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Plant pathogens secrete an arsenal of small secreted proteins ( SSPs ) acting as effectors that modulate host immunity to facilitate infection . SSP-encoding genes are often located in particular genomic environments and show waves of concerted expression at diverse stages of plant infection . To date , little is known...	Effectors are key players in pathogenicity of microbes toward plants . Effector genes usually show concerted expression during plant infection but how this concerted expression is generated remains a largely unexplored research topic . Epigenetic mechanisms are involved in genome maintenance and integrity but are incre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "functional", "genomics", "host-pathogen", "interaction", "microbiology", "genome", "analysis", "tools", "fungi", "plant", "science", "plant", "pathology", "epigenetics", "chromatin", "mycology", "microbial", "pathogens", "biology", "pa...	2014	Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans
Mutation rates can evolve through genetic drift , indirect selection due to genetic hitchhiking , or direct selection on the physicochemical cost of high fidelity . However , for many systems , it has been difficult to disentangle the relative impact of these forces empirically . In RNA viruses , an observed correlatio...	Why organisms have different mutation rates is a longstanding question in evolutionary biology . The polymerases of RNA viruses generally lack proofreading activity and exhibit extremely high mutation rates . Because most mutations are deleterious and mutation rates are typically tuned by natural selection , we asked w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "hela", "cells", "pathogens", "biological", "cultures", "microbiology", "viruses", "animal", "models", "mutation", "model", "organisms", "rna", "viruses", "...	2018	A speed–fidelity trade-off determines the mutation rate and virulence of an RNA virus
The rate of progress in human neurosciences is limited by the inability to easily apply a wide range of analysis methods to the plethora of different datasets acquired in labs around the world . In this work , we introduce a framework for creating , testing , versioning and archiving portable applications for analyzing...	Magnetic Resonance Imaging ( MRI ) is a non-invasive way to measure human brain structure and activity that has been used for over 25 years . There are thousands MRI studies performed every year generating a substantial amount of data . At the same time , many new data analysis methods are being developed every year . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "engineering", "and", "technology", "neuroscience", "magnetic", "resonance", "imaging", "brain", "morphometry", "brain", "mapping", "information", "techno...	2017	BIDS apps: Improving ease of use, accessibility, and reproducibility of neuroimaging data analysis methods
Muffs and beard ( Mb ) is a phenotype in chickens where groups of elongated feathers gather from both sides of the face ( muffs ) and below the beak ( beard ) . It is an autosomal , incomplete dominant phenotype encoded by the Muffs and beard ( Mb ) locus . Here we use genome-wide association ( GWA ) analysis , linkage...	Genetic variation is a key part for the study of evolution , development and differentiation . In domestic animals , many breeds display striking phenotypes that differentiate them from their wild ancestors . Several of these have been related to structural variations , including Fibromelanosis and Rose-comb in chicken...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "livestock", "vertebrates", "animals", "feathers", "animal", "anatomy", "molecular", "biology", "techniques", "zoology", "research", "and", "analysis", "methods", "genomics", "birds", "artificial", "gene", "amplification", "and", "extension", "proteins", "gene", "expres...	2016	A Complex Structural Variation on Chromosome 27 Leads to the Ectopic Expression of HOXB8 and the Muffs and Beard Phenotype in Chickens
Mathematical modeling provides the predictive ability to understand the metabolic reprogramming and complex pathways that mediate cancer cells’ proliferation . We present a mathematical model using a multiscale , multicellular approach to simulate avascular tumor growth , applied to pancreatic cancer . The model spans ...	Cancer cells expertly alter their metabolism in order to sustain growth , a hallmark of cancer . Quantitative details about this metabolic reprogramming are difficult to obtain without the use of predictive mathematical models . Here , we present a robust computational model of avascular tumor growth . The novel aspect...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "chemical", "compounds", "cell", "cycle", "and", "cell", "division", "cell", "processes", "metabolic", "networks", "carbohydrates", "cell", "metabolism", "organic", "compounds", "glucose", "metabolism", "glucose", "sim...	2019	Metabolic reprogramming dynamics in tumor spheroids: Insights from a multicellular, multiscale model
Previous findings indicate that susceptibility to Leishmania ( Viannia ) panamensis infection of monocyte-derived macrophages from patients and asymptomatically infected individuals were associated with the adaptive immune response and clinical outcome . To understand the basis for this difference we examined different...	Leishmania parasites cause a spectrum of diseases ( cutaneous , visceral and the deforming forms—chronic cutaneous and mucocutaneous ) known as leishmaniasis . The macrophage , a key cell in the immune system , is the cellular target of Leishmania parasites in the mammalian host . Previous studies showed the responses ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion", "Conclusions" ]	[ "immunity", "parasitology", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "immune", "response" ]	2012	Human Macrophage Response to L. (Viannia) panamensis: Microarray Evidence for an Early Inflammatory Response
We constantly look for patterns in the environment that allow us to learn its key regularities . These regularities are fundamental in enabling us to make predictions about what is likely to happen next . The physiological study of regularity extraction has focused primarily on repetitive sequence-based rules within th...	Survival crucially depends on our ability to extract information from the environment . This ability relies on learning about regularities that enable us to make predictions about what is likely to happen next . Sensitivity to violations of these regularities is necessary for timely reactions and adaptive responses to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "auditory", "system", "computational", "neuroscience", "biology", "sensory", "systems", "neuroscience" ]	2013	Outlier Responses Reflect Sensitivity to Statistical Structure in the Human Brain
Infection with viruses carrying cross-reactive antigens is associated with break of immunological tolerance and induction of autoimmune disease . Dendritic cells play an important role in this process . However , it remains unclear why autoimmune-tolerance is broken during virus infection , but usually not during expos...	Autoimmune diabetes in humans is linked to infection with viruses , which carry cross-reactive antigens . Virus derived cross-reactive antigens break immunological tolerance to pancreatic islets , which initiates disease . Several other non-viral sources of cross-reactive antigens are known , however they usually fail ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Usp18 Driven Enforced Viral Replication in Dendritic Cells Contributes to Break of Immunological Tolerance in Autoimmune Diabetes
Retroviruses normally infect the somatic cells of their host and are transmitted horizontally , i . e . , in an exogenous way . Occasionally , however , some retroviruses can also infect and integrate into the genome of germ cells , which may allow for their vertical inheritance and fixation in a given species; a proce...	Retroviruses are RNA viruses that are reverse transcribed into DNA and inserted into the host's genome . Though this process happens most frequently in somatic cells ( e . g . , immune cells for HIV ) , retroviruses can occasionally be integrated in the genome of the host's germ cells . Such viral insertions may thus b...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "genetics", "and", "genomics", "virology/virus", "evolution", "and", "symbiosis", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2009	Parallel Germline Infiltration of a Lentivirus in Two Malagasy Lemurs
The obligate intracellular , gram-negative bacterium Chlamydophila pneumoniae ( Cpn ) has impact as a human pathogen . Little is known about changes in the Cpn transcriptome during its biphasic developmental cycle ( the acute infection ) and persistence . The latter stage has been linked to chronic diseases . To analyz...	Chlamydophila ( Chlamydia ) pneumoniae ( Cpn ) accounts for approximately one-tenth of the cases of community-acquired pneumonia worldwide , and persistent Cpn infections are thought to be associated with a variety of chronic diseases . Little is known about Cpn transcriptome changes during its biphasic developmental c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biotechnology", "infectious", "diseases", "cell", "biology", "microbiology", "computational", "biology", "eukaryotes", "genetics", "and", "genomics", "eubacteria" ]	2007	Gene Expression Profiles of Chlamydophila pneumoniae during the Developmental Cycle and Iron Depletion–Mediated Persistence
Models of neocortical networks are increasingly including the diversity of excitatory and inhibitory neuronal classes . Significant variability in cellular properties are also seen within a nominal neuronal class and this heterogeneity can be expected to influence the population response and information processing in n...	Neurons are the fundamental components of the nervous system and a quantitative description of their properties is a prerequisite to understanding the complex structures they comprise , from microcircuits to networks . Mathematical modelling provides an essential tool to this end and there has been intense effort direc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations
The association of the major histocompatibility complex ( MHC ) with SLE is well established yet the causal variants arising from this region remain to be identified , largely due to inadequate study design and the strong linkage disequilibrium demonstrated by genes across this locus . The majority of studies thus far ...	Systemic lupus erythematosus ( SLE/lupus ) is a complex autoimmune disease in which the body's immune system attacks its own tissues , causing inflammation in a variety of different organs such as the skin , joints , and kidneys . The cause of lupus is not known , but genes play a significant role in the predisposition...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics", "rheumatology" ]	2007	Identification of Two Independent Risk Factors for Lupus within the MHC in United Kingdom Families
