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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Direct and referral patients with leprosy reactions were interviewed in two of Nepal's leprosy hospitals . We also collected quantitative and qualitative data from clinical examination and case-note review to document the patient pathway . Seventy-five patients were interviewed . On development of reaction symptoms 39%...	The global strategy for leprosy has moved patient care to general health services with the aim of improving access to treatment . We suspected that leprosy patients with a common complication , leprosy reactions , are not being diagnosed and treated promptly in integrated services . Leprosy reactions cause nerve damage...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "leprosy" ]	2013	Diagnosis and Treatment of Leprosy Reactions in Integrated Services - The Patients' Perspective in Nepal
HIV-infected individuals may experience fever episodes . Fever is an elevation of the body temperature accompanied by inflammation . It is usually beneficial for the host through enhancement of immunological defenses . In cultures , transient non-physiological heat shock ( 42–45°C ) and Heat Shock Proteins ( HSPs ) mod...	Fever is a complex reaction triggered in response to pathogen infection . It induces diverse effects on the human body and especially on the immune system . The functions of immune cells are positively affected by fever , helping them to fight infection . Fever consists in a physiological elevation of temperature and i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "virology", "hiv", "biology", "microbiology", "viral", "diseases" ]	2012	Hyperthermia Stimulates HIV-1 Replication
E2 ubiquitin-conjugating enzymes are crucial mediators of protein ubiquitination , which strongly influence the ultimate fate of the target substrates . Recently , it has been shown that the activity of several enzymes of the ubiquitination pathway is finely tuned by phosphorylation , an ubiquitous mechanism for cellul...	A major mechanism for promoting protein regulation in eukaryotes involves the labeling with ubiquitin molecules of target proteins . Protein ubiquitination is involved in almost all aspects of eukaryotic cellular functions and is mediated , at the molecular level , by a hierarchical cascade of three different enzymes ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biochemical", "simulations", "biochemistry", "simulations", "biophysic", "al", "simulations", "enzymes", "enzyme", "regulation", "biology", "computational", "biology" ]	2011	An Acidic Loop and Cognate Phosphorylation Sites Define a Molecular Switch That Modulates Ubiquitin Charging Activity in Cdc34-Like Enzymes
In Africa , relapsing fever borreliae are neglected vector-borne pathogens that cause mild to deadly septicemia and miscarriage . Screening vectors for the presence of borreliae currently requires technically demanding , time- and resource-consuming molecular methods . Matrix-assisted laser desorption/ionization time-o...	In Africa , relapsing fever borreliae are neglected vector-borne infections that cause mild to deadly septicemia and miscarriage . The causative relapsing fever borreliae are transmitted by the bite of soft ticks , except for Borrelia recurrentis which is transmitted by body lice . Screening vectors for these relapsing...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "bacterial", "pathogens" ]	2014	MALDI-TOF Mass Spectrometry Detection of Pathogens in Vectors: The Borrelia crocidurae/Ornithodoros sonrai Paradigm
Recent studies demonstrated a strong influence of rare genetic variants on several lipid-related traits . However , their impact on free fatty acid ( FFA ) plasma concentrations , as well as the role of rare variants in a general population , has not yet been thoroughly addressed . The adipose triglyceride lipase ( ATG...	The nature of the genetic variation underlying common traits is not yet completely understood . Recently , there has been a shift in the genetic research focus towards the elucidation of the influence of rare variants , which are thought to exert a strong impact on common traits . Circulating free fatty acids are immed...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/functional", "genomics" ]	2010	Investigation and Functional Characterization of Rare Genetic Variants in the Adipose Triglyceride Lipase in a Large Healthy Working Population
The Influenza A virus genome consists of eight negative sense , single-stranded RNA segments . Although it has been established that most virus particles contain a single copy of each of the eight viral RNAs , the packaging selection mechanism remains poorly understood . Influenza viral RNAs are synthesized in the nucl...	Influenza A viruses cause one of the major respiratory infection diseases in humans . The viruses possess a genome consists of eight different RNA segments and the incorporation of all the eight RNA segments is required for the generation of an infectious virus particle . The precise process of how these eight viral RN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "virology", "viral", "structure", "biology", "microbiology", "viral", "packaging", "viral", "replication", "viral", "nucleic", "acid" ]	2013	Colocalization of Different Influenza Viral RNA Segments in the Cytoplasm before Viral Budding as Shown by Single-molecule Sensitivity FISH Analysis
The liver X receptors ( LXRs ) are a family of nuclear receptor transcription factors that are activated by oxysterols and have defined roles in both lipid metabolism and cholesterol regulation . LXRs also affect antimicrobial responses and have anti-inflammatory effects in macrophages . As mice lacking LXRs are more s...	Leishmania spp . are protozoan single-cell parasites that are transmitted to humans by the bite of an infected sand fly , and can cause a wide spectrum of disease , ranging from self-healing skin lesions to potentially fatal systemic infections . Certain species of Leishmania that cause visceral ( systemic ) disease ar...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases", "microbiology/immunity", "to", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/innate", "immunity", "immunology/innate", "immunity", "immunology", "micr...	2010	LXR Deficiency Confers Increased Protection against Visceral Leishmania Infection in Mice
Coxiella burnetii , the causative agent of human Q fever , is an intracellular pathogen that replicates in an acidified vacuole derived from the host lysosomal network . This pathogen encodes a Dot/Icm type IV secretion system that delivers bacterial proteins called effectors to the host cytosol . To identify new effec...	Coxiella burnetii is a Gram-negative intracellular bacterium that can cause the human disease Q fever . A type IV secretion system in C . burnetii called Dot/Icm is functionally similar to the Dot/Icm system of Legionella pneumophila . Here we used L . pneumophila to screen a C . burnetii library for genes encoding eff...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbial", "evolution", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction" ]	2011	The Coxiella burnetii Dot/Icm System Delivers a Unique Repertoire of Type IV Effectors into Host Cells and Is Required for Intracellular Replication
Animal studies generate valuable hypotheses that lead to the conduct of preventive or therapeutic clinical trials . We assessed whether there is evidence for excess statistical significance in results of animal studies on neurological disorders , suggesting biases . We used data from meta-analyses of interventions depo...	Studies have shown that the results of animal biomedical experiments fail to translate into human clinical trials; this could be attributed either to real differences in the underlying biology between humans and animals , to shortcomings in the experimental design , or to bias in the reporting of results from the anima...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "spinal", "cord", "diseases", "clinical", "epidemiology", "epidemiology", "neurology", "parkinson", "disease", "dementia" ]	2013	Evaluation of Excess Significance Bias in Animal Studies of Neurological Diseases
Hotspots of meiotic recombination can change rapidly over time . This instability and the reported high level of inter-individual variation in meiotic recombination puts in question the accuracy of the calculated hotspot map , which is based on the summation of past genetic crossovers . To estimate the accuracy of the ...	In eukaryotes genetic crossovers are responsible for generating genetic diversity and ensuring the proper segregation of chromosomes . Genetic crossovers are tightly clustered in hotspots . Although the existence of hotspots in humans is clearly proven , mechanisms of their formation and the regulation of meiotic recom...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/recombination", "genetics", "and", "genomics/chromosome", "biology", "evolutionary", "biology/genomics", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/population", "genetics" ]	2010	Genetic Crossovers Are Predicted Accurately by the Computed Human Recombination Map
