasite and its different disease forms ...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "medicine", "and", "health", "sciences", "education", "sociology", "vertebrates", "social", "sciences", "diet", "parasitic", "diseases", "animals", "mammals", "parasitology", "health", "care", "animal", "products", "developmental", "biology", "nutrition", "meat", "amnio...	2019	Effects of ‘The Vicious Worm’ educational tool on Taenia solium knowledge retention in Zambian primary school students after one year
The 2020 Sustainable Development goals call for 100% certified interruption or control of the three main forms of Chagas disease transmission in Latin America . However , how much will achieving these goals to varying degrees control Chagas disease; what is the potential impact of missing these goals and if they are ac...	While World Health Organization’s ( WHO ) London Declaration on Neglected Tropical Diseases has proposed 2020 goals of 100% certified interruption or control of the three main forms of Chagas disease transmission ( vectorial , congenital , and transfusional ) in Latin America , the impact of achieving and/or missing th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "animal", "types", "medicine", "and", "health", "sciences", "domestic", "animals", "tropical", "diseases", "vector-borne", "diseases", "vertebrates", "parasitic", "diseases", "parasitic", "protozoans", "animals", "mammals", "dogs", "pets", "and", "companion", "animals",...	2018	Are the London Declaration’s 2020 goals sufficient to control Chagas disease?: Modeling scenarios for the Yucatan Peninsula
The increasing incidence of osteoporosis worldwide requires anabolic treatments that are safe , effective , and , critically , inexpensive given the prevailing overburdened health care systems . While vigorous skeletal loading is anabolic and holds promise , deficits in mechanotransduction accrued with age markedly dim...	Post-menopausal and age-related osteoporosis afflicts large segments of the population and can markedly increase skeletal fragility . Bone fractures that occur as a consequence substantially increase health care expenditures and raise levels of morbidity . While strategies that prevent further loss of bone exist , opti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physiology/cell", "signaling", "computational", "biology/transcriptional", "regulation", "biophysics/theory", "and", "simulation", "computational", "biology/signaling", "networks" ]	2010	Rescuing Loading Induced Bone Formation at Senescence
The small Rho-family GTPase Cdc42 is critical for cell polarization and polarizes spontaneously in absence of upstream spatial cues . Spontaneous polarization is thought to require dynamic Cdc42 recycling through Guanine nucleotide Dissociation Inhibitor ( GDI ) -mediated membrane extraction and vesicle trafficking . H...	Cell polarization is a critical feature of most cells that underlies their functional organization . A central polarity factor called Cdc42 , a small GTPase targeted to the plasma membrane by prenylation , promotes cell polarization in its active GTP-bound form . Cdc42 is a key polarity factor because it accumulates at...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Spontaneous Cdc42 Polarization Independent of GDI-Mediated Extraction and Actin-Based Trafficking
Antigen B ( EgAgB ) is the most abundant and immunogenic antigen produced by the larval stage ( metacestode ) of Echinococcus granulosus . It is a lipoprotein , the structure and function of which have not been completely elucidated . EgAgB apolipoprotein components have been well characterised; they share homology wit...	The larva of the cestode parasite Echinococcus granulosus affects a wide range of livestock mammals and humans , causing cystic echinococcosis ( hydatid disease ) , a zoonosis with significant economic and public health impact . The disease is characterised by the growth of a fluid-filled cyst in the host's viscera ( m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology" ]	2012	Characterisation of the Native Lipid Moiety of Echinococcus granulosus Antigen B
Visuospatial working memory enables us to maintain access to visual information for processing even when a stimulus is no longer present , due to occlusion , our own movements , or transience of the stimulus . Here we show that , when localizing remembered stimuli , the precision of spatial recall does not rely solely ...	Human capacity to maintain spatial information over brief interruptions is strongly limited . However , while studies of visual working memory typically examine recall in sparse displays , consisting only of the stimuli to remember , natural scenes are commonly filled with other objects that—although not required to be...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "social", "sciences", "neuroscience", "learning", "and", "memory", "cognitive", "neuroscience", "cognition", "memory", "vision", "research", "and", "analysis", "methods", "information", "retrieval", "sensory", "physiology", "memo...	2019	Independent working memory resources for egocentric and allocentric spatial information
Mammalian bile acids ( BAs ) are oxidized metabolites of cholesterol whose amphiphilic properties serve in lipid and cholesterol uptake . BAs also act as hormone-like substances that regulate metabolism . The Caenorhabditis elegans clk-1 mutants sustain elevated mitochondrial oxidative stress and display a slow defecat...	Cholesterol metabolism , in particular the transport of cholesterol in the blood by lipoproteins , is an important determinant of human cardiovascular health . Bile acids are breakdown products of cholesterol that have detergent properties and are secreted into the gut by the liver . Bile acids carry out three distinct...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "biochemistry", "model", "organisms", "biology" ]	2012	Mitochondrial Oxidative Stress Alters a Pathway in Caenorhabditis elegans Strongly Resembling That of Bile Acid Biosynthesis and Secretion in Vertebrates
The extent to which epigenetic variation affects complex traits in natural populations is not known . We addressed this question using transcriptome and DNA methylation data from a sample of 135 sequenced A . thaliana accessions . Across individuals , expression was significantly associated with cis-methylation for hun...	It has been demonstrated experimentally that epigenetic variation , in particular DNA methylation , can transmit information across generations . However , it is difficult to evaluate the importance of such effects in natural populations due to complex genetic background effects , making experimental the separation of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "brassica", "social", "sciences", "dna", "transcription", "model", "organisms", "genome", "analysis", "epigenetics", "dna", "plants", "dna", "methylation", "chromatin", "arabidopsis", "thaliana", "research", "and", "analysis", "m...	2016	Limited Contribution of DNA Methylation Variation to Expression Regulation in Arabidopsis thaliana
HIV-1 arose as the result of spillover of simian immunodeficiency viruses ( SIVs ) from great apes in Africa , namely from chimpanzees and gorillas . Chimpanzees and gorillas were , themselves , infected with SIV after virus spillover from African monkeys . During spillover events , SIV is thought to require adaptation...	Multiple times , HIV-1 has entered the human population after emerging from a viral reservoir that exists in African primates . First , simian immunodeficiency virus ( SIV ) made the jump from monkeys into African great apes , and then from apes ( namely , chimpanzees and gorillas ) into humans . It is well appreciated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "biological", "cultures", "microbiology", "vertebrates", "animals", "mammals", "retroviruses", "viruses", "immunodeficiency", "viruses", "primates", "rna",...	2018	Species-specific vulnerability of RanBP2 shaped the evolution of SIV as it transmitted in African apes