Contributions of null and hypomorphic alleles of Apc in mice produce both developmental and pathophysiological phenotypes . To ascribe the resulting genotype-to-phenotype relationship unambiguously to the Wnt/β-catenin pathway , we challenged the allele combinations by genetically restricting intracellular β-catenin ex...	Germline or somatic mutations in genes are the underlying cause of many human diseases , most notably cancer . Interestingly though , even in situations where every cell of every tissue of an organism carries the same mutation ( as is the case for germline mutations ) , some tissues are more susceptible to the developm...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "developmental", "biology", "cell", "biology/cell", "signaling", "developmental", "biology/pattern", "formation", "gastroenterology", "and", "hepatology", "genetics", "and", "genomics/genetics", "of", "disease", "oncology/gastrointestinal", ...	2010	Genetic Dissection of Differential Signaling Threshold Requirements for the Wnt/β-Catenin Pathway In Vivo
Infection of susceptible hosts by the encapsulated Gram-negative bacterium Burkholderia pseudomallei ( Bp ) causes melioidosis , with septic patients attaining mortality rates ≥40% . Due to its high infectivity through inhalation and limited effective therapies , Bp is considered a potential bioweapon . Thus , there is...	Burkholderia pseudomallei is the causative agent of melioidosis , which is a major cause of septic death in endemic areas of Southeast Asia and northern Australia . This range now appears to be expanding , and with the increased incidence of diabetes , which is a major predisposing factor for B . pseudomallei infection...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "melioidosis", "immunology", "burkholderia", "infection", "microbiology", "animal", "models", "bacterial", "diseases", "model", "organ...	2014	Delineating the Importance of Serum Opsonins and the Bacterial Capsule in Affecting the Uptake and Killing of Burkholderia pseudomallei by Murine Neutrophils and Macrophages
Functional protein-protein interactions are crucial in most cellular processes . They enable multi-protein complexes to assemble and to remain stable , and they allow signal transduction in various pathways . Functional interactions between proteins result in coevolution between the interacting partners , and thus in c...	Functional protein-protein interactions are at the heart of most intra-cellular processes . Mapping these interactions is thus crucial to a systems-level understanding of cells , and has broad applications to areas such as drug targeting . Systematic experimental identification of protein interaction partners is still ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "interactions", "statistics", "applied", "mathematics", "split-decomposition", "method", "simulation", "and", "modeling", "algorithms", "multiple", "alignment", "calculation", "mathematics", "protein", "structure", "prediction", "protein", "structure", "research", ...	2018	Inferring interaction partners from protein sequences using mutual information
It is well known that the dinucleotide CpG is under-represented in the genomic DNA of many vertebrates . This is commonly thought to be due to the methylation of cytosine residues in this dinucleotide and the corresponding high rate of deamination of 5-methycytosine , which lowers the frequency of this dinucleotide in ...	Viruses are obligate intracellular parasites that use different strategies to sequester host cell machinery and avoid the host immune system . In this paper we explore the genomes of viruses that encode their genetic information in single-stranded RNA , a different material than the one used by their hosts ( double-str...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/virus", "evolution", "and", "symbiosis", "virology/host", "antiviral", "responses" ]	2008	Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses
Government-administered adulticiding is frequently conducted in response to dengue transmission worldwide . Anecdotal evidence suggests that spraying may create a “false sense of security” for residents . Our objective was to determine if there was an association between residents’ reporting outdoor spatial insecticide...	Outdoor spatial spraying is commonly practiced by local governments as a prevention strategy for dengue and other Aedes-borne viruses . However , it has been publically criticized for its potential to reduce community-level actions such as clearance of mosquito habitat due to a resulting “false sense of security” . Thi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "larvicides", "invertebrates", "medicine", "and", "health", "sciences", "tropical", "diseases", "animals", "developmental", "biology", "pupae", "pest", "control", "neglected", "tropical", "diseases", "infectious", "disease", "control", "insect", "vectors", "zoology", "i...	2017	Outdoor spatial spraying against dengue: A false sense of security among inhabitants of Hermosillo, Mexico
Extraparenchymal neurocysticercosis ( ExPNCC ) , an infection caused by Taenia solium cysticerci that mainly occurs in the ventricular compartment ( Ve ) or the basal subarachnoid space ( SAb ) , is more severe but less frequent and much less studied than parenchymal neurocysticercosis ( ParNCC ) . Demographic , clinic...	Neurocysticercosis ( NCC ) is caused by the establishment of Taenia solium larvae in the human central nervous system . While NCC diagnosis , treatment , and prevention have clearly improved in the last 40 years , the disease still causes significant morbidity and mortality in endemic regions of Latin America , Asia , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "neurocysticercosis", "demography", "nervous", "system", "immunology", "tropical", "diseases", "geographical", "locations", "parasitic", "di...	2017	Extraparenchymal neurocysticercosis: Demographic, clinicoradiological, and inflammatory features
Excessive neutrophil infiltration of the lungs is a common contributor to immune-related pathology in many pulmonary disease states . In response to pathogenic infection , airway epithelial cells produce hepoxilin A3 ( HXA3 ) , initiating neutrophil transepithelial migration . Migrated neutrophils amplify this recruitm...	Pseudomonas aeruginosa is an opportunistic pathogen that causes acute pneumonia in immune compromised patients , and infects 70–80% of patients suffering from cystic fibrosis . Infections can result in excessive airway inflammation , which lead to immune-mediated lung damage , in particular through the action of recrui...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "neurochemistry", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "eicosanoids", "immunology", "vector-borne", "diseases", "microbiology", "neuroscience", "toxicology", "epithelial", ...	2017	Pseudomonas aeruginosa ExoU augments neutrophil transepithelial migration
Identification of functional genetic variation associated with increased susceptibility to complex diseases can elucidate genes and underlying biochemical mechanisms linked to disease onset and progression . For genes linked to genetic diseases , most identified causal mutations alter an encoded protein sequence . Tech...	DNA sequence variations ( polymorphisms ) that affect the expression levels of genes play important roles in the pathogenesis of many complex diseases . Compared with genetic variations that alter the amino acid sequences of encoded proteins , which are relatively easy to identify , sequence variants that affect the re...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mus", "(mouse)", "homo", "(human)", "genetics", "and", "genomics", "computational", "biology" ]	2008	In Silico Detection of Sequence Variations Modifying Transcriptional Regulation
Ankyrin repeat containing proteins are one of the most abundant solenoid folds . Usually implicated in specific protein-protein interactions , these proteins are readily amenable for design , with promising biotechnological and biomedical applications . Studying repeat protein families presents technical challenges due...	Some natural proteins are formed with repetitions of similar amino acid stretches . Ankyrin-repeat proteins constitute one of the most abundant families of this class of proteins that serve as model systems to analyze how variations in sequences exert effects in structures and biological functions . We present an in-de...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Structural and Energetic Characterization of the Ankyrin Repeat Protein Family
Drug-induced liver injury ( DILI ) is a significant concern in drug development due to the poor concordance between preclinical and clinical findings of liver toxicity . We hypothesized that the DILI types ( hepatotoxic side effects ) seen in the clinic can be translated into the development of predictive in silico mod...	Translational research involves utilization of clinical data to address challenges in drug discovery and development . The rationale behind this study is that the side effects observed in clinical trial and post-marketing surveillance can be translated into a screening system for use in drug discovery . As a proof-of-c...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "medicine", "biochemistry", "text", "mining", "predictive", "toxicology", "drug", "research", "and", "development", "drugs", "and", "devices", "adverse", "reactions", "drug", "discovery", "biology", "computational", "biology", "pharmacology", "toxicology" ]	2011	Translating Clinical Findings into Knowledge in Drug Safety Evaluation - Drug Induced Liver Injury Prediction System (DILIps)
Adenosine-5’-triphosphate ( ATP ) is an important phosphate metabolite abundantly found in Mycobacterium leprae bacilli . This pathogen does not derive ATP from its host but has its own mechanism for the generation of ATP . Interestingly , this molecule as well as several antigenic proteins act as bio-markers for the d...	Mycobacterium leprae is the causative organism of the disease so called leprosy . It posses global health challenge due to the emergence of drug resistant M . leprae bacilli . In search for new drug targeting strategies , study of bacterial energy metabolism is significant . Reports claim that M . leprae generates ATP ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Interaction of ATP with a Small Heat Shock Protein from Mycobacterium leprae: Effect on Its Structure and Function
Coxsackievirus B3 ( CVB3 ) , a member of the picornavirus family and enterovirus genus , causes viral myocarditis , aseptic meningitis , and pancreatitis in humans . We genetically engineered a unique molecular marker , “fluorescent timer” protein , within our infectious CVB3 clone and isolated a high-titer recombinant...	Enteroviruses are significant human pathogens , causing myocarditis , aseptic meningitis and encephalitis . The mechanisms of enterovirus dissemination in the host and cell-to-cell spread may be critical factors influencing viral pathogenesis . Here , we have generated a recombinant coxsackievirus expressing “fluoresce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "neural", "stem", "cells", "stem", "cells", "animal", "cells", "cell", "biology", "viral", "transmission", "and", "infection", "virology", "biology", "and", "life", "sciences", "cellular", "types", "microbiology", "viral", "replication", ...	2014	Coxsackievirus B Exits the Host Cell in Shed Microvesicles Displaying Autophagosomal Markers