Oseltamivir ( Tamiflu ) is currently the frontline antiviral drug employed to fight the flu virus in infected individuals by inhibiting neuraminidase , a flu protein responsible for the release of newly synthesized virions . However , oseltamivir resistance has become a critical problem due to rapid mutation of the flu...	Oseltamivir ( Tamiflu ) is the main antiviral drug used to fight viral influenza outbreaks such as the recent swine flu ( H1N1pdm ) global pandemic and avian ( H5N1 ) outbreak in Asia . Oseltamivir inhibits a protein on the surface of flu viruses called neuraminidase , which is responsible for releasing newly formed vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "biophysics/macromolecular", "assemblies", "and", "machines", "infectious", "diseases", "biophysics/theory", "and", "simulation", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/ant...	2010	Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases
Parental genomic imprinting causes preferential expression of one of the two parental alleles . In mammals , differential sex-dependent deposition of silencing DNA methylation marks during gametogenesis initiates a new cycle of imprinting . Parental genomic imprinting has been detected in plants and relies on DNA methy...	Imprinting in plants and mammals involves a process whereby one of the two inherited gene variants ( alleles ) is inactivated . During imprinting , the transcriptional silencing of one allele is mediated by histone modifications or DNA methylation . The expressed parental allele is activated during gametogenesis by poo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "plant", "biology" ]	2008	Retinoblastoma and Its Binding Partner MSI1 Control Imprinting in Arabidopsis
Overnutrition caused by overeating is associated with insulin and leptin resistance through IKKβ activation and endoplasmic reticulum ( ER ) stress in the hypothalamus . Here we show that physical exercise suppresses hyperphagia and associated hypothalamic IKKβ/NF-κB activation by a mechanism dependent upon the pro-inf...	The hypothalamus is a brain region that gathers information on the body's nutritional status and governs the release of multiple metabolic signaling molecules such as insulin and leptin to maintain homeostasis . Overeating and obesity are associated with insulin and leptin resistance in the hypothalamus , and recent st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physiology/neuronal", "signaling", "mechanisms", "diabetes", "and", "endocrinology/obesity" ]	2010	IL-6 and IL-10 Anti-Inflammatory Activity Links Exercise to Hypothalamic Insulin and Leptin Sensitivity through IKKβ and ER Stress Inhibition
IFNγ signaling drives dendritic cells ( DCs ) to promote type I T cell ( Th1 ) immunity . Here , we show that activation of DCs by IFNγ is equally crucial for the differentiation of a population of T-bet+ regulatory T ( Treg ) cells specialized to inhibit Th1 immune responses . Conditional deletion of IFNγ receptor in ...	In order to mount a protective response against numerous and enormously diverse microbial pathogens , T cells are able to differentiate into functionally distinct helper T ( Th ) subsets . To control different types of T cell immunity in a given inflammatory setting , regulatory T ( Treg ) cells have emerged as a dedic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	IFNγ Signaling Endows DCs with the Capacity to Control Type I Inflammation during Parasitic Infection through Promoting T-bet+ Regulatory T Cells
Microbial biotransformations have a major impact on contamination by toxic elements , which threatens public health in developing and industrial countries . Finding a means of preserving natural environments—including ground and surface waters—from arsenic constitutes a major challenge facing modern society . Although ...	Microorganisms play a crucial role in nutrient biogeochemical cycles . Arsenic is found throughout the environment from both natural and anthropogenic sources . Its inorganic forms are highly toxic and impair the physiology of most higher organisms . Arsenic contamination of groundwater supplies is giving rise to incre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "archaea", "ecology", "microbiology", "computational", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	A Tale of Two Oxidation States: Bacterial Colonization of Arsenic-Rich Environments
Virus-host interactions are frequently studied in bulk cell populations , obscuring cell-to-cell variation . Here we investigate endogenous herpesvirus gene expression at the single-cell level , combining a sensitive and robust fluorescent in situ hybridization platform with multiparameter flow cytometry , to study the...	The gammaherpesviruses are a group of DNA tumor viruses that establish lifelong infection . How these viruses infect and manipulate cells has frequently been studied in bulk populations of cells . While these studies have been incredibly insightful , there is limited understanding of how virus infection proceeds within...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "microbiology", "fibroblasts", "organisms", "viruses", "rna", "viruses", "connective", "tissue", "cells", "microbial", "genetics", "research", "and", "anal...	2019	Multidimensional analysis of Gammaherpesvirus RNA expression reveals unexpected heterogeneity of gene expression
Fundamental to the function of nervous systems is the ability to reorganize to cope with changing sensory input . Although well-studied in single neurons , how such adaptive versatility manifests in the collective population dynamics and function of cerebral cortex remains unknown . Here we measured population neural a...	The cerebral cortex is versatile; depending on changes in behavioral context , the same neural circuit can exhibit dramatically different neural activity and perform different functions . A long-standing hypothesis at the interface of physics and neuroscience posits that such shifts in cortical operation are governed b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "nervous", "system", "population", "dynamics", "membrane", "potential", "brain", "vertebrates", "social", "sciences", "electrophysiology", "neuroscience", "animals", "testudines", "reptiles", "cognition", "v...	2017	Adaptation towards scale-free dynamics improves cortical stimulus discrimination at the cost of reduced detection
The fungus Cryptococcus is a major cause of meningoencephalitis in HIV-infected as well as HIV-uninfected individuals with mortalities in developed countries of 20% and 30% , respectively . In HIV-related disease , defects in T-cell immunity are paramount , whereas there is little understanding of mechanisms of suscept...	Cryptococcus is an important cause of fungal meningitis with significant mortality globally . Susceptibility to the fungus in humans has been related to T-lymphocyte defects in HIV-infected individuals , but little is known about possible immune defects in non HIV-infected patients including previously healthy individu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Paradoxical Immune Responses in Non-HIV Cryptococcal Meningitis
Chagas disease caused by Trypanosoma cruzi is a complex disease that is endemic and an important problem in public health in Latin America . The T . cruzi parasite is classified into six discrete taxonomic units ( DTUs ) based on the recently proposed nomenclature ( TcI , TcII , TcIII , TcIV , TcV and TcVI ) . The disc...	Trypanosoma cruzi the aetiological agent of Chagas disease infects over 8 million people in Latin America . Currently , six genetic groups or DTUs have been identified in this highly genetic and diverse parasite . Many authors have considered that disease installation is induced by this genetic variability in T . cruzi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/parasitology" ]	2010	Chagas Cardiomyopathy Manifestations and Trypanosoma cruzi Genotypes Circulating in Chronic Chagasic Patients
Classical Marr-Albus theories of cerebellar learning employ only cortical sites of plasticity . However , tests of these theories using adaptive calibration of the vestibulo–ocular reflex ( VOR ) have indicated plasticity in both cerebellar cortex and the brainstem . To resolve this long-standing conflict , we attempte...	Our ability to learn skilled movements depends crucially on the cerebellum , hence understanding cerebellar plasticity is central to theories of motor learning . The adaptation of the vestibulo-ocular reflex ( VOR ) is often used to test these theories . This reflex stabilizes the retinal image by moving the eyes to co...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "primates", "physiology", "computational", "biology", "neuroscience", "mammals" ]	2007	Cerebellar Motor Learning: When Is Cortical Plasticity Not Enough?