In the ciliate Paramecium tetraurelia , differentiation of the somatic nucleus from the zygotic nucleus is characterized by massive and reproducible deletion of transposable elements and of 45 , 000 short , dispersed , single-copy sequences . A specific class of small RNAs produced by the germline during meiosis , the ...	The unicellular eukaryote Paramecium tetraurelia provides an extraordinary model for studying the mechanisms involved in zygotic genome rearrangements . At each sexual cycle , differentiation of the somatic nucleus from the zygotic nucleus is characterized by extensive remodeling of the entire somatic genome , which in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Local Effect of Enhancer of Zeste-Like Reveals Cooperation of Epigenetic and cis-Acting Determinants for Zygotic Genome Rearrangements
In the Drosophila brain , the neuropeptide PIGMENT DISPERSING FACTOR ( PDF ) is expressed in the small and large Lateral ventral neurons ( LNvs ) and regulates circadian locomotor behavior . Interestingly , PDF immunoreactivity at the dorsal terminals changes across the day as synaptic contacts do as a result of a rema...	Circadian clocks have evolved as mechanisms that allow organisms to adapt to the day/night cyclical changes , a direct consequence of the rotation of the Earth . In the last two decades , and due to its amazing repertoire of genetic tools , Drosophila has been at the leading front in the discovery of genes that account...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "specimen", "preparation", "and", "treatment", "mechanical", "treatment", "of", "specimens", "biochemistry", "cellular", "neuroscience", "neurochemistry", "behavioral", "neuroscience", "specimen", "disruption", "neuronal", "morphology", "biology", "and", "life", "sciences",...	2014	Mmp1 Processing of the PDF Neuropeptide Regulates Circadian Structural Plasticity of Pacemaker Neurons
Perception of extracellular signals by cell surface receptors is of central importance to eukaryotic development and immunity . Kinases that are associated with the receptors or are part of the receptors themselves modulate signaling through phosphorylation events . The rice ( Oryza sativa L . ) XA21 receptor kinase is...	Resistance to pathogens is critical to plant and animal survival . Plants , unlike animals , lack an adaptive immune system and instead rely on the innate immune response to protect against infection . To elucidate the molecular mechanism of plant innate immunity , we are studying the signaling cascade mediated by the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "plant", "biology", "immunology" ]	2008	Rice XB15, a Protein Phosphatase 2C, Negatively Regulates Cell Death and XA21-Mediated Innate Immunity
Systematic mappings of the effects of protein mutations are becoming increasingly popular . Unexpectedly , these experiments often find that proteins are tolerant to most amino acid substitutions , including substitutions in positions that are highly conserved in nature . To obtain a more realistic distribution of the ...	Understanding and predicting the effects of single nucleotide polymorphisms ( SNPs ) is of fundamental importance in many fields . Systematic experimental mappings of the effects of such mutations within a given gene/protein comprise an essential experimental tool for determining protein function and for refining model...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations
Current Chagas disease vector control strategies , based on chemical insecticide spraying , are growingly threatened by the emergence of pyrethroid-resistant Triatoma infestans populations in the Gran Chaco region of South America . We have already shown that the entomopathogenic fungus Beauveria bassiana has the abili...	Triatomine bugs are the causative agent of Chagas disease ( American trypanosomiasis ) , they transmit the parasite Trypanosoma cruzi by infectious blood-sucking . In the southern Cone of South America , Triatoma infestans is the major disease vector . The efficacy of chemical control strategies is mostly based on pyre...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Discussion" ]	[]	2015	Biological Control of the Chagas Disease Vector Triatoma infestans with the Entomopathogenic Fungus Beauveria bassiana Combined with an Aggregation Cue: Field, Laboratory and Mathematical Modeling Assessment
Despite the importance of intracellular signaling networks , there is currently no consensus regarding the fundamental nature of the protein complexes such networks employ . One prominent view involves stable signaling machines with well-defined quaternary structures . The combinatorial complexity of signaling networks...	Intracellular signaling networks are central to a cell's ability to adapt to its environment . Developing the capacity to effectively manipulate such networks would have a wide range of applications , from cancer therapy to synthetic biology . This requires a thorough understanding of the mechanisms of signal transduct...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes
Nutrition is known to interact with genotype in human metabolic syndromes , obesity , and diabetes , and also in Drosophila metabolism . Plasticity in metabolic responses , such as changes in body fat or blood sugar in response to changes in dietary alterations , may also be affected by genotype . Here we show that var...	Normal individual differences in the foraging ( for ) gene of the fruit fly Drosophila melanogaster result in two behavioral types called rover and sitter . Larval rovers show a greater behavioral response to changes in their food environment than sitters . The for gene makes an enzyme called PKG , which is found in th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/animal", "behavior" ]	2009	The Drosophila foraging Gene Mediates Adult Plasticity and Gene–Environment Interactions in Behaviour, Metabolites, and Gene Expression in Response to Food Deprivation
Protein Direct Coupling Analysis ( DCA ) , which predicts residue-residue contacts based on covarying positions within a multiple sequence alignment , has been remarkably effective . This suggests that there is more to learn from sequence correlations than is generally assumed , and calls for deeper investigations into...	The success of Direct Coupling Analysis ( DCA ) for protein structure prediction suggests that multiple sequence alignments implicitly contain more structural information than had previously been realized , and prompts deeper investigations of the sequence correlations uncovered by either DCA or other approaches . To a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "quantum", "chemistry", "crystal", "structure", "enzymes", "split-decomposition", "method", "dna", "clamps", "condensed", "matter", "physics", "enzymology", "multiple", "alignment", "calculation", "protein", "structure", "dna", "dna", "structure", "crystallography", "grou...	2018	Statistical investigations of protein residue direct couplings
Nucleophosmin ( NPM ) is a multifunctional nuclear phosphoprotein and a histone chaperone implicated in chromatin organization and transcription control . Oncogenic Kaposi's sarcoma herpesvirus ( KSHV ) is the etiological agent of Kaposi's sarcoma , primary effusion lymphoma ( PEL ) and multicentric Castleman disease (...	Latency is the predominant mode of viral persistence in KS and PEL tumors , and has a fundamental impact on KSHV tumorigenesis . Establishment and maintenance of latency involves a number of viral and cellular factors . This study provides a novel functional link between LANA and v-cyclin by showing that phosphorylatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hematology/lymphomas", "and", "chronic", "lymphoblastic", "leukemia", "virology/persistence", "and", "latency", "virology/viral", "replication", "and", "gene", "regulation", "cell", "biology", "virology/viruses", "and", "cancer" ]	2010	Nucleophosmin Phosphorylation by v-Cyclin-CDK6 Controls KSHV Latency
Cells of the immune system are derived from hematopoietic stem cells ( HSCs ) residing in the bone marrow . HSCs become activated in response to stress , such as acute infections , which adapt the bone marrow output to the needs of the immune response . However , the impact of infection-adapted HSC activation and diffe...	Hematopoietic stem cells ( HSCs ) are responsible for the generation of all blood cells and thus play an important but often underappreciated role in the host response to infections . HSCs are normally dormant , but they can become activated in response to stress , such as infections . This stress response is meant to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "bone", "marrow", "cells", "organisms", "protozoans", "leishmania", "...	2017	Infection-adapted emergency hematopoiesis promotes visceral leishmaniasis