Prediction of drug combinations that effectively target cancer cells is a critical challenge for cancer therapy , in particular for triple-negative breast cancer ( TNBC ) , a highly aggressive breast cancer subtype with no effective targeted treatment . As signalling pathway networks critically control cancer cell beha...	We applied a systems modelling approach combining mechanistic modelling and biological experimentation to identify effective drug combinations for triple-negative breast cancer ( TNBC ) , an aggressive subtype of breast cancer with no approved targeted treatment . The model predicted and prioritized the synergistic com...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "signal", "transduction", "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "signal", "inhibition", "pharmaceutics", "cell", "biology", "network", "analysis", "dose", "prediction", "methods", "cancer", "treatment", "biolo...	2018	Systems modelling of the EGFR-PYK2-c-Met interaction network predicts and prioritizes synergistic drug combinations for triple-negative breast cancer
Genetic heterogeneity in a mixed sample of tumor and normal DNA can confound characterization of the tumor genome . Numerous computational methods have been proposed to detect aberrations in DNA samples from tumor and normal tissue mixtures . Most of these require tumor purities to be at least 10–15% . Here , we presen...	Allelic imbalance , or a deviation from the expected 1-to-1 ratio of alleles where both were present in the germline , can result when there has been an acquired deletion or duplication of part of a chromosome and is a hallmark of cancer genomes . Tumor genomic profiling studies often involve analysis of samples that c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "statistics", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism
The mitochondrial protein SLC25A46 has been recently identified as a novel pathogenic cause in a wide spectrum of neurological diseases , including inherited optic atrophy , Charcot-Marie-Tooth type 2 , Leigh syndrome , progressive myoclonic ataxia and lethal congenital pontocerebellar hypoplasia . SLC25A46 is an outer...	Neurodegenerative diseases encompass a wide range of clinical conditions remaining incurable while the genetic and molecular basis of most of these conditions remains unknown due to their heterogeneity and the lack of animal models . Mutations in nuclear genes encoding mitochondrial proteins have recently emerged as no...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "brain", "electrophysiology", "neuroscience", "animal", "models", "membrane", "proteins", "model", "organisms", "outer", "membrane", "proteins", "experimental", "organism", "systems", "nerve", "fibers", "mito...	2017	Novel insights into SLC25A46-related pathologies in a genetic mouse model
In recent years , there has been a huge rise in the number of publicly available transcriptional profiling datasets . These massive compendia comprise billions of measurements and provide a special opportunity to predict the function of unstudied genes based on co-expression to well-studied pathways . Such analyses can...	A major challenge in modern genomics research is to link the thousands of unstudied genes to the pathways and complexes within which they operate . A popular strategy to infer the function of an unstudied gene is to search for co-expressing genes of known function using a single transcriptional profiling dataset . Toda...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gene", "regulation", "metabolic", "processes", "oxidative", "phosphorylation", "probability", "distribution", "mathematics", "immunoprecipitation", "genome", "analysis", "mitochondria", "bioassays", "and", "physiological", "analysis", "bioenergetics", "co-immunoprecipitation", ...	2017	CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets
Prostaglandin E2 plays important roles in the maintenance of colonic homeostasis . The recently identified prostaglandin E receptor ( EP ) 4–associated protein ( EPRAP ) is essential for an anti-inflammatory function of EP4 signaling in macrophages in vitro . To investigate the in vivo roles of EPRAP , we examined the ...	Inflammatory bowel disease ( IBD ) is one of the most prevalent and serious gastrointestinal diseases in Western countries and associates with cancer development . EP4 receptor signaling can suppress intestinal inflammation and shows promise as a target for the development of novel therapies for IBD . To date , however...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	EP4 Receptor–Associated Protein in Macrophages Ameliorates Colitis and Colitis-Associated Tumorigenesis
The ability of a New World ( NW ) clade B arenavirus to enter cells using human transferrin receptor 1 ( TfR1 ) strictly correlates with its ability to cause hemorrhagic fever . Amapari ( AMAV ) and Tacaribe ( TCRV ) , two nonpathogenic NW clade B arenaviruses that do not use human TfR1 , are closely related to the NW ...	Several arenaviruses found in the New World cause hemorrhagic fever when they are transmitted from their natural reservoirs to humans . These pathogenic arenaviruses use human transferrin receptor 1 ( TfR1 ) , a protein involved in cellular iron uptake , to infect human cells . The nonpathogenic New World arenaviruses ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/host", "invasion", "and", "cell", "entry", "virology/emerging", "viral", "diseases" ]	2009	Host-Species Transferrin Receptor 1 Orthologs Are Cellular Receptors for Nonpathogenic New World Clade B Arenaviruses
The four dengue virus serotypes ( DENV-1–DENV-4 ) have a large impact on global health , causing 50–100 million cases of dengue fever annually . Herein , we describe the first kinetic T cell response to a low-dose DENV-1 vaccination study ( 10 PFU ) in humans . Using flow cytometry , we found that proinflammatory cytok...	40% of the world's population is at risk for developing dengue fever , an acute febrile illness caused by the 4 serotypes of dengue viruses ( DENV ) . Though most of the 50–100 million annual DENV infections resolve without medical intervention , approximately 500 , 000 cases are severe and require hospitalization . Su...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunity", "global", "health", "dengue", "fever", "neglected", "tropical", "diseases", "immunology", "biology", "viral", "diseases", "dengue", "infectious", "disease", "control", "immune", "response" ]	2012	Primary Vaccination with Low Dose Live Dengue 1 Virus Generates a Proinflammatory, Multifunctional T Cell Response in Humans
Strongyloidiasis can be fatal in immunocompromised patients , but few epidemiological studies investigated the burden of this neglected tropical disease among these populations , particularly in low- and middle-income countries such as Bolivia . This study aimed to fill in this gap by estimating prevalence rate and ris...	Strongyloidiasis is an understudied chronic intestinal infection and one of the most overlooked of the neglected tropical diseases , particularly in countries such as Bolivia . The strongyloidiasis usually remains paucisymptomatic for decades in immunocompetent persons , but may lead to severe conditions with high mort...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "oncology", "developmental", "biology", "neglected", "tropical", "diseases", "s...	2019	Epidemiology of Strongyloides stercoralis infection in Bolivian patients at high risk of complications
Dietary factors , including meat , fruits , vegetables and fiber , are associated with colorectal cancer; however , there is limited information as to whether these dietary factors interact with genetic variants to modify risk of colorectal cancer . We tested interactions between these dietary factors and approximately...	High intake of red and processed meat and low intake of fruits , vegetables and fiber are associated with a higher risk of colorectal cancer . We investigate if the effect of these dietary factors on colorectal cancer risk is modified by common genetic variants across the genome ( total of about 2 . 7 million genetic v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gastroenterology", "and", "hepatology", "medicine", "and", "health", "sciences", "epidemiology" ]	2014	Genome-Wide Diet-Gene Interaction Analyses for Risk of Colorectal Cancer
Several parameters should be addressed before incriminating a vector for Leishmania transmission . Those may include its ability to become infected by the same Leishmania species found in humans , the degree of attractiveness for reservoirs and humans and capacity to sustain parasite infection under laboratory conditio...	Leishmaniasis is a vector-borne disease caused by the Leishmania parasite . It is transmitted by phlebotomine sand flies when infected females take a bloodmeal from a mammalian host . The transmission of Leishmania species involves complex ecological interactions between parasite–vector and vector–host . Until recently...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "vector-borne", "diseases", "vertebrates", "sand", "flies", "parasitic", "diseases", "animals", "mammals", "dogs", "parasitic", "protozoans", "protozoans", "leishmania", "insect", "ve...	2017	Experimental infection and transmission of Leishmania by Lutzomyia cruzi (Diptera: Psychodidae): Aspects of the ecology of parasite-vector interactions
Recent genome-wide meta-analyses identified 157 loci associated with cross-sectional lipid traits . Here we tested whether these loci associate ( singly and in trait-specific genetic risk scores [GRS] ) with longitudinal changes in total cholesterol ( TC ) and triglyceride ( TG ) levels in a population-based prospectiv...	Although large cross-sectional studies have proven highly successful in identifying gene variants related to lipid levels and other cardiometabolic traits , very few examples of well-designed longitudinal studies exist where associations between genotypes and long-term changes in lipids have been assessed . Here we und...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "biomarker", "epidemiology", "cardiovascular", "anatomy", "population", "genetics", "quantitative", "traits", "clinical", "epidemiology", "atherosclerosis", "genetic", "epidemiology", "cardiology", "public", "and", "occupational", "h...	2014	Genetic Determinants of Long-Term Changes in Blood Lipid Concentrations: 10-Year Follow-Up of the GLACIER Study
Schistosomiasis causes long-term illness and significant economic burden . Morbidity control through integration within existing health care delivery systems is considered a potentially sustainable and cost-effective approach , but there is paucity of information about health-seeking behaviour . A questionnaire-based s...	The World Health Organization recommends that long-term benefit of schistosomiasis control should include treatment in local health facilities . This means that patients should visit a hospital or clinic with their complaints . However , little is known about whether they do so . We conducted a study in three regions o...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Discussion" ]	[ "science", "policy/education", "public", "health", "and", "epidemiology", "public", "health", "and", "epidemiology/health", "policy", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/he...	2010	Health Seeking Behaviour and Utilization of Health Facilities for Schistosomiasis-Related Symptoms in Ghana
Recent serological studies of seasonal influenza A in humans suggest a striking characteristic profile of immunity against age , which holds across different countries and against different subtypes of influenza . For both H1N1 and H3N2 , the proportion of the population seropositive to recently circulated strains peak...	The way in which a population builds immunity to influenza affects outbreak size and the emergence of new strains . However , although age-specific immunity has been widely discussed for the 2009 influenza pandemic , the age profile of immunity to seasonal influenza remains little understood . In contrast to many infec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "immunity", "population", "modeling", "epidemiology", "infectious", "disease", "epidemiology", "immunology", "biology", "computational", "biology", "infectious", "disease", "modeling", "population", "biology" ]	2012	The Role of Social Contacts and Original Antigenic Sin in Shaping the Age Pattern of Immunity to Seasonal Influenza