West Nile virus ( WNV ) is a re-emerging pathogen that can cause fatal encephalitis . In mice , susceptibility to WNV has been reported to result from a single point mutation in oas1b , which encodes 2′–5′ oligoadenylate synthetase 1b , a member of the type I interferon-regulated OAS gene family involved in viral RNA d...	When humans are exposed to infectious agents , the outcome may vary: some remain uninfected , some who become infected remain asymptomatic , and symptomatic individuals may develop clinical manifestations that vary in number and severity . Both host and environmental factors are thought to influence outcome . Here we s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "virology/host", "antiviral", "responses", "immunology/innate", "immunity" ]	2009	Genetic Variation in OAS1 Is a Risk Factor for Initial Infection with West Nile Virus in Man
Complex cognition and relatively large brains are distributed across various taxa , and many primarily verbal hypotheses exist to explain such diversity . Yet , mathematical approaches formalizing verbal hypotheses would help deepen the understanding of brain and cognition evolution . With this aim , we combine element...	Complex cognition and relatively large brains occur in a diversity of mammal , bird , and fish species among others , and there is a large number of mostly verbal hypotheses to explain what causes their evolution in certain species but not others . However , these hypotheses have scarcely exploited the power of formula...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "learning", "urology", "medicine", "and", "health", "sciences", "social", "sciences", "mathematical", "models", "neuroscience", "learning", "and", "memory", "age", "groups", "developmental", "biology", "adults", "cognitive", "psychology", "cognition", "memory", "bioener...	2017	A model for brain life history evolution
Sodalis glossinidius , a maternally inherited endosymbiont of the tsetse fly , maintains genes encoding homologues of the PhoP-PhoQ two-component regulatory system . This two-component system has been extensively studied in facultative bacterial pathogens and is known to serve as an environmental magnesium sensor and a...	Mutualistic insect endosymbionts are known to undergo a process of degenerative evolution that streamlines their gene inventory in accordance with the obligate nature of the host associated lifestyle . Here we show that the mutualistic insect endosymbiont Sodalis glossinidius utilizes a two-component regulatory system ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "applied", "microbiology", "microbial", "evolution", "gene", "expression", "genetics", "molecular", "genetics", "biology", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics", "gene", "function" ]	2011	Attenuation of the Sensing Capabilities of PhoQ in Transition to Obligate Insect–Bacterial Association
Many models of classical conditioning fail to describe important phenomena , notably the rapid return of fear after extinction . To address this shortfall , evidence converged on the idea that learning agents rely on latent-state inferences , i . e . an ability to index disparate associations from cues to rewards ( or ...	Computational researchers are increasingly interested in a structured form of learning known as latent-state inferences . Latent-state inferences is a type of learning that involves categorizing , generalizing , and recalling disparate associations between observations in one’s environment and is used in situations whe...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "markov", "models", "classical", "conditioning", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "experimental", "psychology", "fear", "cognitive", "psychology", "mathematics", "cognition", "memory", "researc...	2019	A flexible and generalizable model of online latent-state learning
The discovery and analysis of cis-regulatory modules ( CRMs ) in metazoan genomes is crucial for understanding the transcriptional control of development and many other biological processes . Cross-species sequence comparison holds much promise for improving computational prediction of CRMs , for elucidating their bind...	Interspecies comparison of regulatory sequences is a major focus in the bioinformatics community today . There is extensive ongoing effort toward measuring the extent and patterns of binding site turnover in cis-regulatory modules . A major roadblock in such an analysis has been the fact that traditional alignment meth...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "drosophila", "computational", "biology" ]	2007	MORPH: Probabilistic Alignment Combined with Hidden Markov Models of cis-Regulatory Modules
Netherton Syndrome ( NS ) is a rare and severe autosomal recessive skin disease which can be life-threatening in infants . The disease is characterized by extensive skin desquamation , inflammation , allergic manifestations and hair shaft defects . NS is caused by loss-of-function mutations in SPINK5 encoding the LEKTI...	Netherton Syndrome ( NS ) is a severe form of ichthyosis characterized by desquamation , inflammation and multiple allergies , which can be life-threatening in infants . NS is caused by loss-of-function mutations in SPINK5 encoding the LEKTI serine protease inhibitor . Current treatment options for this orphan disease ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	KLK5 Inactivation Reverses Cutaneous Hallmarks of Netherton Syndrome
The enteric bacterial pathogen Salmonella enterica serovar Typhimurium ( S . Typhimurium ) , utilizes two type III secretion systems ( T3SSs ) to invade host cells , survive and replicate intracellularly . T3SS1 and its dedicated effector proteins are required for bacterial entry into non-phagocytic cells and establish...	Pathogenic bacteria that adopt an intracellular lifestyle must create a specialized niche that supports their replication while avoiding detection and killing by the host . The foodborne pathogen , S . Typhimurium , invades epithelial cells lining the intestine and establishes residence within a host-derived membrane-b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "vacuoles", "viral", "transmission", "and", "infection", "hela", "cells", "pathogens", "biological", "cultures", "microbiology", "light", "microscopy", "bacterial", "diseases", "fungi...	2019	SopF, a phosphoinositide binding effector, promotes the stability of the nascent Salmonella-containing vacuole
During the last decade , French Guiana has been affected by major dengue fever outbreaks . Although this arbovirus has been a focus of many awareness campaigns , very little information is available about beliefs , attitudes and behaviors regarding vector-borne diseases among the population of French Guiana . During th...	Although dengue fever has been a focus of many awareness campaigns in Latin America , very little information is available about beliefs , attitudes and behaviors regarding vector-borne diseases among the population of French Guiana . At the initial onset of the first chikungunya outbreak , a quantitative survey was co...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "chikungunya", "infection", "togaviruses", "pathogens", "sociology", "tropical", "diseases", "vector-borne", "diseases", "social", "sciences", "microbiology"...	2016	Knowledge, Attitude and Practices of Vector-Borne Disease Prevention during the Emergence of a New Arbovirus: Implications for the Control of Chikungunya Virus in French Guiana
How splicing factors are recruited to nascent transcripts in the nucleus in order to assemble spliceosomes on newly synthesised pre-mRNAs is unknown . To address this question , we compared the intranuclear trafficking kinetics of small nuclear ribonucleoprotein particles ( snRNP ) and non-snRNP proteins in the presenc...	Understanding the genomic program of an organism requires knowledge of how the information encoded in DNA is processed to generate messenger RNAs that can be translated into proteins . The initial products of gene transcription are extensively modified in the cell nucleus , and a major processing reaction consists of s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "homo", "(human)", "molecular", "biology", "computational", "biology" ]	2007	A Stochastic View of Spliceosome Assembly and Recycling in the Nucleus