Host cell attachment by Toxoplasma gondii is dependent on polarized secretion of apical adhesins released from the micronemes . Subsequent translocation of these adhesive complexes by an actin-myosin motor powers motility and host cell invasion . Invasion and motility are also accompanied by shedding of surface adhesin...	Apicomplexan parasites invade host cells using a multi-step process that depends on regulated secretion of adhesins , attachment to the cell , and active penetration . Coordinating these activities requires control of proper timing and release of surface proteins that mediate adhesion . Parasites like Toxoplasma gondii...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/parasitology" ]	2010	Rhomboid 4 (ROM4) Affects the Processing of Surface Adhesins and Facilitates Host Cell Invasion by Toxoplasma gondii
Japanese encephalitis ( JE ) virus ( JEV ) causes severe epidemic encephalitis across Asia , for which the live attenuated vaccine SA14-14-2 is being used increasingly . JEV is a flavivirus , and is closely related to dengue virus ( DENV ) , which is co-endemic in many parts of Asia , with clinically relevant interacti...	The Flavivirus genus member Japanese encephalitis ( JE ) virus ( JEV ) , causes severe brain disease in tens of thousands of children across Asia every year . JE is vaccine preventable , and the immune response to JEV plays a major role in disease outcome . However , the response to JEV is hard to study as JE affects y...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "immunology", "vaccines", "preventive", "medicine", "peptide", "libraries", "cytotoxic", "t", "cells", "vaccination", "and", "immunization...	2017	Cellular Immune Responses to Live Attenuated Japanese Encephalitis (JE) Vaccine SA14-14-2 in Adults in a JE/Dengue Co-Endemic Area
p53 , which regulates cell-cycle arrest and apoptosis , is a crucial target for viruses to release cells from cell-cycle checkpoints or to protect cells from apoptosis for their own benefit . Viral evasion mechanisms of aquatic viruses remain mysterious . Here , we report the spring viremia of carp virus ( SVCV ) degra...	Upon viral infiltration , host cells employ p53 to defend against infection . Thus , viruses need to inhibit these antiviral surveillance mechanisms in the host to efficiently spread to new hosts . To date , the evasion mechanisms against fish p53 remain unclear . In this study , we reveal that SVCV modulates host p53 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "rna", "extraction", "microbiology", "protein", "expression", "molecular", "biology", "techniques", "synthesis", "phase", "extraction", "techniques", "research", "a...	2019	Spring viraemia of carp virus modulates p53 expression using two distinct mechanisms
Defining the precise cellular mechanisms of neutralization by potently inhibitory antibodies is important for understanding how the immune system successfully limits viral infections . We recently described a potently inhibitory monoclonal antibody ( MAb E16 ) against the envelope ( E ) protein of West Nile virus ( WNV...	Antibodies are essential components of the immune response against many pathogens , including viruses . A greater understanding of the mechanisms by which the most strongly inhibitory antibodies act may influence the design and production of novel vaccines or antibody-based therapies . Our group recently generated a hi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "immunology/immune", "response", "infectious", "diseases/viral", "infections", "microbiology", "immunology/immunity", "to", "infections" ]	2009	A Therapeutic Antibody against West Nile Virus Neutralizes Infection by Blocking Fusion within Endosomes
The Fanconi Anemia ( FA ) pathway is a multi-step DNA repair process at stalled replication forks in response to DNA interstrand cross-links ( ICLs ) . Pathological mutation of key FA genes leads to the inherited disorder FA , characterized by progressive bone marrow failure and cancer predisposition . The study of FA ...	Fanconi anemia ( FA ) is a devastating disease of children that leads to birth defects , bone marrow failure , and a variety of cancers early in their lives . Germ-line mutations in FA genes disrupt the DNA repair process , namely the FA pathway , resulting in genome instability and clinical features of FA patients . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "gene", "regulation", "293t", "cells", "enzymes", "biological", "cultures", "enzymology", "plasmid", "construction", "phosphatases", "isomerism", "dna", "construction", "dna", "molecular", "biology", "techniques", "isomerization", "research", "and", "an...	2019	Prolyl isomerization of FAAP20 catalyzed by PIN1 regulates the Fanconi anemia pathway
Because of the parallels found with human language production and acquisition , birdsong is an ideal animal model to study general mechanisms underlying complex , learned motor behavior . The rich and diverse vocalizations of songbirds emerge as a result of the interaction between a pattern generator in the brain and a...	Brain Machine Interfaces ( BMIs ) decode motor instructions from neuro-physiological recordings and feed them to bio-mimetic effectors . Many applications achieve high accuracy on a limited number of tasks by applying statistical methods to these data to extract features corresponding to certain motor instructions . We...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "signal", "processing", "biomimetics", "biomechanics", "biological", "systems", "engineering", "mathematics", "computational", "neuroscience", "coding", "mechanisms", "bioengineering", "biology", "nonlinear", "dynamics", "biophysics", "speech", "signal", "pro...	2012	Prosthetic Avian Vocal Organ Controlled by a Freely Behaving Bird Based on a Low Dimensional Model of the Biomechanical Periphery
Molecular chaperones are essential elements of the protein quality control machinery that governs translocation and folding of nascent polypeptides , refolding and degradation of misfolded proteins , and activation of a wide range of client proteins . The prokaryotic heat-shock protein DnaK is the E . coli representati...	Molecular chaperones are essential elements of the protein quality control machinery that governs translocation and folding of nascent polypeptides , refolding and degradation of misfolded proteins , and activation of a wide range of client proteins . This variety of functions results from the existence of multiple cha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "computational", "biology/sequence", "motif", "analysis", "biochemistry/protein", "folding", "biophysics/biomacromolecule-ligand", "interactions", "computational", "biology/macromolecular", "sequence", "analysis", "b...	2009	Accurate Prediction of DnaK-Peptide Binding via Homology Modelling and Experimental Data
Atopic dermatitis ( AD ) is a common chronic inflammatory skin disorder and a major manifestation of allergic disease . AD typically presents in early childhood often preceding the onset of an allergic airway disease , such as asthma or hay fever . We previously mapped a susceptibility locus for AD on Chromosome 3q21 ....	Atopic dermatitis ( AD , eczema ) is a common chronic inflammatory skin disorder and a major manifestation of allergic disease . Typically , AD first occurs in early childhood , often preceding the onset of allergic airways disease , such as asthma and hay fever . A family history of allergic disorders is the single st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "dermatology", "pediatrics", "and", "child", "health", "homo", "(human)", "genetics", "and", "genomics" ]	2007	Variants in a Novel Epidermal Collagen Gene (COL29A1) Are Associated with Atopic Dermatitis