We characterized the establishment of an Epidermal Growth Factor Receptor ( EGFR ) organizing center ( EOC ) during leg development in Drosophila melanogaster . Initial EGFR activation occurs in the center of leg discs by expression of the EGFR ligand Vn and the EGFR ligand-processing protease Rho , each through single...	The EGFR signaling pathway plays a major role in innumerable developmental processes in all animals and its deregulation leads to different types of cancer , as well as many other developmental diseases in humans . Here we explored the integration of inputs from the Wnt- and TGF-beta signaling pathways and the leg-spec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome", "expression", "analysis", "invertebrates", "medicine", "and", "health", "sciences", "legs", "egfr", "signaling", "limbs", "(anatomy)", "cloning", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "ge...	2018	cis-regulatory architecture of a short-range EGFR organizing center in the Drosophila melanogaster leg
SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity . Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates , although pr...	Restriction endonucleases protect their bacterial hosts from viral infection by cleaving any invading viral DNA . One such enzyme , SgrAI , cleaves DNA very slowly but can be activated to cleave DNA 200 times more rapidly . Activation occurs when the enzyme interacts with two or more copies of DNA containing its recogn...	[ "Abstract", "Results", "Discussion", "Methods" ]	[ "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/macromolecular", "assemblies", "and", "machines" ]	2010	Domain Swapping in Allosteric Modulation of DNA Specificity
Cancer results from genetic alterations that disturb the normal cooperative behavior of cells . Recent high-throughput genomic studies of cancer cells have shown that the mutational landscape of cancer is complex and that individual cancers may evolve through mutations in as many as 20 different cancer-associated genes...	Cancer is a disease of multicellular organisms that is characterized by a breakdown of cooperation between individual cells . The progression of cancer proceeds from a single genetically altered cell to billions of invasive cells through a series of clonal expansions . During tumorigenesis the cancer cells undergo repl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "computational", "biology", "evolutionary", "biology", "cancer", "genetics", "and", "genomics" ]	2007	Genetic Progression and the Waiting Time to Cancer
The circadian clock plays a pervasive role in the temporal regulation of plant physiology , environmental responsiveness , and development . In contrast , the phytohormone auxin plays a similarly far-reaching role in the spatial regulation of plant growth and development . Went and Thimann noted 70 years ago that plant...	Most higher organisms , including plants and animals , have developed a time-keeping mechanism that allows them to anticipate daily fluctuations of environmental parameters such as light and temperature . This circadian clock efficiently coordinates plant growth and metabolism with respect to time of day by producing s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "arabidopsis", "(thale", "cress)", "plant", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	The Circadian Clock Regulates Auxin Signaling and Responses in Arabidopsis
Dengue is a vector-borne viral disease of humans that endemically circulates in many tropical and subtropical regions worldwide . Infection with dengue can result in a range of disease outcomes . A considerable amount of research has sought to improve our understanding of this variation in disease outcomes and to ident...	Dengue is an important vector-borne disease that infects four-hundred million individuals annually . Infection results in a wide range of clinical symptoms . Though many risk factors of dengue are known , the mechanisms explaining why an individual will suffer severe symptoms are poorly understood . Clinical studies ha...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "viral", "transmission", "and", "infection", "immunology", "tropical", "diseases", "microbiology", "simulation", "and", "modeling", "neglected", "tropical", "diseases",...	2016	Drivers of Inter-individual Variation in Dengue Viral Load Dynamics
In Trypanosoma cruzi , the etiologic agent of Chagas disease , Rad51 ( TcRad51 ) is a central enzyme for homologous recombination . Here we describe the different roles of TcRad51 in DNA repair . Epimastigotes of T . cruzi overexpressing TcRAD51 presented abundant TcRad51-labeled foci before gamma irradiation treatment...	Trypanosoma cruzi is the causative agent of Chagas disease , a tropical neglected illness that affects 6 million people worldwide , mostly in Latin America . Our research group focuses on the elucidation of DNA repair and metabolism of T . cruzi , and on the possible implications of those mechanisms in both parasite ge...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "gamma", "radiation", "immunology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "fibroblasts", "protozoan", "life", "cycles", "radiation", "developmental", "biology", "...	2018	The in vivo and in vitro roles of Trypanosoma cruzi Rad51 in the repair of DNA double strand breaks and oxidative lesions
Evaluation of therapeutic response in chronic Chagas disease is a major challenge , due to prolonged persistence of Trypanosoma cruzi-specific antibodies , lack of sensitivity of parasitological tests , and need for long-term follow-up to observe negative seroconversion of conventional serological tests ( CS ) . The ob...	Evaluation of therapeutic response in chronic Chagas disease is a major challenge , particularly in the early post-treatment phase , due to prolonged persistence of Trypanosoma cruzi-specific antibodies and lack of sensitivity of available parasitological tests . The main limitation in evaluating Chagas disease treatme...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitology", "pediatrics", "neglected", "tropical", "diseases", ...	2019	Longitudinal follow up of serological response in children treated for Chagas disease
The yaws treponemes , Treponema pallidum ssp . pertenue ( TPE ) strains , are closely related to syphilis causing strains of Treponema pallidum ssp . pallidum ( TPA ) . Both yaws and syphilis are distinguished on the basis of epidemiological characteristics , clinical symptoms , and several genetic signatures of the co...	Spirochete Treponema pallidum ssp . pertenue ( TPE ) is the causative agent of yaws while strains of Treponema pallidum ssp . pallidum ( TPA ) cause syphilis . Both yaws and syphilis are distinguished on the basis of epidemiological characteristics and clinical symptoms . Neither treponeme can reproduce outside the hos...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "genome", "analysis", "tools", "genomics", "tropical", "diseases", "(non-neglected)", "biology", "computational", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence
Differentiation of lung vascular smooth muscle cells ( vSMCs ) is tightly regulated during development or in response to challenges in a vessel specific manner . Aberrant vSMCs specifically associated with distal pulmonary arteries have been implicated in the pathogenesis of respiratory diseases , such as pulmonary art...	The pathogenesis of some vascular diseases , such as PAH is selectively associated with aberrant differentiation and proliferation of vSMCs of distal arteries . While significant progresses have been made in understanding the core mechanism of differentiation and proliferation of vSMCs , little is known regarding vesse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Disruption of miR-29 Leads to Aberrant Differentiation of Smooth Muscle Cells Selectively Associated with Distal Lung Vasculature
Chagas disease is caused by the parasite Trypanosoma cruzi , and it begins with a short acute phase characterized by high parasitemia followed by a life-long chronic phase with scarce parasitism . Cardiac involvement is the most prominent manifestation , as 30% of infected subjects will develop abnormal ventricular rep...	Chagas’ disease is caused by the protozoan parasite Trypanosoma cruzi and affects 8 million individuals worldwide . The life-long infection begins with a short acute phase , which is associated to parasites circulating in the bloodstream , tissue parasitism , and various signs and symptoms including those related to my...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	MicroRNA Transcriptome Profiling in Heart of Trypanosoma cruzi-Infected Mice: Parasitological and Cardiological Outcomes
The ubiquitin-like modifier ISG15 is one of the most predominant proteins induced by type I interferons ( IFN ) . In this study , murine embryo fibroblast ( MEFs ) and mice lacking the gene were used to demonstrate a novel role of ISG15 as a host defense molecule against vaccinia virus ( VACV ) infection . In MEFs , th...	Modification of proteins by ubiquitin ( UB ) and ubiquitin-like proteins ( UBL ) represents a key regulatory process of innate and adaptive immune responses . Interferon-stimulated gene product 15 ( ISG15 ) is a member of UBL molecules that can reversibly be conjugated to proteins mediating considerable antiviral respo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immune", "evasion", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology/host", "antiviral", "responses", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance" ]	2008	Vaccinia Virus E3 Protein Prevents the Antiviral Action of ISG15
Contrast is the most fundamental property of images . Consequently , any comprehensive model of biological vision must incorporate this attribute and provide a veritable description of its impact on visual perception . Current theoretical and computational models predict that vision should modify its characteristics at...	We can view cortex from two fundamentally different perspectives: a powerful device for performing optimal inference , or an assembly of biological components not built for achieving statistical optimality . The former approach is attractive thanks to its elegance and potentially wide applicability , however the basic ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "social", "sciences", "light", "neuroscience", "electromagnetic", "radiation", "simulation", "and", "modeling", "mathematics", "luminance", "algebra", "visible", "light", "vision", "research", "and", "analysis", "methods", "behavior", "physics", "psychology", "eigenvector...	2018	The empirical characteristics of human pattern vision defy theoretically-driven expectations