In-silico identification of potential target genes for disease is an essential aspect of drug target discovery . Recent studies suggest that successful targets can be found through by leveraging genetic , genomic and protein interaction information . Here , we systematically tested the ability of 12 varied algorithms ,...	The use of biological network data has proven its effectiveness in many areas from computational biology . Networks consist of nodes , usually genes or proteins , and edges that connect pairs of nodes , representing information such as physical interactions , regulatory roles or co-occurrence . In order to find new can...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "machine", "learning", "algorithms", "medicine", "and", "health", "sciences", "genetic", "networks", "applied", "mathematics", "simulation", "and", "modeling", "algorithms", "mathematics", "artificial", "intelligence", "network", "analysis", "genome", "analysis", "pharmac...	2019	Benchmarking network propagation methods for disease gene identification
The developmental transition from a vegetative to a reproductive phase ( i . e . , flowering ) is timed by the seasonal cue day length or photoperiod in many plant species . Through the photoperiod pathway , inductive day lengths trigger the production of a systemic flowering signal , florigen , to provoke the floral t...	The timing of the developmental transition from a vegetative to a reproductive phase is critically important for reproductive success in flowering plants . Plants synchronize the timing of their floral transition with the changing seasons to flower at a suitable time . The change in day length , or photoperiod , is a k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "growth", "and", "development", "genetics", "plant", "genetics", "epigenetics", "biology", "histone", "modification" ]	2013	Photoperiodic Regulation of Flowering Time through Periodic Histone Deacetylation of the Florigen Gene FT
It has been hypothesized that neural activities in the primary visual cortex ( V1 ) represent a saliency map of the visual field to exogenously guide attention . This hypothesis has so far provided only qualitative predictions and their confirmations . We report this hypothesis’ first quantitative prediction , derived ...	It has been hypothesized that neural activities in the primary visual cortex represent a saliency map of the visual field to exogenously guide attention . This hypothesis has so far provided only qualitative predictions and their confirmations . We report this hypothesis’ first quantitative prediction , derived without...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Primary Visual Cortex as a Saliency Map: A Parameter-Free Prediction and Its Test by Behavioral Data
Sleep plays an important role in the consolidation of recent memories . However , the cellular and synaptic mechanisms of consolidation during sleep remain poorly understood . In this study , using a realistic computational model of the thalamocortical network , we tested the role of Non-Rapid Eye Movement ( NREM ) sle...	We spend a third of our lives sleeping . During sleep , human and animal brains are decoupled from the external sensory input , however , brain activity remains high and varies across sleep stages . It is believed that one of the important sleep functions is the consolidation of recent memories to organize them for lon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "learning", "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "sleep", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "physiological", "processes", "cognitive", "psychol...	2018	Differential roles of sleep spindles and sleep slow oscillations in memory consolidation
A . aegypti production and human density may vary considerably in dengue endemic areas . Understanding how interactions between these factors influence the risk of transmission could improve the effectiveness of the allocation of vector control resources . To evaluate the combined impacts of variation in A . aegypti pr...	In the urban dengue system the life history of the mosquito vector , Aedes aegypti , transpires mainly inside and around human residences . In this study we integrated field data from an endemic city of Colombia into a simulation model to assess how natural variation in A . aegypti production and household human densit...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "social", "and", "behavioral", "sciences", "infectious", "disease", "epidemiology", "demography", "sociology", "population", "modeling", "neglected", "tropical", "diseases", "population", "biology", "infectious", "dis...	2012	The Interactive Roles of Aedes aegypti Super-Production and Human Density in Dengue Transmission
Activation of CD4+ T cells requires the recognition of peptides that are presented by HLA class II molecules and can be assessed experimentally using the ELISpot assay . However , even given an individual’s HLA class II genotype , identifying which class II molecule is responsible for a positive ELISpot response to a g...	When studying the host immune response , a central question is: “which peptides elicit CD4+ T cell responses ? ” ELISpot assays are used to assess if subjects have responded to a given peptide . However , to determine which of the HLA-II molecules coded by the host HLA genotype is responsible for the reaction requires ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "animal", "models", "immunodefic...	2016	BIITE: A Tool to Determine HLA Class II Epitopes from T Cell ELISpot Data
While the neurobiology of simple and habitual choices is relatively well known , our current understanding of goal-directed choices and planning in the brain is still limited . Theoretical work suggests that goal-directed computations can be productively associated to model-based ( reinforcement learning ) computations...	Computational reinforcement learning theories have contributed to advance our understanding of how the brain implements decisions—and especially simple and habitual choices . However , our current understanding of the neural and computational principles of complex and flexible ( goal-directed ) choices is comparatively...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "decision", "making", "nervous", "system", "brain", "social", "sciences", "vertebrates", "neuroscience", "learning", "and", "memory", "animals", "mammals", "simulation", "and", "modeling", "cognitive", "psychology", ...	2018	Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis
Highly pathogenic avian influenza ( HPAI ) viruses of the H5N1 subtype often cause severe pneumonia and multiple organ failure in humans , with reported case fatality rates of more than 60% . To develop a clinical antibody therapy , we generated a human-mouse chimeric monoclonal antibody ( MAb ) ch61 that showed strong...	The H5N1 highly pathogenic avian influenza virus has been circulating in poultry in Asia , the Middle East , and Africa since its first appearance in southern China in 1996 . This virus occasionally infects humans with a high case mortality rate and poses a significant pandemic threat . Since neutralizing antibodies ge...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "microbiology", "vertebrates", "orthomyxoviruses", "animals", "mammals", "primates", "animal", "models", "model", "organisms", "antibodies", "veterinary", "science", "immunotherapy",...	2014	Protective Efficacy of Passive Immunization with Monoclonal Antibodies in Animal Models of H5N1 Highly Pathogenic Avian Influenza Virus Infection
One of the most powerful techniques for studying the function of a gene is to disrupt the expression of that gene using genetic engineering strategies such as targeted recombination or viral integration of gene trap cassettes . The tremendous utility of these tools was recognized this year with the awarding of the Nobe...	To determine the function of a gene , it is often informative to first disrupt the expression of that gene through targeted recombination or the insertion of gene trap cassettes . In our study , we point out that these approaches may be confounded by the presence of small non-coding elements known as microRNAs . MicroR...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "vertebrates", "plants", "eukaryotes", "computational", "biology" ]	2008	Unintentional miRNA Ablation Is a Risk Factor in Gene Knockout Studies: A Short Report