Children of mothers infected with soil-transmitted helminths ( STH ) may have an increased susceptibility to STH infection . We did a case-control study nested in a birth cohort in Ecuador . Data from 1 , 004 children aged 7 months to 3 years were analyzed . Cases were defined as children with Ascaris lumbricoides and/...	Soil-transmitted helminths ( intestinal worms ) are among the most common childhood infections worldwide and are a significant cause of morbidity particularly among poor populations living in developing countries . The potent immune modulatory effects of these parasites have been suggested to be a determinant of the ep...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "immunology", "parasitic", "diseases", "helminth", "infection", "global", "health", "neglected", "tropical", "diseases", "immunomodulation", "infectious", "diseases", "soil-transmitted", "helminths", "disease", "ecology...	2012	Maternal Geohelminth Infections Are Associated with an Increased Susceptibility to Geohelminth Infection in Children: A Case-Control Study
Dengue remains the most prevalent arthropod-borne viral disease in humans . While probing for blood vessels , Aedes aegypti and Ae . albopictus mosquitoes transmit the four serotypes of dengue virus ( DENV1-4 ) by injecting virus-containing saliva into the skin . Even though arthropod saliva is known to facilitate tran...	Mosquitoes inject saliva into the skin while probing for blood vessels . Saliva facilitates blood feeding and can contain pathogens when the mosquito is infected . In tropical regions , Aedes mosquitoes transmit the four serotypes of dengue virus ( DENV1-4 ) and infect almost 400 million humans every year . DENV causes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "blood", "cells", "dermatology", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "integumentary", "system", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "immune", "cells", "ears", "immunology", "saliva", "an...	2016	Mosquito Saliva Increases Endothelial Permeability in the Skin, Immune Cell Migration, and Dengue Pathogenesis during Antibody-Dependent Enhancement
Bacterial cells maintain sophisticated levels of intracellular organization that allow for signal amplification , response to stimuli , cell division , and many other critical processes . The mechanisms underlying localization and their contribution to fitness have been difficult to uncover , due to the often challengi...	The development of multicellularity requires specialization and differentiation of individual cells . The process of differentiation requires the breaking of cellular symmetry , which can be achieved via asymmetric localization of proteins; cell division then gives rise to cells with different compositions and hence po...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemical", "simulations", "biology", "computational", "biology", "microbiology", "microbial", "growth", "and", "development" ]	2012	Interplay between the Localization and Kinetics of Phosphorylation in Flagellar Pole Development of the Bacterium Caulobacter crescentus
Pathway analysis is widely used to gain mechanistic insights from high-throughput omics data . However , most existing methods do not consider signal integration represented by pathway topology , resulting in enrichment of convergent pathways when downstream genes are modulated . Incorporation of signal flow and integr...	21st-century biotechnology has enabled measurements of genes and proteins at large scale by RNA sequencing and proteomics technologies . In particular , RNA-sequencing has become a first step of unbiased interrogation . These studies frequently produce a long list of differentially abundant genes , which become interpr...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "genetic", "networks", "applied", "mathematics", "signaling", "networks", "genetic", "algorithms", "simulation", "and", "modeling", "algorithms", "mathematics", "network", "analysis", "genome", "analysis", "pharmacology", "research...	2019	Executable pathway analysis using ensemble discrete-state modeling for large-scale data
RNA silencing or interference ( RNAi ) is a gene regulation mechanism in eukaryotes that controls cell differentiation and developmental processes via expression of microRNAs . RNAi also serves as an innate antiviral defence response in plants , nematodes , and insects . This antiviral response is triggered by virus-sp...	Cells have evolved mechanisms to protect themselves from virus infection . A well-known antiviral mechanism in mammals is the interferon ( IFN ) response of the innate immune system . In plants , insects , and worms , RNA silencing or RNA interference ( RNAi ) is a strong antiviral defence mechanism . It is still debat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "infectious", "diseases", "cell", "biology", "virology", "immunology", "eukaryotes", "homo", "(human)" ]	2007	The Ebola Virus VP35 Protein Is a Suppressor of RNA Silencing
The Dobzhansky-Muller model of incompatibilities explains reproductive isolation between species by incorrect epistatic interactions . Although the mechanisms of speciation are of great interest , no incompatibility has been characterized at the gene level in mammals . The Hybrid sterility 1 gene ( Hst1 ) participates ...	Disturbed gametogenesis in the progeny of two fertile parental forms is called hybrid sterility; it is an important part of reproductive barriers between species . The Dobzhansky-Muller model of incompatibilities explains reproductive isolation between species by incorrect interactions between genes . Hybrid sterility ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "animal", "genetics", "quantitative", "traits", "epistasis", "speciation", "biology", "hybridization", "evolutionary", "genetics", "trait", "locus", "heredity", "animal", "evolution", "genetics", "haploinsufficiency", "evolutionary", "biology", "e...	2012	Interallelic and Intergenic Incompatibilities of the Prdm9 (Hst1) Gene in Mouse Hybrid Sterility
Polyomaviruses are a family of small non-enveloped DNA viruses that encode oncogenes and have been associated , to greater or lesser extent , with human disease and cancer . Currently , twelve polyomaviruses are known to circulate within the human population . To further examine the diversity of human polyomaviruses , ...	Polyomaviruses are able to cause severe disease in immunocompromised individuals . The discovery of Merkel cell polyomavirus and its association with Merkel cell carcinoma has increased interest in these viruses , resulting in the identification of several novel human polyomaviruses in recent years . The existence of o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "emerging", "infectious", "diseases", "virology", "biology", "microbiology", "viral", "diseases" ]	2013	Novel Polyomaviruses of Nonhuman Primates: Genetic and Serological Predictors for the Existence of Multiple Unknown Polyomaviruses within the Human Population
Adaptation from standing genetic variation or recurrent de novo mutation in large populations should commonly generate soft rather than hard selective sweeps . In contrast to a hard selective sweep , in which a single adaptive haplotype rises to high population frequency , in a soft selective sweep multiple adaptive ha...	Evolutionary adaptation is a process in which beneficial mutations increase in frequency in response to selective pressures . If these mutations were previously rare or absent from the population , adaptation should generate a characteristic signature in the genetic diversity around the adaptive locus , known as a sele...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps
We present a new approach to modeling languages for computational biology , which we call the layer-oriented approach . The approach stems from the observation that many diverse biological phenomena are described using a small set of mathematical formalisms ( e . g . differential equations ) , while at the same time di...	The pursuit for understanding of neural function by computational modeling has produced a variety of software tools , with each tool targeting specific audiences and often requiring input in its own distinct language . Consequently , comprehending and communicating neuroscience models is a difficult and time-consuming ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "simulation", "languages", "computer", "science", "programming", "languages", "biophysic", "al", "simulations", "computational", "neuroscience", "single", "neuron", "function", "biology", "computational", "biology" ]	2012	The Layer-Oriented Approach to Declarative Languages for Biological Modeling