Multiple rare variants either within or across genes have been hypothesised to collectively influence complex human traits . The increasing availability of high throughput sequencing technologies offers the opportunity to study the effect of rare variants on these traits . However , appropriate and computationally effi...	Rapid advances in sequencing technology mean that it is now possible to directly assay rare genetic variation . In addition , the availability of almost fully sequenced human genomes by the 1000 Genomes Project allows genotyping at rare variants that are not present on arrays commonly used in genome-wide association st...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "genome", "analysis", "tools", "genomics", "genetic", "mutation", "genetic", "association", "studies", "genetics", "biology", "human", "genetics", "genetics", "of", "disease", "gene", "function" ]	2013	A Flexible Approach for the Analysis of Rare Variants Allowing for a Mixture of Effects on Binary or Quantitative Traits
We sequenced and compared the genomes of the Dothideomycete fungal plant pathogens Cladosporium fulvum ( Cfu ) ( syn . Passalora fulva ) and Dothistroma septosporum ( Dse ) that are closely related phylogenetically , but have different lifestyles and hosts . Although both fungi grow extracellularly in close contact wit...	We compared the genomes of two closely related pathogens with very different lifestyles and hosts: C . fulvum ( Cfu ) , a biotroph of tomato , and D . septosporum ( Dse ) , a hemibiotroph of pine . Some differences in gene content were identified that can be directly related to their different hosts , such as the prese...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "plant", "biology", "microbiology", "plant", "science", "plant", "pathology", "molecular", "genetics", "structural", "genomics", "mycology", "comparative", "genomics", "biology", "genetics", "genomics", "computational", "biology", "genetics", "an...	2012	The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry
Clotting systems are required in almost all animals to prevent loss of body fluids after injury . Here , we show that despite the risks associated with its systemic activation , clotting is a hitherto little appreciated branch of the immune system . We compared clotting of human blood and insect hemolymph to study the ...	One of the main functions of immune systems is to prevent the dissemination of microbes and the resulting sepsis . Blood clotting during sepsis has until now been primarily regarded as harmful , leading to the formation of widespread clots in blood vessels and as a result to organ failure . Here we show that clotting a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "immunology/immune", "response", "hematology/coagulation", "disorders", "genetics", "a...	2010	Pathogen Entrapment by Transglutaminase—A Conserved Early Innate Immune Mechanism
Drug screening studies typically involve assaying the sensitivity of a range of cancer cell lines across an array of anti-cancer therapeutics . Alongside these sensitivity measurements high dimensional molecular characterizations of the cell lines are typically available , including gene expression , copy number variat...	A core tenant of precision medicine is that treatment should be tailored to the patient . In the context of cancer , large-scale screens , assaying the sensitivity of many cell-lines to panels of drugs , have the potential to enable discovery of biomarkers of sensitivity to specific therapeutics . However , existing co...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "statistics", "gene", "regulation", "computational", "biology", "basic", "cancer", "research", "oncology", "mathematics", "forecasting", "copy", "number", "variation", "mapk", "signaling", "cascades", "resea...	2019	Sparse discriminative latent characteristics for predicting cancer drug sensitivity from genomic features
The ability of Taenia solium to modulate the immune system likely contributes to their longevity in the human host . We tested the hypothesis that the nature of the immune response is related to the location of parasite and clinical manifestations of infection . Peripheral blood mononuclear cells ( PBMC ) were obtained...	Cysticercosis is a parasitic disease caused by the larval cysts of the pork tapeworm Taenia solium following accidental ingestion of tapeworm eggs . Neurocysticercosis is a leading cause of seizures and epilepsy in developing countries . The clinical manifestations depend on many factors including the number , size , l...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Comparative Study of Peripheral Immune Responses to Taenia solium in Individuals with Parenchymal and Subarachnoid Neurocysticercosis
Ancestral state reconstructions in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection ( BSSVS ) framework . Recently , this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model ( GLM ...	For the better part of the last decade , epidemiological researchers have employed a Bayesian framework to reconstruct phylogenetic trees and determine the spatiotemporal relationships between clades of viruses . Recently , an extension of this framework has enabled direct assessment of how various demographic , geogra...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "biogeography", "taxonomy", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "influenza", "atmospheric", "science", "pathogens", "population", "genetics", "immunology", "microbiology", "o...	2017	Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction
In contrast to Trypanosoma brucei gambiense and T . b . rhodesiense ( the causative agents of human African trypanosomiasis ) , T . b . brucei is lysed by apolipoprotein-L1 ( apoL1 ) -containing human serum trypanolytic factors ( TLF ) , rendering it non-infectious to humans . While the mechanisms of TLF1 uptake , apoL...	Expression of the trypanolytic serum component , apolipoprotein-L1 ( apoL1 ) , by humans and the concomitant evolution of countermeasures by two African trypanosome sub-species defines their ability to cause disease in humans . A genome-scale RNAi screen identified more than 60 proteins that sensitise non-human infecti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cdna", "libraries", "cdna", "library", "screening", "lysosomes", "rna", "interference", "parasitic", "protozoans", "membrane", "proteins", "protozoans", "forms", "of", "dna", "dna", "libraries", "epigenetics", "molecular", "biology", "techniques", "dna", "cellular", ...	2018	Decoding the network of Trypanosoma brucei proteins that determines sensitivity to apolipoprotein-L1
Dietary restriction ( DR ) , limiting nutrient intake from diet without causing malnutrition , delays the aging process and extends lifespan in multiple organisms . The conserved life-extending effect of DR suggests the involvement of fundamental mechanisms , although these remain a subject of debate . To help decipher...	Dietary restriction has been shown to extend lifespan in diverse , evolutionarily distant species , yet its underlying mechanisms remain unknown . We first constructed a database of genes essential for the life-extending effects of dietary restriction in various model organisms and then studied their interactions using...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genomics", "model", "organisms", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes
Rhinolophidae or Horseshoe bats emit long and narrowband calls . Fluttering insect prey generates echoes in which amplitude and frequency shifts are present , i . e . glints . These glints are reliable cues about the presence of prey and also encode certain properties of the prey . In this paper , we propose that these...	Rhinolophidae are echolocating bats that hunt among vegetation . The foliage returns clutter echoes that potentially mask the echoes of insect prey . However , prey introduces frequency and amplitude shifts , called glints , into the echo to which these bats are highly sensitive . Therefore , these glints are used by R...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary", "ecology", "animal", "behavior", "theoretical", "biology", "ecology", "evolutionary", "biology", "computational", "neuroscience", "biology", "computational", "biology", "sensory", "systems", "neuroscience", "sensory", "perception", "behavioral", "ecology" ]	2011	Dominant Glint Based Prey Localization in Horseshoe Bats: A Possible Strategy for Noise Rejection
PIKfyve , VAC14 , and FIG4 form a complex that catalyzes the production of PI ( 3 , 5 ) P2 , a signaling lipid implicated in process ranging from lysosome maturation to neurodegeneration . While previous studies have identified VAC14 and FIG4 mutations that lead to both neurodegeneration and coat color defects , how PI...	In order for a cell to develop and maintain functional organelles , proteins must be delivered to developing organelles in a precise , sequential fashion . In this study , we used a well-established model for organelle biogenesis ( the melanosome ) to understand how phosphoinositides regulate vesicle trafficking and me...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "lysosomes", "vesicles", "integumentary", "system", "pigments", "epithelial", "cells", "animal", "models", "model", "organisms", "microscopy", "materials", "science", "experimental", "organism", "systems", "chromatophores", "cellul...	2018	PIKfyve regulates melanosome biogenesis
The differential programming of sperm and eggs in gonads is a fundamental topic in reproductive biology . Although the sexual fate of germ cells is believed to be determined by signaling factors from sexually differentiated somatic cells in fetal gonads , the molecular mechanism that determines germ cell fate is poorly...	Mammalian sex depends on a male-specific gene , sex-determining region Y ( SRY ) , which is located on the Y chromosome . Individuals lacking this gene will develop as female . Accordingly , germ cell fate also changes from male to female in the absence of SRY . Therefore , it is thought that somatic cells regulate ger...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cell", "differentiation", "germ", "cells", "developmental", "biology", "morphogenesis", "animal", "cells", "chromosome", "bi...	2016	Sexual Fate Change of XX Germ Cells Caused by the Deletion of SMAD4 and STRA8 Independent of Somatic Sex Reprogramming
Variants resistant to compounds specifically targeting HCV are observed in clinical trials . A multi-variant viral dynamic model was developed to quantify the evolution and in vivo fitness of variants in subjects dosed with monotherapy of an HCV protease inhibitor , telaprevir . Variant fitness was estimated using a mo...	Hepatitis C virus ( HCV ) infects an estimated 170 million people worldwide . Current treatment for HCV is 48 weeks of peginterferon and ribavirin of which patient response has large variability . Recently , specifically targeted antiviral therapies for HCV ( STAT-C ) are under clinical development and have shown poten...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/persistence", "and", "latency", "pharmacology/drug", "resistance", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "pharmacology/drug", "development", "virology", "computational", "biology/evolutionary", "modeling", "virology/antivirals,",...	2010	A Multi-Variant, Viral Dynamic Model of Genotype 1 HCV to Assess the in vivo Evolution of Protease-Inhibitor Resistant Variants
Recent functional genomics studies including genome-wide small interfering RNA ( siRNA ) screens demonstrated that hepatitis C virus ( HCV ) exploits an extensive network of host factors for productive infection and propagation . How these co-opted host functions interact with various steps of HCV replication cycle and...	Hepatitis C virus ( HCV ) is a positive strand RNA virus that belongs to the Flaviridae family . Chronic HCV infection is a leading cause of end-stage liver disease , which is associated with significant morbidity and mortality in the world . Our recent genome-wide siRNA screen has revealed that HCV depends extensively...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "viral", "classification", "pathogens", "microbiology", "liver", "diseases", "viruses", "viral", "attachment", "infectious...	2014	Integrative Functional Genomics of Hepatitis C Virus Infection Identifies Host Dependencies in Complete Viral Replication Cycle