Cellulose represents the most abundant biopolymer in nature and has great economic importance . Cellulose chains pack laterally into crystalline forms , stacking into a complicated crystallographic structure . However , the mechanism of cellulose crystallization is poorly understood . Here , via functional characteriza...	Cellulose is an important natural resource with great economic value . Plant cellulose packs laterally into a complicated crystallographic structure , which determines cellulose quality and commercial uses . However , the mechanism of cellulose crystallization is poorly understood . Here we report that Brittle Culm1 ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "cell", "biology", "plant", "cell", "wall", "biology", "molecular", "cell", "biology" ]	2013	Brittle Culm1, a COBRA-Like Protein, Functions in Cellulose Assembly through Binding Cellulose Microfibrils
Gene expression of DNA viruses requires nuclear import of the viral genome . Human Adenoviruses ( Ads ) , like most DNA viruses , encode factors within early transcription units promoting their own gene expression and counteracting cellular antiviral defense mechanisms . The cellular transcriptional repressor Daxx prev...	To initiate infection , DNA viruses deliver their genome to the nucleus and express viral genes required for genome replication . Efficient transport is achieved by packing the viral genome as a condensed , transcriptionally inactive nucleo-protein complex . However , for most DNA viruses , including Adenoviruses ( Ads...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "transmission", "and", "infection", "virology", "biology", "microbiology", "viral", "replication" ]	2012	Transcriptional Activation of the Adenoviral Genome Is Mediated by Capsid Protein VI
Profound knowledge of demographic history is a prerequisite for the understanding and inference of processes involved in the evolution of population differentiation and speciation . Together with new coalescent-based methods , the recent availability of genome-wide data enables investigation of differentiation and dive...	Demographic processes leave specific and detectable signatures within species genomes . Analysis of patterns of variation within and between closely related species can be used to unravel their divergence history and is crucial for understanding evolutionary processes such as speciation . We applied a set of novel popu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Demographic Divergence History of Pied Flycatcher and Collared Flycatcher Inferred from Whole-Genome Re-sequencing Data
Advances in neuronal recording techniques are leading to ever larger numbers of simultaneously monitored neurons . This poses the important analytical challenge of how to capture compactly all sensory information that neural population codes carry in their spatial dimension ( differences in stimulus tuning across neuro...	The ever growing size of neural populations simultaneously recorded in electrophysiological experiments calls for urgent analytical progress in understanding how to compactly describe all sensory information present both in the spatial and temporal structure of single-trial neural population activity . Here we show the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "ocular", "anatomy", "computational", "biology", "social", "sciences", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "ganglion", "cells", "computational", "ne...	2016	Using Matrix and Tensor Factorizations for the Single-Trial Analysis of Population Spike Trains
Type III secretion systems ( T3SS ) are central virulence factors for many pathogenic Gram-negative bacteria , and secreted T3SS effectors can block key aspects of host cell signaling . To counter this , innate immune responses can also sense some T3SS components to initiate anti-bacterial mechanisms . The Yersinia pes...	Many pathogenic Gram-negative bacteria express type III secretion systems ( T3SS ) that translocate bacterial proteins into host cells with the potential of altering normal cell processes . Yersinia pestis , the causative agent of plague , harbors a T3SS which is particularly effective in suppressing innate immunity an...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "cell", "death", "innate", "immune", "system", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "immunology", "cell", "processes", "microbiology", "enzymology", "secretion", "systems", "yersin...	2016	The Yersinia pestis Effector YopM Inhibits Pyrin Inflammasome Activation
Lignocellulosic biomass can be a significant source of renewable clean energy with continued improvement in biomass yield and bioconversion strategies . In higher plants , the leaf blade is the central energy convertor where solar energy and CO2 are assimilated to make the building blocks for biomass production . Here ...	The leaf blade of higher plants serves as a solar panel in which it captures solar energy and carbon dioxide to produce chemical energy in the process of photosynthesis . Thus , the ultimate source of food and feed for most heterotrophic organisms , including humans , comes from the photosynthetic activity of leaves . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "engineering", "and", "technology", "bioenergy", "cell", "processes", "hormones", "plant", "science", "rice", "plant", "hormones", "genetically", "modified", "plants", "experimental", "organism", "systems", "plants", "genetic", "engi...	2017	Overexpression of the WOX gene STENOFOLIA improves biomass yield and sugar release in transgenic grasses and display altered cytokinin homeostasis
Insulin and insulin-like growth factor signaling ( IIS ) regulates cell death , repair , autophagy , and renewal in response to stress , damage , and pathogen challenge . Therefore , IIS is fundamental to lifespan and disease resistance . Previously , we showed that insulin-like growth factor 1 ( IGF1 ) within a physio...	The complexity of the malaria parasite life cycle makes it an elusive target for drug and vaccine development . Thus , targeting the parasite in the mosquito vector is an attractive alternative . When consuming an infective blood meal the mosquito ingests not only the blood proteins and parasites , but a range of host ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "innate", "immune", "system", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cell", "processes", "immunology", "microbiology", "plasmodium", "falciparum", "parasitic", "diseases",...	2014	Human IGF1 Regulates Midgut Oxidative Stress and Epithelial Homeostasis to Balance Lifespan and Plasmodium falciparum resistance in Anopheles stephensi
Through national efforts and regional cooperation under the umbrella of the Regional Program for the Elimination of Rabies , dog and human rabies have decreased significantly in Latin America and Caribbean ( LAC ) countries over the last three decades . To achieve this decline , LAC countries had to develop national pl...	Globally , dog-mediated rabies kills over 55 , 000 people on an annual basis and disproportionally affects socio-economically disadvantaged populations . For over 4 decades , the Latin America and Caribbean ( LAC ) region have worked towards the elimination of dog-mediated rabies succeeding in a substantial reduction o...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "geographical", "locations", "dogs", "animals", "mammals", "vaccines", "preventive", "medicine", "virus...	2018	Rabies in the Americas: 1998-2014
Neurogenesis is a key developmental event through which neurons are generated from neural stem/progenitor cells . Chromatin remodeling BAF ( mSWI/SNF ) complexes have been reported to play essential roles in the neurogenesis of the central nervous system . However , whether BAF complexes are required for neuron generat...	The stepwise differentiation of oNSCs to immature and mature ORNs is driven by a defined set of transcription factors . Yet , how these transcription factors act in concert with epigenetic and chromatin-remodeling cofactors to orchestrate OE neurogenesis is unknown . In this study , we identified subunits of chromatin-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurogenesis", "neuronal", "differentiation", "neuroscience", "cell", "differentiation", "developmental", "biology", "nerve", "fibers", "embryos", "immunologic", "techniques", "research", "and", "analysis", "methods", "embryology", "developmental", "neuroscience", "animal", ...	2016	mSWI/SNF (BAF) Complexes Are Indispensable for the Neurogenesis and Development of Embryonic Olfactory Epithelium