The halophilic archaeon Haloferax volcanii has a multireplicon genome , consisting of a main chromosome , three secondary chromosomes , and a plasmid . Genes for the initiator protein Cdc6/Orc1 , which are commonly located adjacent to archaeal origins of DNA replication , are found on all replicons except plasmid pHV2 ...	Haloferax volcanii is a member of the archaea , which are renowned for thriving in extreme environments . Archaea have circular chromosomes like bacteria but use enzymes similar to those found in eukaryotes to replicate their DNA . Few archaeal species have systems for genetics , and this has limited our understanding ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "archaea", "microbiology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	Genetic and Physical Mapping of DNA Replication Origins in Haloferax volcanii
Antisense ( as ) lncRNAs can regulate gene expression but the underlying mechanisms and the different cofactors involved remain unclear . Using Native Elongating Transcript sequencing , here we show that stabilization of antisense Exo2-sensitivite lncRNAs ( XUTs ) results in the attenuation , at the nascent transcripti...	Examples of regulatory antisense ( as ) lncRNAs acting on gene expression have been reported in multiple model organisms . However , despite their regulatory importance , aslncRNAs have been poorly studied , and the molecular bases for aslncRNAs-mediated regulation remain incomplete . One reason for the lack of global ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "small", "nucleolar", "rnas", "oxidative", "stress", "gene", "regulation", "dna-binding", "proteins", "dna", "transcription", "fungi", "model", "organisms", "experimental", "organism", "systems", "epigenetics", "chromatin", "schizosaccharomyces", "research", "and", "analy...	2018	Bases of antisense lncRNA-associated regulation of gene expression in fission yeast
Recent evidence suggests that the timing of DNA replication is coordinated across megabase-scale domains in metazoan genomes , yet the importance of this aspect of genome organization is unclear . Here we show that replication timing is remarkably conserved between human and mouse , uncovering large regions that may ha...	During S-phase of the cell cycle , chromosomal DNA is replicated in a complex process involving the coordinated activity of thousands of replication forks , each of which duplicates a long stretch of DNA . Recent experiments revealed that the genome is replicating as a mosaic of large-scale early and late chromosomal d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "cell", "biology/cell", "growth", "and", "division", "computational", "biology/genomics", "cell", "biology/nuclear", "structure", "and", "function" ]	2010	Comparative Analysis of DNA Replication Timing Reveals Conserved Large-Scale Chromosomal Architecture
RNA interference-related silencing mechanisms concern very diverse and distinct biological processes , from gene regulation ( via the microRNA pathway ) to defense against molecular parasites ( through the small interfering RNA and the Piwi-interacting RNA pathways ) . Small non-coding RNAs serve as specificity factors...	The fine-tuning of gene expression required for the normal development of multicellular organisms involves small RNAs that are called microRNAs ( miRNAs ) . MiRNAs can reduce the stability or the activity of the many cellular messenger RNAs that contain miRNA complementary sequences . In animal gonads , the harmful exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	MicroRNA-Dependent Transcriptional Silencing of Transposable Elements in Drosophila Follicle Cells
Control programs for trachoma use mass antibiotic distributions to treat ocular Chlamydia trachomatis in an effort to eliminate this disease worldwide . To determine whether children infected with ocular Chlamydia are more likely to present later for examination than those who are uninfected , we compare the order of p...	Trachoma is the most common cause of blindness from an infection in the world . The bacterium that causes trachoma is called Chlamydia trachomatis and it can be treated with the antibiotic azithromycin . Experts recommend trying to reach at least 80% of children for treatment in a community but it is unknown if this is...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "eye", "infections", "medicine", "bacterial", "diseases", "infectious", "diseases", "ophthalmology", "neglected", "tropical", "diseases", "trachoma" ]	2013	The Easiest Children to Reach Are Most Likely to Be Infected with Ocular Chlamydia trachomatis in Trachoma Endemic Areas of Niger
The fate of neural progenitor cells ( NPCs ) during corticogenesis is determined by a complex interplay of genetic or epigenetic components , but the underlying mechanism is incompletely understood . Here , we demonstrate that Suppressor of Mek null ( Smek ) interact with methyl-CpG–binding domain 3 ( Mbd3 ) and the co...	Neural progenitor cells are self-renewing , multipotent cells that generate major neural cell types , including neurons and glia . Their fate during development of the cerebral cortex is determined by a complex interplay of genetic and epigenetic components . It has been shown that Suppressor of Mek null ( Smek ) prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "molecular", "probe", "techniques", "gene", "regulation", "neuronal", "differentiation", "immunoblotting", "cell", "differentiation", "developmental", "biology", "immunoprecipitation", "stem", "cells", "molecular", "biology", "techniques", "research", "and", "analysis", "me...	2017	Smek promotes corticogenesis through regulating Mbd3’s stability and Mbd3/NuRD complex recruitment to genes associated with neurogenesis
Helminthiases are a group of disabling neglected tropical diseases that affect billions of people worldwide . Current control methods use preventative chemotherapy but reinfection is common and an inter-sectoral approach is required if elimination is to be achieved . Household and community scale water treatment can be...	Helminth infections are currently controlled by mass administration of anthelmintic drugs which are effective at treating the diseases but cannot prevent reinfection . As we work to eliminate these diseases , complimentary control methods such as improving access to water , sanitation , and hygiene will be crucial to r...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "ultraviolet", "radiation", "helminths", "database", "searching", "light", "disinfection", "animals", "electromagnetic", "radiation", "health", "care", "preventive", "medicine...	2019	Ultraviolet sensitivity of WASH (water, sanitation, and hygiene) -related helminths: A systematic review
Approximately 10% of genes in the human genome are distributed such that their transcription start sites are located less than 1 kb apart on opposite strands . These divergent gene pairs have a single intergenic segment of DNA , which in some cases appears to share regulatory elements , but it is unclear whether these ...	Surveys of the locations of genes in the human genome have revealed that a surprising number of genes , greater than 10% , have transcription start sites within 1 kb of one another on opposite strands . These divergent gene pairs , sometimes referred to as bidirectional genes , are common in organisms such as bacteria ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "in", "vitro", "homo", "(human)", "genetics", "and", "genomics", "mammals" ]	2007	The ets-Related Transcription Factor GABP Directs Bidirectional Transcription
Cells trigger massive changes in gene expression upon environmental fluctuations . The Hog1 stress-activated protein kinase ( SAPK ) is an important regulator of the transcriptional activation program that maximizes cell fitness when yeast cells are exposed to osmostress . Besides being associated with transcription fa...	Cells coordinate various intracellular activities in response to sudden changes in the environment to maximize survival and cell fitness . Clear examples of this are the regulation of gene expression and cell cycle progression . Stress-Activated Protein Kinase ( SAPK ) signaling pathway acts as the central core for the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "cellular", "stress", "responses", "gene", "regulation", "cell", "processes", "dna", "transcription", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "transcriptional", "control", "artificial", "gene", "amplification", "a...	2017	Regulation of transcription elongation in response to osmostress