HIV-1 virions infect target cells by first establishing contact between envelope glycoprotein trimers on the virion's surface and CD4 receptors on a target cell , recruiting co-receptors , fusing with the cell membrane and finally releasing the genetic material into the target cell . Specific experimental setups allow ...	A large part of the research on the Human Immunodeficiency Virus focuses on how virus particles attach and enter their target cells , and how entry can be inhibited by antibodies or antiretroviral drugs . Because virus particles are too small to be observed in action the inference of the details of HIV entry has to be ...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "mathematics/statistics", "mathematics", "computational", "biology" ]	2010	Estimating the Stoichiometry of HIV Neutralization
Actin is a highly versatile , abundant , and conserved protein , with functions in a variety of intracellular processes . Here , we describe a novel role for insect cytoplasmic actin as an extracellular pathogen recognition factor that mediates antibacterial defense . Insect actins are secreted from cells upon immune c...	Actin is one of the best studied , evolutionary conserved and most abundant intracellular proteins . Actin can exists in globular and filamentous functionally distinct forms , and is involved in a variety of biological processes , such as muscle contraction , cell motility , cell division , vesicle and organelle moveme...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Cytoplasmic Actin Is an Extracellular Insect Immune Factor which Is Secreted upon Immune Challenge and Mediates Phagocytosis and Direct Killing of Bacteria, and Is a Plasmodium Antagonist
Plasmacytoid dendritic cells ( pDCs ) were initially considered as critical for innate immunity to viruses . However , our group has shown that pDCs bind to and inhibit the growth of Aspergillus fumigatus hyphae and that depletion of pDCs renders mice hypersusceptible to experimental aspergillosis . In this study , we ...	While plasmacytoid dendritic cells ( pDCs ) are known to be important immune cells involved in protection from viruses and tumors , their role in protection against fungal infections is less clear . Our laboratory has been studying the interplay between pDCs and the fungal pathogen , Aspergillus fumigatus . Our previou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Recognition of Aspergillus fumigatus Hyphae by Human Plasmacytoid Dendritic Cells Is Mediated by Dectin-2 and Results in Formation of Extracellular Traps
A key feature of signalling in dendritic spines is the synapse-specific transduction of short electrical signals into biochemical responses . Ca2+ is a major upstream effector in this transduction cascade , serving both as a depolarising electrical charge carrier at the membrane and an intracellular second messenger . ...	Experiences change neuronal circuits , and these circuit changes outlast the initial experiences . This means that , in neurons , the fast electrical activity encoding experiences needs to be transduced into longer-lived biochemical and structural changes . A key mediator between these two timescales of neuronal activi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ryanodine Receptor Activation Induces Long-Term Plasticity of Spine Calcium Dynamics
New treatments are needed for neglected tropical diseases ( NTDs ) such as Human African trypanosomiasis ( HAT ) , Chagas disease , and schistosomiasis . Through a whole organism high-throughput screening campaign , we previously identified 797 human kinase inhibitors that grouped into 59 structural clusters and showed...	Human African trypanosomiasis ( HAT ) is a parasitic disease prevalent in sub-Saharan Africa . Current treatments cause severe toxicity , are difficult to administer , and are susceptible to resistance . In order to quickly discover new leads for HAT drug discovery , we screened human kinase inhibitors against Trypanos...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "african", "trypanosomiasis", "drugs", "cytotoxicity", "assay", "tropical", "diseases", "microbiology", "enzymology", "parasitic", "diseases", "parasitic", "protozoans",...	2019	Evaluation of a class of isatinoids identified from a high-throughput screen of human kinase inhibitors as anti-Sleeping Sickness agents
In the social amoeba Dictyostelium discoideum , thousands of cells aggregate upon starvation to form a multicellular fruiting body , and approximately 20% of them die to form a stalk that benefits the others . The aggregative nature of multicellular development makes the cells vulnerable to exploitation by cheaters , a...	In social amoebae such as Dictyostelium discoideum , cells aggregate to form a multicellular slug that migrates and then forms a fruiting body , which contains live spores ( which go on to make new amoebae ) and dead stalk cells . Unlike animals where all the cells descend from one fertilized egg , social amoeba fruiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology" ]	2008	Kin Discrimination Increases with Genetic Distance in a Social Amoeba
Modeling the complex collective behavior is a challenging issue in several material and life sciences . The collective motion has been usually modeled by simple interaction rules and explained by global statistics . However , it remains difficult to bridge the gap between the dynamic properties of the complex interacti...	Modeling complex collective motions is a challenging problem such as in biology , physics , and human behavior because the rules governing the motion are sometimes unclear . Then , researchers have usually used simple interaction model and explain global statistics . However , it remains difficult to bridge the gap bet...	[ "Abstract", "Results", "Discussion", "Materials", "and", "methods" ]	[ "recreation", "collective", "animal", "behavior", "sports", "applied", "mathematics", "social", "sciences", "geometry", "simulation", "and", "modeling", "algorithms", "systems", "science", "mathematics", "animal", "behavior", "zoology", "research", "and", "analysis", "m...	2018	Prediction and classification in equation-free collective motion dynamics
Taenia spp . infections , particularly cysticercosis , cause considerable health impacts in endemic countries . Despite previous evidence of spatial clustering in cysticercosis and the role of environmental factors ( e . g . temperature and humidity ) in the survival of eggs , little research has explored these aspects...	Taenia spp . can cause tapeworm infections in the human gut , and infection with the larval stage of Taenia solium ( cysticercosis ) can lead to serious outcomes , such as epilepsy . Transmission occurs in areas with poor sanitation and a lack of adequate meat inspection practices , although there are still gaps in our...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	The Influence of Socio-economic, Behavioural and Environmental Factors on Taenia spp. Transmission in Western Kenya: Evidence from a Cross-Sectional Survey in Humans and Pigs
Control initiatives have successfully reduced the prevalence and intensity of schistosomiasis transmission in several localities around the world . However , individuals that release low numbers of eggs in their feces may not be detected by classical methods that are limited by low sensitivity . Given that accurate est...	Schistosomiasis is a parasitic infection that is caused by flatworms that live inside venous vessels . The parasite eggs are eliminated with human feces . They hatch in the water and the free swimming larvae infect snails . The larvae develop in the snail tissues and , on reaching an infective stage , are released into...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "urine", "neglected", "tropical", "diseases", "south"...	2018	Study of diagnostic accuracy of Helmintex, Kato-Katz, and POC-CCA methods for diagnosing intestinal schistosomiasis in Candeal, a low intensity transmission area in northeastern Brazil
The nucleosome repeat length ( NRL ) is an integral chromatin property important for its biological functions . Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins , both in vitro and in vivo , but a systematic theoret...	The DNA molecule of a human or mouse can be up to two meters long , if stretched . However , it is stored inside the small volume of the nucleus in the living cell . DNA compaction is achieved at different hierarchical levels with the help of a number of architectural proteins . The elementary unit of compaction is the...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "theory", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Regulation of the Nucleosome Repeat Length In Vivo by the DNA Sequence, Protein Concentrations and Long-Range Interactions
Designed peptides that bind to major histocompatibility protein I ( MHC-I ) allomorphs bear the promise of representing epitopes that stimulate a desired immune response . A rigorous bioinformatical exploration of sequence patterns hidden in peptides that bind to the mouse MHC-I allomorph H-2Kb is presented . We exempl...	Future success in vaccine development will critically depend on identifying potent epitopes with reduced side effects . Among such candidate molecules , immunogenic peptides binding to major histocompatibility protein I ( MHC-I ) represent a preferred class of biomolecules for vaccine design . Computational models assi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "computer", "applications", "sequence", "analysis", "computer", "science", "medicinal", "chemistry", "computer", "modeling", "major", "histocompatibility", "complex", "antigen", "processing", "and", "recognition", "immunology", "chemistry", "biology", "comp...	2013	Scrutinizing MHC-I Binding Peptides and Their Limits of Variation
Tissue invasive helminth infections and tuberculosis ( TB ) are co-endemic in many parts of the world and can trigger immune responses that might antagonize each other . We have previously shown that helminth infections modulate the Th1 and Th17 responses to mycobacterial-antigens in latent TB . To determine whether he...	While it has long been recognized that helminth infections alter the pathophysiology of allergic and autoimmune disease , data suggest that helminth infections also exert an important immunological effect on concomitant infections and vaccine responses . In particular , helminth coinfection can modulate the severity , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "diseases", "infectious", "diseases", "helminth", "infections", "medicine", "and", "health", "sciences", "tuberculosis", "biology", "and", "life", "sciences", "immunology", "parasitic", "diseases", "immunomodulation", "immune", "response" ]	2014	Helminth Infections Coincident with Active Pulmonary Tuberculosis Inhibit Mono- and Multifunctional CD4+ and CD8+ T Cell Responses in a Process Dependent on IL-10