Although Toll-like receptor ( TLR ) 4 signals from the cell surface of myeloid cells , it is restricted to an intracellular compartment and requires ligand internalization in intestinal epithelial cells ( IECs ) . Yet , the functional consequence of cell-type specific receptor localization and uptake-dependent lipopoly...	The mammalian host recognizes infection by the detection of particular microbial structures . Recognition of these structures leads to activation of host defense effector mechanisms that in turn combat infection . A very potent activating microbial structure is lipopolysaccharide , a cell wall component released by man...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "immunology/innate", "immunity" ]	2009	O-Antigen Delays Lipopolysaccharide Recognition and Impairs Antibacterial Host Defense in Murine Intestinal Epithelial Cells
Tm-22 is a coiled coil-nucleotide binding-leucine rich repeat resistance protein that confers durable extreme resistance against Tomato mosaic virus ( ToMV ) and Tobacco mosaic virus ( TMV ) by recognizing the viral movement protein ( MP ) . Here we report that the Nicotiana benthamiana J-domain MIP1 proteins ( NbMIP1s...	Plant pathogens cause considerable yield losses in many vegetables and crops; therefore , understanding the mechanisms of disease resistance can enable crop improvements and provide substantial economic benefits . Here , we examine the signaling pathways of Tm-22 , a tomato resistance protein that confers resistance to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Type I J-Domain NbMIP1 Proteins Are Required for Both Tobacco Mosaic Virus Infection and Plant Innate Immunity
Pathogenesis of severe fever with thrombocytopenia syndrome ( SFTS ) has not been well described yet . Recent studies indicate that SFTSV could replicate in endothelial cells . Here we performed a case-control study to determine whether endothelial activation/dysfunction occurred in SFTSV infection and to identify the ...	Severe fever with thrombocytopenia syndrome ( SFTS ) is a tick-borne viral disease and first reported in the rural areas of China . Pathogenesis of the disease has not been well described yet . Recent studies indicated that SFTSV replicated in endothelial cells . So , we performed a case-control study to explore whethe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "endothelial", "cells", "immunology", "biomarkers", "epithelial", "cells", "developmental", "biology", "signs", "and...	2017	Endothelial activation and dysfunction in severe fever with thrombocytopenia syndrome
Zeins , the predominent storage proteins in maize endosperm , are encoded by multiple genes and gene families . However , only a few transcriptional factors for zein gene regulation have been functionally characterized . In this study , a MADS-box protein , namely ZmMADS47 , was identified as an Opaque2 ( O2 ) interact...	A newly identified transcription factor of seed storage proteins can engage its transactivation ability after interacting with another seed storage protein transcription factor in maize .	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "plant", "anatomy", "rna", "interference", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "endosperm", "cereal", "crops", "plant", "science", "model", "organisms", "transcription", "factors", "crops", "sequence", "...	2016	ZmMADS47 Regulates Zein Gene Transcription through Interaction with Opaque2
Giardia lamblia is a parasitic protozoan that infects a wide range of vertebrate hosts including humans . Trophozoites are non-invasive but associate tightly with the enterocyte surface of the small intestine . This narrow ecological specialization entailed extensive morphological and functional adaptations during host...	In canonical clathrin mediated endocytosis ( CME ) models , the concerted action of ca . 50 proteins mediates the uptake of extracellular components . The key player in this process is clathrin which coats transport intermediates called clathrin coated vesicles ( CCV ) . The intestinal parasite Giardia lamblia has unde...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "trophozoites", "parasite", "groups", "giardia", "light", "microscopy", "parasitic", "protozoans", "parasitology", "membrane", "proteins", "apicomplexa", "protozoans", "microscopy", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "...	2016	Static Clathrin Assemblies at the Peripheral Vacuole—Plasma Membrane Interface of the Parasitic Protozoan Giardia lamblia
Drosophila clock neurons are self-sustaining cellular oscillators that rely on negative transcriptional feedback to keep circadian time . Proper regulation of organismal rhythms of physiology and behavior requires coordination of the oscillations of individual clock neurons within the circadian control network . Over t...	The regulation of the daily fluctuations that characterize an organism's physiology and behavior requires coordination of the cellular oscillations of individual “clock” neurons within the circadian control network . Clock neurons that secrete a neuropeptide called pigment dispersing factor ( PDF ) calibrate , or entra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "physiology" ]	2008	Phase Coupling of a Circadian Neuropeptide With Rest/Activity Rhythms Detected Using a Membrane-Tethered Spider Toxin
Entamoeba histolytica , a protozoan parasite of humans , produces dysenteric diarrhea , intestinal mucosa damage and extraintestinal infection . It has been proposed that the intestinal microbiota composition could be an important regulatory factor of amebic virulence and tissue invasion , particularly if pathogenic ba...	Entamoeba histolytica ameba/bacteria mixed intestinal infections are common in endemic regions of Amebiasis . Recent investigations support the idea that pathogen interplay in these infections may have a role in invasive disease , activating signals that increase intestinal inflammation . We have studied interactions o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "immunology", "microbiology", "host-pathogen", "interaction", "parastic", "protozoans", "emerging", "infectious", "diseases", "gastroenterology", "and", "hepatology", "bacterial", "pathogens", "inflammation", "entamoeba", "histolytica", "biology", "gastrointestinal"...	2013	Toll-like Receptor Signaling Activation by Entamoeba histolytica Induces Beta Defensin 2 in Human Colonic Epithelial Cells: Its Possible Role as an Element of the Innate Immune Response
Legionella pneumophila is the causative agent of Legionnaires’ disease , a potentially fatal lung infection . Alveolar macrophages support intracellular replication of L . pneumophila , however the contributions of other immune cell types to bacterial killing during infection are unclear . Here , we used recently descr...	Legionnaires’ Disease , a leading cause of community-acquired pneumonia resulting in significant morbidity and death , develops after infection with Legionella bacteria that replicate inside specialised sentinel cells of the lung . Although some factors that help combat Legionella infection are known , an overall view ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "signs", "and", "symptoms", "phagocytes", "bacteria", "neutrophils", "bacterial", ...	2016	Cooperation between Monocyte-Derived Cells and Lymphoid Cells in the Acute Response to a Bacterial Lung Pathogen
Complement receptor 3 ( CR3 , CD11b/CD18 ) is a major macrophage phagocytic receptor . The biochemical pathways through which CR3 regulates immunologic responses have not been fully characterized . Francisella tularensis is a remarkably infectious , facultative intracellular pathogen of macrophages that causes tularemi...	The highly virulent Francisella tularensis can cause respiratory disease in humans with less than 10 bacteria . In vivo , it replicates mainly within macrophages . Evasion and/or suppression of the host protective immune response is essential to Francisella's virulence in mammals . However , the detailed molecular mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immunology", "microbiology", "host-pathogen", "interaction", "bacterial", "diseases", "immunoregulation", "immunomodulation", "bacterial", "pathogens", "infectious", "diseases", "microbial", "pathogens", "biology", "immune", "response", "immunity", "innate", "imm...	2013	Fine Tuning Inflammation at the Front Door: Macrophage Complement Receptor 3-mediates Phagocytosis and Immune Suppression for Francisella tularensis