The recent emergence of zoonotic diseases such as Highly Pathogenic Avian Influenza ( HPAI ) and Severe Acute Respiratory Syndrome ( SARS ) have contributed to dominant Global Health narratives around health securitisation and pandemic preparedness , calling for greater co-operation between the health , veterinary and ...	The One Health movement requires more robust evidence around its practical implementation if it is to truly become a way forwards for addressing health issues at the human , animal and ecosystem interface . The research in this paper discusses some of the recent successes and challenges with both Emerging and Neglected...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "public", "and", "occupational", "health", "political", "science", "infectious", "diseases", "veterinary", "diseases", "medicine", "and", "health", "sciences", "global", "health", "biology", "and", "life", "sciences", "social", "sciences", "veterinary", "science" ]	2014	One Health: Past Successes and Future Challenges in Three African Contexts
Cryptococcus neoformans is a common life-threatening human fungal pathogen . The size of cryptococcal cells is typically 5 to 10 µm . Cell enlargement was observed in vivo , producing cells up to 100 µm . These morphological changes in cell size affected pathogenicity via reducing phagocytosis by host mononuclear cells...	Cryptococcus neoformans is a common life-threatening opportunistic human fungal pathogen . C . neoformans grows as a budding yeast in vitro with typical cell sizes ranging from 5 to 10 µm in diameter . Early reports suggested the presence of enlarged cells in human infections yet the identity of these cells and their r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "cell", "biology/cell", "signaling", "infectious", "diseases/fungal", "infections", "cell", "biology/morphogenesis", "and", "cell", "biology", "neurological", "disorders/infectious", "diseases"...	2010	Cryptococcal Cell Morphology Affects Host Cell Interactions and Pathogenicity
Lack of surveillance systems and accurate data impede evidence-based decisions on treatment and prevention of enteric fever , caused by Salmonella Typhi/Paratyphi . The WHO coordinates a global Invasive Bacterial–Vaccine Preventable Diseases ( IB-VPD ) surveillance network but does not monitor enteric fever . We evalua...	Typhoid/paratyphoid fever imposes a major global burden , specifically in low-and-middle-income countries ( LMICs ) . However , it is challenging to implement evidence-based decisions for treatment and prevention because of lack of data from comprehensive surveillance systems , which are often expensive and difficult t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "salmonella", "typhi", "pulmonology", "vaccines", "pneumonia", "bacterial", "diseases", "signs", "and", "sym...	2017	Integration of enteric fever surveillance into the WHO-coordinated Invasive Bacterial-Vaccine Preventable Diseases (IB-VPD) platform: A low cost approach to track an increasingly important disease
Neglected tropical diseases , including diseases caused by trypanosomatid parasites such as Trypanosoma brucei , cost tens of millions of disability-adjusted life-years annually . As the current treatments for African trypanosomiasis and other similar infections are limited , new therapeutics are urgently needed . RNA ...	African sleeping sickness is a devastating disease that plagues sub-Saharan Africa . Neglected tropical diseases like African sleeping sickness cause significant death and suffering in the world's poorest countries . Current treatments for African sleeping sickness either have high costs , terrible side effects , or li...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "biophysics/theory", "and", "simulation", "pharmacology/drug", "development", "infectious", "diseases/protozoal", "infections", "computational", "biology/molecular", "dynamics" ]	2010	Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1
The aim of this work is to elucidate how physical principles of protein design are reflected in natural sequences that evolved in response to the thermal conditions of the environment . Using an exactly solvable lattice model , we design sequences with selected thermal properties . Compositional analysis of designed mo...	What mechanisms does Nature use in her quest for thermophilic proteins ? It is known that stability of a protein is mainly determined by the energy gap , or the difference in energy , between native state and a set of incorrectly folded ( misfolded ) conformations . Here we show that Nature makes thermophilic proteins ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "in", "vitro", "molecular", "biology", "eubacteria", "computational", "biology" ]	2007	Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins
Wolbachia are the most widespread maternally-transmitted bacteria in the animal kingdom . Their global spread in arthropods and varied impacts on animal physiology , evolution , and vector control are in part due to parasitic drive systems that enhance the fitness of infected females , the transmitting sex of Wolbachia...	Male killing is an adaptive trait for bacteria that are maternally transmitted through host populations . Such bacteria are common in arthropods and resultantly have significant impacts on host population size , mating strategy , and evolution . Moreover , male-killing bacteria are under recent scrutiny as a symbiotic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Statistical", "analyses" ]	[ "invertebrates", "bacteriophages", "animals", "wolbachia", "animal", "models", "viruses", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "population", "biology", "embryos", "bacteria", "drosophila", "re...	2019	The phage gene wmk is a candidate for male killing by a bacterial endosymbiont
A number of nonclassical MHC Ib molecules recognizing distinct microbial antigens have been implicated in the immune response to Mycobacterium tuberculosis ( Mtb ) . HLA-E has been identified to present numerous Mtb peptides to CD8+ T cells , with multiple HLA-E-restricted cytotoxic T lymphocyte ( CTL ) and regulatory ...	The disease tuberculosis ( TB ) is caused by the microbe Mycobacterium tuberculosis ( Mtb ) , and remains a major public health concern . More research is needed to understand the diverse immune responses against Mtb to develop better vaccines . Mouse Qa-1 and its human counterpart HLA-E are nonclassical MHC I molecule...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "animal", "models", "model", "organisms", "clinical", "medicine", "experimental", "organism", "systems", "cytotoxic", "t", "cells", "bacteria", "research", "and", "analysis", ...	2017	MHC Ib molecule Qa-1 presents Mycobacterium tuberculosis peptide antigens to CD8+ T cells and contributes to protection against infection
The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data . The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects ...	WikiPathways is a crowd-sourced online platform for biological pathways . It is based on the same underlying platform as Wikipedia . Pathways are saved as graphical images embedded in a set of meta data elements ( i . e . references , list of pathways elements , and context annotations ) . Pathways are used as proxies ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "linguistics", "medicine", "and", "health", "sciences", "protein", "metabolism", "metabolic", "processes", "social", "sciences", "glycolysis", "diabetes", "mellitus", "endocrine", "disorders", "computer", "and", "information", "sciences", "endocrinology", "metabolic", "pa...	2016	Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources
African swine fever ( ASF ) is caused by a large and highly pathogenic DNA virus , African swine fever virus ( ASFV ) , which provokes severe economic losses and expansion threats . Presently , no specific protection or vaccine against ASF is available , despite the high hazard that the continued occurrence of the dise...	ASFV is a highly pathogenic zoonotic virus , which can cause severe economic losses and bioterrorism threats . No vaccine against ASFV is available so far . A strong hazard of ASFV dissemination through EU countries from Caucasian areas has recently emerged , thus making urgent to acquire knowledge and tools for protec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cellular", "structures", "signal", "transduction", "cellular", "stress", "responses", "molecular", "cell", "biology", "cell", "biology", "viral", "immune", "evasion", "veterinary", "microbiology", "virology", "biology", "microbiology", "host-pathogen", "interaction", "mo...	2012	African Swine Fever Virus Uses Macropinocytosis to Enter Host Cells
Spain has one of the world’s largest pools of organ donors and is a global leader in terms of the number of transplants it performs . The current outbreak of leishmaniasis in Fuenlabrada ( in the southwest of the region of Madrid , Spain ) has involved 600 clinical cases since late 2009 ( prevalence 0 . 2% ) . It may t...	We have used cytokine release assays to determine the prevalence of Leishmania infantum infection in solid organ transplant ( SOT ) recipients living in an area where the organism is endemic following an outbreak . Some 21 . 05% of SOT recipients with no previous history of leishmaniasis had been in contact with the pa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Cytokine Release Assays as Tests for Exposure to Leishmania, and for Confirming Cure from Leishmaniasis, in Solid Organ Transplant Recipients
Outcome of host-pathogen encounter is determined by the complex interplay between protective bacterial and host defense strategies . This complexity further amplifies with the existence of cell-to-cell phenotypic heterogeneity in pathogens which remains largely unexplored . In this study , we illustrated that heterogen...	Streptococcus pneumoniae , the Gram-positive diplococci , is the primary etiological agent of bacterial meningitis . In order to cause central nervous system ( CNS ) infections , SPN has to breach the blood-brain barrier , however , the pneumococcal determinants involved in this process remain unidentified . Here , we ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "flow", "cytometry", "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "body", "fluids", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "cardiovascular", "anatomy", "pathogens", "cell", "processes", "...	2018	Heterogeneity in pneumolysin expression governs the fate of Streptococcus pneumoniae during blood-brain barrier trafficking
Natural populations are known to differ not only in DNA but also in their chromatin-associated epigenetic marks . When such inter-individual epigenomic differences ( or “epi-polymorphisms” ) are observed , their stability is usually not known: they may or may not be reprogrammed over time or upon environmental changes ...	Chemical modifications of chromatin , such as DNA methylation , incorporation of histone variants , or post-translational modifications of histone proteins , constitute the “epigenome” and confer specific properties to genome functions . Epigenomes differ from one individual to another , opening the exciting perspectiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "expression", "analysis", "genetic", "networks", "functional", "genomics", "genome", "scans", "statistics", "population", "genetics", "microbiology", "histone", "modification", "genome", "analysis", "tools", "model", "organisms", "mathematics", "trait", "locus",...	2012	Genetic Modifiers of Chromatin Acetylation Antagonize the Reprogramming of Epi-Polymorphisms
Type I interferons ( IFN ) are important for antiviral responses . Melanoma differentiation-associated gene 5 ( MDA-5 ) and retinoic acid-induced gene I ( RIG-I ) proteins detect cytosolic double-stranded RNA ( dsRNA ) or 5′-triphosphate ( 5′-ppp ) RNA and mediate IFN production . Cytosolic 5′-ppp RNA and dsRNA are gen...	Type I interferons ( IFN ) are critical for mounting effective antiviral responses by the host cells . For RNA viruses , it is believed that IFN is triggered exclusively by viral double-stranded RNA ( dsRNA ) or RNA containing a 5′-triphosphate ( 5′-ppp ) that is produced during viral genome replication or transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "transmission", "and", "infection", "viral", "classification", "enzymes", "viral", "enzymes", "immunology", "host-pathogen", "interaction", "microbiology", "animal", "models", "model", "organisms", "rna", "viruses", "signaling", "pathways", "viral", "nucleic", ...	2013	RIG-I and MDA-5 Detection of Viral RNA-dependent RNA Polymerase Activity Restricts Positive-Strand RNA Virus Replication
Lujo virus ( LUJV ) is a novel member of the Arenaviridae family that was first identified in 2008 after an outbreak of severe hemorrhagic fever ( HF ) . In what was a small but rapidly progressing outbreak , this previously unknown virus was transmitted from the critically ill index patient to 4 attending healthcare w...	The pathogenic arenaviruses are a diverse group of human pathogens capable of causing a wide range of human illness ranging from encephalitis to severe hemorrhagic fever throughout the New and Old World . In 2008 , a previously unknown virus ( now named Lujo virus ) caused a high case fatality outbreak ( 80% ) in south...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "spleen", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "animal", "models", "viruses", "model", "organisms", ...	2012	Severe Hemorrhagic Fever in Strain 13/N Guinea Pigs Infected with Lujo Virus
Parasitic flatworms of the genus Schistosoma cause schistosomiasis , a neglected tropical disease that affects hundreds of millions . Treatment of schistosomiasis depends almost entirely on the drug praziquantel ( PZQ ) . Though essential to treating and controlling schistosomiasis , a major limitation of PZQ is that i...	Schistosomes are parasitic flatworms that cause schistosomiasis , a tropical disease affecting hundreds of millions worldwide . Praziquantel ( PZQ ) is the current drug of choice against schistosomiasis , and , indeed , is the only approved antischistosomal treatment available in most parts of the world . Though effect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "helminth", "infections", "schistosomiasis", "medicine", "and", "health", "sciences", "drug", "research", "and", "development", "drug", "discovery", "for", "neglected", "diseases", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "pharmacology"...	2014	Inhibition or Knockdown of ABC Transporters Enhances Susceptibility of Adult and Juvenile Schistosomes to Praziquantel
A century after the discovery of Trypanosoma cruzi in a child living in Lassance , Minas Gerais , Brazil in 1909 , many uncertainties remain with respect to factors determining the pathogenesis of Chagas disease ( CD ) . Herein , we simultaneously investigate the contribution of both host and parasite factors during ac...	Chagas disease , a life-long parasitic disease caused by the flagellate protozoan Trypanosoma cruzi , was discovered a century ago by the Brazilian physician Carlos Chagas , and remains one of the most neglected tropical diseases , affecting 13 million people in Latin America . Disease is characterized by distinct clin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/protozoal", "infections", "molecular", "biology", "immunology/immunity", "to", "infections", "patho...	2010	Coinfection with Different Trypanosoma cruzi Strains Interferes with the Host Immune Response to Infection
The natural history and potential impact of mosquito-specific flaviviruses on the transmission efficiency of West Nile virus ( WNV ) is unknown . The objective of this study was to determine whether or not prior infection with Culex flavivirus ( CxFV ) Izabal altered the vector competence of Cx . quinquefasciatus Say f...	Unlike most known flaviviruses ( Family , Flaviviridae: Genus , Flavivirus ) , insect-only flaviviruses are a unique group of flaviviruses that only infect invertebrates . The study of insect-only flaviviruses has increased in recent years due to the discovery and characterization of numerous novel flaviviruses from a ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology" ]	2010	Transmission of West Nile Virus by Culex quinquefasciatus Say Infected with Culex Flavivirus Izabal