D-aminoacyl-tRNA deacylase ( DTD ) removes D-amino acids mischarged on tRNAs and is thus implicated in enforcing homochirality in proteins . Previously , we proposed that selective capture of D-aminoacyl-tRNA by DTD’s invariant , cross-subunit Gly-cisPro motif forms the mechanistic basis for its enantioselectivity . We...	Proteins are composed of 20 different amino acids , 19 of which have L-chirality and one , glycine , that is achiral . A polypeptide consisting of both D- and L-amino acids cannot assume its proper three-dimensional conformation and is therefore non-functional . Since the cellular milieu contains both D- and L-amino ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfer", "rna", "medicine", "and", "health", "sciences", "crystal", "structure", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "aliphatic", "amino", "acids", "absorption", "spectroscopy", "nmr", "spectroscopy", "condensed", "matter", "physics...	2016	Elongation Factor Tu Prevents Misediting of Gly-tRNA(Gly) Caused by the Design Behind the Chiral Proofreading Site of D-Aminoacyl-tRNA Deacylase
The genome of Epstein-Barr virus ( EBV ) encodes 86 proteins , but only a limited set is expressed in EBV–growth transformed B cells , termed lymphoblastoid cell lines ( LCLs ) . These cells proliferate via the concerted action of EBV nuclear antigens ( EBNAs ) and latent membrane proteins ( LMPs ) , some of which are ...	Epstein-Barr virus ( EBV ) infects primary human B cells and establishes a latent infection , which leads to permanently growing B cell cultures . These growth transformed B cells express a well defined set of latent viral genes , which are also expressed in post-transplant lymphomas of immunosuppressed patients . In a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression" ]	2009	Differential Gene Expression Patterns of EBV Infected EBNA-3A Positive and Negative Human B Lymphocytes
One of the challenges to understand the organization of the nervous system has been to determine how axon guidance molecules govern axon outgrowth . Through an unbiased genetic screen , we identified a conserved Wnt pathway which is crucial for anterior-posterior ( A/P ) outgrowth of neurites from RME head motor neuron...	How do individual nerve fibers find their way along specific paths in a complex environment such as the developing central nervous system ? A principal mechanism in axon guidance is binding of a receptor protein on the axon surface to a guidance molecule . However , it remains a mystery exactly how a limited number of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/neurodevelopment" ]	2010	A Wnt-Frz/Ror-Dsh Pathway Regulates Neurite Outgrowth in Caenorhabditis elegans
Transcellular Mg2+ transport across epithelia , involving both apical entry and basolateral extrusion , is essential for magnesium homeostasis , but molecules involved in basolateral extrusion have not yet been identified . Here , we show that CNNM4 is the basolaterally located Mg2+ extrusion molecule . CNNM4 is strong...	Magnesium is an essential element for living organisms . Its absorption occurs at the intestine through the barrier comprised of epithelial cells . In this process , transcellular Mg2+ transport across epithelia , involving both entry from one side and extrusion from the other side , is important . Previous studies hav...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Basolateral Mg2+ Extrusion via CNNM4 Mediates Transcellular Mg2+ Transport across Epithelia: A Mouse Model
Basic helix-loop-helix ( bHLH ) transcription factors play critical roles in lymphoid and erythroid development; however , little is known about their role in myeloid lineage development . In this study , we identify the bHLH transcription factor Twist-2 as a key negative regulator of myeloid lineage development , as m...	Hematopoiesis is coordinated by transcription factors that regulate proliferation , differentiation , and cell fate determinations . Myelopoiesis refers to the development of all white blood cells , excluding lymphocytes ( B and T cells ) ; however , the molecular regulation of this developmental process is still incom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hematology", "immunology" ]	2008	Twist-2 Controls Myeloid Lineage Development and Function
The goal of elimination of the human filariases would benefit greatly from the use of a macrofilaricidal agent . In vivo trials in humans and many experimental animal models suggest that flubendazole ( FLBZ ) is a highly efficacious macrofilaricide . However , since serious injection site reactions were reported in hum...	Lymphatic filariasis and onchocerciasis are tropical parasitic diseases caused by filarial nematodes , which constitute a serious public health issue in tropical regions . Lymphatic filariasis causes debilitating lymphedema and hydrocele , resulting in temporary or permanent disability . Onchocerciasis ( also known as ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "veterinary", "science" ]	2014	Exploring the Potential of Flubendazole in Filariasis Control: Evaluation of the Systemic Exposure for Different Pharmaceutical Preparations
Visceral leishmaniasis ( VL ) in the Indian subcontinent is a fatal disease if left untreated . Between 1994 to 2013 , the Ministry of Health of Bangladesh reported 1 , 09 , 266 cases of VL and 329 VL related deaths in 37 endemic districts . Indoor residual spraying ( IRS ) using dichlorodiphenyltrichloroethane ( DDT )...	The visceral leishmaniasis ( VL ) elimination programme was launched in the Indian subcontinent ( Bangladesh , India and Nepal ) in 2005 . Although the integrated vector management ( IVM ) system is one of the important elements highlighted in the Regional VL elimination strategy , indoor residual spraying ( IRS ) is t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "india", "sand", "flies", "parasitic", "diseases", "ddt", "neglected", "tropical", "diseases", "infectious", "disease", "control", "insect", "vectors", "bangladesh...	2018	Indoor residual spraying for kala-azar vector control in Bangladesh: A continuing challenge
Influenza pandemics in the last century were characterized by successive waves and differences in impact and timing between different regions , for reasons not clearly understood . The 2009 H1N1 pandemic showed rapid global spread , but with substantial heterogeneity in timing within each hemisphere . Even within Europ...	The 2009 H1N1pdm influenza pandemic spread rapidly but heterogeneously . A notable pattern occurred in Europe , with the UK exhibiting a first wave in early summer and a second wave in autumn , while all other European countries experienced a single wave in autumn/winter , resulting in a clear West to East pattern of s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "population", "modeling", "epidemiology", "infectious", "disease", "epidemiology", "biology", "computational", "biology", "infectious", "disease", "modeling" ]	2011	Determinants of the Spatiotemporal Dynamics of the 2009 H1N1 Pandemic in Europe: Implications for Real-Time Modelling
The increasing use of malaria diagnostic tests reveals a growing proportion of patients with fever but no malaria . Clinicians and health care workers in low-income countries have few tests to diagnose causes of fever other than malaria although several diseases share common symptoms . We propose here to assess etiolog...	Febrile illnesses have many origins , but infectious agents are the most important cause . Pathogens such as viruses and bacteria can cause various diseases , but associated signs and symptoms are generally non-specific and can overlap between diseases . Treatments of infectious diseases rely on the diagnostic of the c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "respiratory", "infections", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "parasitic", "diseases", "pulmonology"...	2018	Study on causes of fever in primary healthcare center uncovers pathogens of public health concern in Madagascar
The aphid Myzus persicae is a globally significant crop pest that has evolved high levels of resistance to almost all classes of insecticide . To date , the neonicotinoids , an economically important class of insecticides that target nicotinic acetylcholine receptors ( nAChRs ) , have remained an effective control meas...	M . persicae is the most economically important aphid pest in many regions of the world due to its large host range and the damage it causes through direct feeding and through the transmission of plant viruses . This species has developed resistance to most classes of insecticide; and although , to date , the neonicoti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "genetics", "and", "genomics" ]	2010	Amplification of a Cytochrome P450 Gene Is Associated with Resistance to Neonicotinoid Insecticides in the Aphid Myzus persicae
Interferon-stimulated gene 15 ( ISG15 ) encodes an ubiquitin-like protein that covalently conjugates protein . Protein modification by ISG15 ( ISGylation ) is known to inhibit the replication of many viruses . However , studies on the viral targets and viral strategies to regulate ISGylation-mediated antiviral response...	Type I IFN response is a front-line defense against virus infection . Activation of type I IFN signaling leads to expression of a subset of cellular proteins encoded by interferon-stimulated genes ( ISGs ) . ISG15 encodes an ubiquitin-like protein that is covalently conjugated to protein lysine residues . ISG15 modific...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "293t", "cells", "pathogens", "immunology", "biological", "cultures", "immunoblotting", "microbiology", "viral", "structure",...	2016	Consecutive Inhibition of ISG15 Expression and ISGylation by Cytomegalovirus Regulators
Loop-mediated isothermal amplification ( LAMP ) is a rapid and sensitive tool used for the diagnosis of a variety of infectious diseases . One of the advantages of this method over the polymerase chain reaction is that DNA amplification occurs at a constant temperature , usually between 60–65°C; therefore , expensive d...	Human African trypanosomiasis ( HAT ) is an endemic protozoan disease affecting many African countries , predominantly in rural areas where the tsetse fly vector is present . HAT diagnosis currently relies on conventional microscopy techniques , which provide relatively low sensitivity and are often unable to distingui...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Direct Blood Dry LAMP: A Rapid, Stable, and Easy Diagnostic Tool for Human African Trypanosomiasis
Nucleosomes in all eukaryotes examined to date adopt a characteristic architecture within genes and play fundamental roles in regulating transcription , yet the identity and precise roles of many of the trans-acting factors responsible for the establishment and maintenance of this organization remain to be identified ....	The genome in eukaryotic cells is packaged into nucleosomes , which play critical roles in regulating where and when different genes are expressed . For example , nucleosomes can physically block access of transcription factor to sites on DNA or direct regulatory proteins to DNA . Consistent with these roles , nucleoso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "chromosome", "biology", "gene", "expression", "genetics", "epigenetics", "yeast", "and", "fungal", "models", "biology", "genomics", "saccharomyces", "cerevisiae", "chromatin", "dna", "transcription", "gene", "function" ]	2013	A Compendium of Nucleosome and Transcript Profiles Reveals Determinants of Chromatin Architecture and Transcription