The existence of viral variants that escape from the selection pressures imposed by cytotoxic T-lymphocytes ( CTLs ) in HIV-1 infection is well documented , but it is unclear when they arise , with reported measures of the time to escape in individuals ranging from days to years . A study of participants enrolled in th...	The cytotoxic T-lymphocyte ( CTL ) arm of the immune response is thought to play a significant role in the control of HIV-1 infection . Mutations within the HIV-1 genome allow the virus to escape recognition by CTLs and so evade the immune response . These escape mutations have been well documented but observed waiting...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Structured Observations Reveal Slow HIV-1 CTL Escape
Multiple complexes protect telomeres . In telomerase-maintained organisms , Shelterin related complexes occupy the duplex region while the CST and Tpp1-Pot1 complexes bind the single stranded overhang of telomeres . Drosophila uses a transposon-based mechanism for end protection . We showed that the HOAP-HipHop complex...	Chromosome ends are protected by the telomere structure maintained by the telomerase enzyme in most organisms . The fruit fly Drosophila has fascinated the field as the only major model organism that relies solely on a telomerase-independent mechanism for end protection . The fly model is arguably the best system to re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "invertebrates", "cell", "fusion", "medicine", "and", "health", "sciences", "chromosome", "structure", "and", "function", "diet", "animals", "animal", "models", "telomeres", "mutation", "drosophila", "melanogaster", "model", "organisms", "nutrition...	2016	MTV, an ssDNA Protecting Complex Essential for Transposon-Based Telomere Maintenance in Drosophila
Lipids are key components in the viral life cycle that affect host-pathogen interactions . In this study , we investigated the effect of HCV infection on sphingolipid metabolism , especially on endogenous SM levels , and the relationship between HCV replication and endogenous SM molecular species . We demonstrated that...	One of the key components for hepatitis C virus ( HCV ) propagation is lipids , some of which comprise membranous replication complexes for HCV replication . Research on cofactors that are involved in the formation of the membranous replication complex has advanced steadily; on the other hand , the lipids constituting ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "drugs", "and", "devices", "gastroenterology", "and", "hepatology" ]	2012	Self-Enhancement of Hepatitis C Virus Replication by Promotion of Specific Sphingolipid Biosynthesis
Expansion of a trinucleotide ( CGG ) repeat element within the 5′ untranslated region ( 5′UTR ) of the human FMR1 gene is responsible for a number of heritable disorders operating through distinct pathogenic mechanisms: gene silencing for fragile X syndrome ( >200 CGG ) and RNA toxic gain-of-function for FXTAS ( ∼55–20...	Expansion of a CGG-repeat element within the human FMR1 gene is responsible for multiple human diseases , including fragile X syndrome and fragile X-associated tremor/ataxia syndrome ( FXTAS ) . These diseases occur in separate ranges of repeat length and are characterized by profoundly different molecular mechanisms ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "gene", "function", "mutation", "x-linked", "traits", "dna", "epigenetics", "molecular", "genetics", "gene", "expression", "biochemistry", "rna", "cell", "biology", "nucleic", "acids", "heredity", "sex", "linkage", "genetics", "biology", "and", ...	2014	Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region
The repair of DNA double-strand breaks ( DSBs ) is critical for the maintenance of genomic integrity and viability for all organisms . Mammals have evolved at least two genetically discrete ways to mediate DNA DSB repair: homologous recombination ( HR ) and non-homologous end joining ( NHEJ ) . In mammalian cells , mos...	Humans utilize at least two major pathways to repair DNA double-strand breaks ( DSBs ) : homologous recombination ( HR ) and non-homologous end joining ( NHEJ ) , and there are at least two genetically discrete sub-pathways of NHEJ: classical-NHEJ ( C-NHEJ ) and alternative-NHEJ ( A-NHEJ ) . Since the products generate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "genetics", "and", "genomics/gene", "function", "molecular", "biology/dna", "repair" ]	2010	Ku Regulates the Non-Homologous End Joining Pathway Choice of DNA Double-Strand Break Repair in Human Somatic Cells
Human immunodeficiency virus ( HIV-1 ) is , like most pathogens , under selective pressure to escape the immune system of its host . In particular , HIV-1 can avoid recognition by cytotoxic T lymphocytes ( CTLs ) by altering the binding affinity of viral peptides to human leukocyte antigen ( HLA ) molecules , the role ...	Our immune system can recognize and kill virus-infected cells by distinguishing between self and virus-derived protein fragments , called peptides , displayed on the surface of each cell . One requirement for a successful recognition is that those peptides bind to the human leukocyte antigen ( HLA ) class I molecules ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "immune", "cells", "major", "histocompatibility", "complex", "antigen", "processing", "and", "recognition", "t", "cells", "immunology", "biology", "evolutionary", "biology", "evolutionary", "immunology", "genetics", "and", "genomics" ]	2012	Estimating the Fitness Cost of Escape from HLA Presentation in HIV-1 Protease and Reverse Transcriptase
The relationship between epigenetic marks on chromatin and the regulation of DNA replication is poorly understood . Mutations of the H3K27 methyltransferase genes , ARABIDOPSIS TRITHORAX-RELATED PROTEIN5 ( ATXR5 ) and ATXR6 , result in re-replication ( repeated origin firing within the same cell cycle ) . Here we show ...	Before cell division the genome is required to replicate once to ensure that each daughter cell inherits a full copy of genomic DNA . Eukaryotic DNA is wrapped around histones to form nucleosomes . Chemical modifications of DNA and histones are known to regulate gene expression . There is growing evidence that these mo...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	DNA Methyltransferases Are Required to Induce Heterochromatic Re-Replication in Arabidopsis
Yellow fever ( YF ) virtually disappeared in francophone West African countries as a result of YF mass vaccination campaigns carried out between 1940 and 1953 . However , because of the failure to continue mass vaccination campaigns , a resurgence of the deadly disease in many African countries began in the early 1980s...	This article describes the use of an original modeling approach to assess the risk of yellow fever ( YF ) epidemics . YF is a viral hemorrhagic fever responsible in past centuries for devastating outbreaks . Since the 1930s , a vaccine has been available that protects the individual for at least 10 years , if not for l...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "public", "health", "and", "epidemiology", "infectious", "diseases/neglected", "tropical", "diseases", "mathematics", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infections", "public", "health", "and", "...	2009	Assessment of Yellow Fever Epidemic Risk: An Original Multi-criteria Modeling Approach
Optimization of the types and timing of avoidance behaviors depending on the intensity of a noxious stimulus is essential for survival; however , processing in the central nervous system and its developmental basis are largely unknown . Here , we report that Caenorhabditis elegans preferentially selects one of three di...	For survival , animals exhibit appropriate behaviors depending on the type and strength of a stimulus; however , processing in the central nervous system and its developmental basis are largely unknown . Here , we performed RNA interference screening of 210 transcription factors by observing the avoidance behaviors evo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "nervous", "system", "caenorhabditis", "neuronal", "differentiation", "junctional", "complexes", "electrophysiology", "neuroscience", "animals", "cell", "...	2018	OFF-responses of interneurons optimize avoidance behaviors depending on stimulus strength via electrical synapses