Replicative DNA polymerases are frequently stalled by DNA lesions . The resulting replication blockage is released by homologous recombination ( HR ) and translesion DNA synthesis ( TLS ) . TLS employs specialized TLS polymerases to bypass DNA lesions . We provide striking in vivo evidence of the cooperation between DN...	DNA replication is a fragile biochemical reaction , as the replicative DNA polymerases are readily stalled by DNA lesions . The resulting replication blockage is released by translesion DNA synthesis ( TLS ) , which employs specialized TLS polymerases to bypass DNA lesions . There are at least seven TLS polymerases kno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "cell", "biology/cellular", "death", "and", "stress", "responses", "molecular", "biology/recombination", "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", ...	2010	Simultaneous Disruption of Two DNA Polymerases, Polη and Polζ, in Avian DT40 Cells Unmasks the Role of Polη in Cellular Response to Various DNA Lesions
Lipids are main fuels for cellular energy and mitochondria their major oxidation site . Yet unknown is to what extent the fuel role of lipids is influenced by their uncoupling effects , and how this affects mitochondrial energetics , redox balance and the emission of reactive oxygen species ( ROS ) . Employing a combin...	Lipids are main sources of energy for liver and cardiac and skeletal muscle . Mitochondria are the main site of lipid oxidation which , in the heart , supplies most of the energy required for its blood pumping function . Paradoxically , however , lipids over supply impair mitochondrial function leading to metabolic syn...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Model", "description" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "simulation", "and", "modeling", "diabetes", "mellitus", "endocrine", "disorders", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods...	2017	Mitochondrial respiration and ROS emission during β-oxidation in the heart: An experimental-computational study
Transcription elongation by RNA polymerase II was often considered an invariant non-regulated process . However , genome-wide studies have shown that transcriptional pausing during elongation is a frequent phenomenon in tightly-regulated metazoan genes . Using a combination of ChIP-on-chip and genomic run-on approaches...	Transcription of DNA–encoded information into RNA is the first step in gene regulation . RNA polymerases initiate transcription at the promoter region and elongate the transcripts traveling throughout the gene until reaching the termination sequences . Classical models of transcriptional regulation were focused on the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "computational", "biology/transcriptional", "regulation", "molecular", "biology/transcription", "elongation", "biochemistry/transcription", "and", "translation" ]	2009	Regulon-Specific Control of Transcription Elongation across the Yeast Genome
Isothermal microcalorimetry is an established tool to measure heat flow of physical , chemical or biological processes . The metabolism of viable cells produces heat , and if sufficient cells are present , their heat production can be assessed by this method . In this study , we investigated the heat flow of two medica...	Microcalorimetry is a technology developed to record minute changes in temperature as a result of physical , chemical or biological reactions over time . The method has been applied to bacterial and eukaryotic cells and it was found that the metabolic activity of living cells in a culture medium produces enough heat fl...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "drug", "research", "and", "development", "drugs", "and", "devices", "protozoology", "biology", "microbiology", "drug", "discovery", "pharmacology", "parasitology" ]	2012	Isothermal Microcalorimetry, a New Tool to Monitor Drug Action against Trypanosoma brucei and Plasmodium falciparum
Efficient sampling of visual information requires a coordination of eye movements and ongoing brain oscillations . Using intracranial and magnetoencephalography ( MEG ) recordings , we show that saccades are locked to the phase of visual alpha oscillations and that this coordination is related to successful mnemonic en...	In everyday life , we constantly move our eyes to sample visual information . In order to make the sampling efficient , these eye movements need to be coordinated with the intrinsic brain dynamics that constrain visual computations . The present study provides novel evidence for how this coordination is achieved at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "social", "sciences", "neuroscience", "learning", "and", "memory", "cognitive", "psychology", "mathematics", "statistics", "(mathematics)", "cognition", "brain", "mapping", "test", "statistics", "memory",...	2017	Saccades are phase-locked to alpha oscillations in the occipital and medial temporal lobe during successful memory encoding
Postweaning multisystemic wasting disease ( PMWS ) in piglets caused by porcine circovirus type 2 ( PCV2 ) is one of the major threats to most pig farms worldwide . Among all the PCV types , PCV2 is the dominant genotype causing PMWS and associated diseases . Considerable efforts were made to study the virus-like-parti...	Porcine circovirus type 2 ( PCV2 ) is considered as one of the most wide-spread pathogens threatening swine production by causing postweaning multisystemic wasting disease ( PMWS ) in piglets worldwide . Several VLP-based PCV2 vaccines are commercially available which significantly reduce the viral burden and virally i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "crystal", "structure", "immunology", "condensed", "matter", "physics", "microbiology", "electron", "cryo-microscopy", "vaccines", "preventive", "medicine", "microscopy", "protein", "structure", "crys...	2019	Structural roles of PCV2 capsid protein N-terminus in PCV2 particle assembly and identification of PCV2 type-specific neutralizing epitope
The pontine neurons ( PN ) represent a major source of mossy fiber projections to the cerebellum . During mouse hindbrain development , PN migrate tangentially and sequentially along both the anteroposterior ( AP ) and dorsoventral ( DV ) axes . Unlike DV migration , which is controlled by the Netrin-1/Dcc attractive p...	In the developing central nervous system , neurons migrate sometimes over long distances from their birthplace to their final location , where they condense in specific nuclei . The precise positioning of migrating neurons is critical to the building of ordered connectivity with their target partners . Little is known ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "developmental", "biology" ]	2008	Hox Paralog Group 2 Genes Control the Migration of Mouse Pontine Neurons through Slit-Robo Signaling
Wolbachia are maternally inherited bacteria that commonly spread through host populations by causing cytoplasmic incompatibility , often expressed as reduced egg hatch when uninfected females mate with infected males . Infected females are frequently less fecund as a consequence of Wolbachia infection . However , theor...	Wolbachia are endosymbiotic bacteria that live inside the cells of their invertebrate hosts . They are transmitted directly from mother to offspring , and spread through populations by manipulating the reproduction of their hosts . The most common reproductive manipulation responsible for the spread of these bacteria ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "ecology", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	From Parasite to Mutualist: Rapid Evolution of Wolbachia in Natural Populations of Drosophila
Epidemics of infectious diseases often occur in predictable limit cycles . Theory suggests these cycles can be disrupted by high amplitude seasonal fluctuations in transmission rates , resulting in deterministic chaos . However , persistent deterministic chaos has never been observed , in part because sufficiently larg...	Measles epidemics continue to pose a significant public health risk wherever vaccination coverage is low . In such populations transmission rates tend to fluctuate seasonally , mirroring patterns of human aggregation , due to the timing of school terms , and/or the migration of workers and their families . Here we show...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.