The fungus Mycosphaerella graminicola has been a pathogen of wheat since host domestication 10 , 000–12 , 000 years ago in the Fertile Crescent . The wheat-infecting lineage emerged from closely related Mycosphaerella pathogens infecting wild grasses . We use a comparative genomics approach to assess how the process of...	The fungal wheat pathogen Mycosphaerella graminicola emerged in the Middle East 11 , 000 years ago , coinciding with host domestication . We sequenced the genome of the closest known endemic relative of M . graminicola infecting wild grass hosts . A comparative genome analysis allowed us to infer how speciation and hos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/genomics" ]	2010	Whole-Genome and Chromosome Evolution Associated with Host Adaptation and Speciation of the Wheat Pathogen Mycosphaerella graminicola
The aim of this study was to explore the mechanisms of resistance against invading Ascaris suum larvae in pigs . Pigs received a low dose of 100 A . suum eggs daily for 14 weeks . This resulted in a >99% reduction in the number of larvae that could migrate through the host after a challenge infection of 5000 A . suum e...	Ascaris lumbricoides and A . suum are common large roundworms that inhabit the small intestine in humans and pigs , respectively . Before the worms establish themselves in the small intestine , they first migrate through the host's liver and lungs , causing significant organ damage . After treatment , people and animal...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "ascariasis", "parasitic", "diseases" ]	2013	A Role for Eosinophils in the Intestinal Immunity against Infective Ascaris suum Larvae
Giardia lamblia is a very common cause of gastrointestinal symptoms worldwide . There are several methods for the diagnosis of Giardia infection , however none are ideal . We aim to find a new , microRNA-based method that will improve the currently available diagnostic methods for giardiasis . Deep-sequence profiling o...	Giardiasis is a major cause of diarrheal disease throughout the world . It is more common in areas with poor sanitation such as in many low-income countries , but it occurs in high-income countries as well . It is the most commonly identified intestinal parasite in the United States and it is endemic in other industria...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "trophozoites", "medicine", "and", "health", "sciences", "parasite", "groups", "biopsy", "giardiasis", "giardia", "natural", "antisense", "transcripts", "gene", "regulation", "tropical", "diseases", "rna", "extraction", "parasitic", "diseases", "parasitic", "protozoans", ...	2019	Giardia lamblia miRNAs as a new diagnostic tool for human giardiasis
TGF-β is widely held to be critical for the maintenance and function of regulatory T ( Treg ) cells and thus peripheral tolerance . This is highlighted by constitutive ablation of TGF-β receptor ( TR ) during thymic development in mice , which leads to a lethal autoimmune syndrome . Here we describe that TGF-β–driven p...	TGF-β is a cytokine thought to be critical for the maintenance and function of tolerance in the immune system . In many studies the disruption of TGF-β signalling in CD4+ T cells ( a type of white blood cell that coordinates immune responses ) has resulted in autoimmune syndromes . We show here that the induced removal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	TGF-β Signalling Is Required for CD4+ T Cell Homeostasis But Dispensable for Regulatory T Cell Function
Transcriptional regulation of some genes involved in xenobiotic detoxification and apoptosis is performed via the human pregnane X receptor ( PXR ) which in turn is activated by structurally diverse agonists including steroid hormones . Activation of PXR has the potential to initiate adverse effects , altering drug pha...	Promiscuous proteins generally bind a large array of diverse ligand structures . This may be facilitated by a very large binding site , multiple binding sites , or a flexible binding site that can adjust to the size of the ligand . These aspects also increase the complexity of predicting whether a molecule will bind or...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "biology/small", "molecule", "chemistry", "computational", "biology/metabolic", "networks", "computational", "biology/signaling", "networks", "computational", "biology/systems", "biology", "chemical", "biology/directed", "molecular", "evolution" ]	2009	Challenges Predicting Ligand-Receptor Interactions of Promiscuous Proteins: The Nuclear Receptor PXR
Interactions between early developing Schistosoma mansoni larval stages and the hemolymph of its snail intermediate host represent the first molecular encounter with the snail’s immune system . To gain a more comprehensive understanding of this early parasite-host interaction , biotinylated sporocyst tegumental membran...	Transmission of the human blood fluke Schistosoma mansoni critically depends on the successful establishment of infections within species of its snail intermediate host , Biomphalaria . One of the most important barriers to infection is the host’s innate immune system , comprised of plasma proteins and immunocytes ( he...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "biomphalaria", "immunology", "animals", "parasitology", "magnetic", "resonance", "imaging", "developmental", "biology", "gastropods", "sporocysts", "snails", "research", "and", "analysis",...	2017	Proteomic analysis of Biomphalaria glabrata plasma proteins with binding affinity to those expressed by early developing larval Schistosoma mansoni
An important component of the World Health Organization's comprehensive trachoma elimination strategy is the provision of repeated annual mass azithromycin distributions , which are directed at reducing the burden of ocular chlamydia . Knowledge of characteristics associated with infection after mass antibiotic treatme...	Trachoma , which is the leading infectious cause of blindness worldwide , is caused by repeated ocular infection with Chlamydia trachomatis . Treatment for trachoma includes mass azithromycin treatments to the entire community . The World Health Organization recommends at least 3 rounds of annual mass antibiotic distri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "research", "design", "cross-sectional", "studies", "global", "health", "neglected", "tropical", "diseases", "trachoma" ]	2011	Risk Factors for Ocular Chlamydia after Three Mass Azithromycin Distributions
Genome-wide maps of transcription factor ( TF ) occupancy and regions of open chromatin implicitly contain DNA sequence signals for multiple factors . We present SeqGL , a novel de novo motif discovery algorithm to identify multiple TF sequence signals from ChIP- , DNase- , and ATAC-seq profiles . SeqGL trains a discri...	Transcriptional regulation is the cell’s primary mode of controlling gene expression . Transcription factors ( TFs ) are proteins that recognize and bind specific DNA sequence signals to regulate the expression of target genes . Recent years have seen the rapid development of genome-wide assays to profile the binding l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps
Hendra virus ( HeV ) is a recently emerged severe human pathogen that belongs to the Henipavirus genus within the Paramyxoviridae family . The HeV genome is encapsidated by the nucleoprotein ( N ) within a helical nucleocapsid . Recruitment of the viral polymerase onto the nucleocapsid template relies on the interactio...	The polymerase of negative strand RNA viruses reads the viral RNA that is associated with the nucleoprotein N forming a helical nucleocapsid . The interaction between N and the cofactor of the polymerase , the phosphoprotein P , is essential for transcription and replication of the viral genome . The mechanism by which...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Atomic Resolution Description of the Interaction between the Nucleoprotein and Phosphoprotein of Hendra Virus
Animals can exhibit complex movement patterns that may be the result of interactions with their environment or may be directly the mechanism by which their behaviour is governed . In order to understand the drivers of these patterns we examine the movement behaviour of individual desert locusts in a homogenous experime...	The movement of organisms is an essential feature of life and is fundamental to almost all ecological and evolutionary processes . The motion of animals can have a significant impact on the environment , for example on the distribution of resources , habitat fragmentation or the spread of pests and diseases . Locusts e...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "animal", "behavior", "mathematics", "ecology", "entomology", "statistics", "applied", "mathematics", "biology", "zoology", "neuroscience", "statistical", "methods", "behavioral", "ecology" ]	2012	Intermittent Motion in Desert Locusts: Behavioural Complexity in Simple Environments
To estimate the prevalence of trachoma in the North Region of Cameroon in order to facilitate the planning of trachoma control activities in this region , a survey was carried out in 2011 and 2012 in 15 health districts ( HDs ) . A cross-sectional , two-stage cluster random sampling survey was carried out . The survey ...	Trachoma is the most common infectious cause of blindness . Recurrent episodes of infection with Chlamydia trachomatis cause conjunctival inflammation in children who go on to develop scarring and blindness as adults . The current effort led by the World Health Organization ( WHO ) and the Alliance for Global Eliminati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "ophthalmology", "trachoma" ]	2014	Prevalence of Trachoma in the North Region of Cameroon: Results of a Survey in 15 Health Districts
HIV causes several forms of immune dysfunction that need to be addressed in a functional cure for HIV . Immune exhaustion describes a dysfunctional phenotype caused by chronic cellular activation . Lymphocyte activation gene-3 ( LAG3 ) is one of several negative coreceptors known as immune checkpoints that contribute t...	Antiviral drugs have transformed HIV infection from a death sentence to a manageable disease . However , millions still lack access to these drugs , which require daily adherence . This allows the HIV epidemic to continue , killing a million people each year . The search for a cure has been long , but researchers now h...	[ "Abstract", "Introduction", "LAG3", "expression", "LAG3", "receptors", "LAG3", "mechanism", "LAG3", "function", "on", "cell", "types", "and", "subsets", "LAG3", "and", "HIV", "disease", "Conclusion" ]	[ "blood", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell-mediated", "immunity", "microbiology", "retroviruses", "viruses", "i...	2019	Roles, function and relevance of LAG3 in HIV infection
As a potent CD8+ T cell activator , peptide vaccine has found its way in vaccine development against intracellular infections and cancer , but not against leishmaniasis . The first step toward a peptide vaccine is epitope mapping of different proteins according to the most frequent HLA types in a population . Six Leish...	Leishmaniasis is currently a serious health as well as economic problem in underdeveloped and developing countries in Africa , Asia , the Near and Middle East , Central and South America and the Mediterranean region . Cutaneous leishmaniasis is highly endemic in Iran , remarkably in Isfahan , Fars , Khorasan , Khozesta...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "leishmaniasis", "neglected", "tropical", "diseases", "immunology", "immune", "response" ]	2011	In Silico Analysis of Six Known Leishmania major Antigens and In Vitro Evaluation of Specific Epitopes Eliciting HLA-A2 Restricted CD8 T Cell Response

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