Huntington’s Disease ( HD ) is an autosomal dominant progressive neurodegenerative disorder characterized by cognitive , behavioral and motor dysfunctions . HD is caused by a CAG repeat expansion in exon 1 of the HD gene that is translated into an expanded polyglutamine tract in the encoded protein , huntingtin ( HTT )...	Huntington’s Disease is a genetic disorder characterized by progressive cognitive , behavioral and motor dysfunctions . Usually the first symptoms appear around 40 years of age , and lead to death within 15–20 years after the onset of symptoms . To date there is no cure for Huntington’s Disease , and current therapeuti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "weight", "gain", "body", "weight", "medicine", "and", "health", "sciences", "neurodegenerative", "diseases", "genetic", "diseases", "brain", "vertebrates", "mice", "animals", "mammals", "physiological", "processes", "physiological", "parameters", "homeostasis", "molecula...	2017	Elimination of huntingtin in the adult mouse leads to progressive behavioral deficits, bilateral thalamic calcification, and altered brain iron homeostasis
Two amino acids ( lysine at position 627 or asparagine at position 701 ) in the polymerase subunit PB2 protein are considered critical for the adaptation of avian influenza A viruses to mammals . However , the recently emerged pandemic H1N1 viruses lack these amino acids . Here , we report that a basic amino acid at po...	Influenza viruses that originate from avian species likely have to acquire adapting amino acid changes to replicate efficiently in mammals . Two amino acid changes in the polymerase PB2 protein—a glutamic acid to lysine change at position 627 or an aspartic acid to asparagine change at position 701—are known to allow i...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/viral", "replication", "and", "gene", "regulation", "virology/animal", "models", "of", "infection", "virology", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetic...	2010	Biological and Structural Characterization of a Host-Adapting Amino Acid in Influenza Virus
Ebolaviruses cause an often rapidly fatal syndrome known as Ebola virus disease ( EVD ) , with average case fatality rates of ~50% . There is no licensed vaccine or treatment for EVD , underscoring the urgent need to develop new anti-ebolavirus agents , especially in the face of an ongoing outbreak in the Democratic Re...	There are no approved vaccines or treatments to combat infections with ebolaviruses , which cause Ebola virus disease ( EVD ) , an often rapidly fatal disease characterized by fever and bleeding that results in death in up to ~90% of cases . Ebolaviruses are among the most pathogenic viruses that cause human disease an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "ebola", "hemorrhagic", "fever", "orthomyxoviruses", "retroviruses", "viruses", "animal", "models", "immunodeficiency", "viruses", "...	2019	Inhibition of Ebola Virus by a Molecularly Engineered Banana Lectin
Heart failure is a leading cause of death , yet its underlying electrophysiological ( EP ) mechanisms are not well understood . In this study , we use a multiscale approach to analyze a model of heart failure and connect its results to features of the electrocardiogram ( ECG ) . The heart failure model is derived by mo...	Ventricular fibrillation ( VF ) is one of the leading causes of sudden death . During VF , the electrical wave of activation in the heart breaks up chaotically . Consequently , the heart is unable to contract synchronously and pump blood to the rest of the body . In our work we formulate and validate a model of heart f...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "muscle", "tissue", "cardiovascular", "anatomy", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "electrocardiography", "bioassays", "and", "physiological", "anal...	2016	Electrophysiology of Heart Failure Using a Rabbit Model: From the Failing Myocyte to Ventricular Fibrillation
Incoming papillomaviruses ( PVs ) depend on mitotic nuclear envelope breakdown to gain initial access to the nucleus for viral transcription and replication . In our previous work , we hypothesized that the minor capsid protein L2 of PVs tethers the incoming vDNA to mitotic chromosomes to direct them into the nascent n...	Papillomaviruses can cause carcinogenic malignancies such as cervical cancer . Like most DNA viruses , papillomaviruses must deliver their genome to the cell nucleus during initial infection , where it is expressed and replicated . However , papillomaviruses make use of unconventional mechanisms for genome delivery . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chromosome", "structure", "and", "function", "metaphase", "pathogens", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "viruses", "mitosis", "dna",...	2017	A central region in the minor capsid protein of papillomaviruses facilitates viral genome tethering and membrane penetration for mitotic nuclear entry
Despite advance in science and technology for prevention , detection and treatment of cholera , this infectious disease remains a major public health problem in many countries in sub-Saharan Africa , Uganda inclusive . The aim of this study was to identify cholera hotspots in Uganda to guide the development of a roadma...	Uganda has regularly reported cholera since its first appearance in 1971 . Although the Government of Uganda implements cholera prevention and control interventions such as provision of safe water , promotion of sanitation and hygiene , health education and healthcare , the disease continues to threaten many districts ...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "rivers", "tropical", "diseases", "geographical", "locations", "uganda", "health", "care", "bacterial", "diseases", "aquatic", "environments", "bodies", "of", "water", "neglected", ...	2017	Identifying cholera "hotspots" in Uganda: An analysis of cholera surveillance data from 2011 to 2016
Protein S-palmitoylation , a lipid modification mediated by members of the palmitoyltransferase family , serves as an important membrane-targeting mechanism in eukaryotes . Although changes in palmitoyltransferase expression are associated with various physiological and disease states , how these changes affect global ...	Palmitoylation is a fatty acid modification , which increases the hydrophobicity of proteins , known to control the membrane trafficking and function of many proteins important for cellular homeostasis and disease . Being a reversible process , palmitoylation is proposed to be a major cellular regulator . While changes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "meiosis", "lipids", "model", "organisms", "molecular", "cell", "biology", "cell", "division", "enzyme", "classes", "enzyme", "regulation", "enzymes", "transferases", "yeast", "and", "fungal", "models", "schizosaccharomyces", "pombe", "biology", "fatty",...	2013	Quantitative Control of Protein S-Palmitoylation Regulates Meiotic Entry in Fission Yeast
Schistosoma japonicum is endemic in the Philippines , China and Indonesia , and infects more than 40 mammalian host species , all of which can act as reservoirs of infection . In China , water buffaloes have been shown to be major reservoirs of human infection . However , in the Philippines , carabao have not been cons...	Schistosomiasis japonica is endemic in China , the Philippines and parts of Indonesia . Extensive research efforts have shown that water buffaloes are major reservoir hosts for transmission of Schistosoma japonicum in China . In contrast , comparatively fewer studies have been undertaken on the reservoir hosts for schi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "microbiology", "parasitology" ]	2012	High Prevalence of Schistosoma japonicum Infection in Carabao from Samar Province, the Philippines: Implications for Transmission and Control
Circadian rhythms are fundamental to life . In mammals , these rhythms are generated by pacemaker neurons in the suprachiasmatic nucleus ( SCN ) of the hypothalamus . The SCN is remarkably consistent in structure and function between species , yet mammalian rest/activity patterns are extremely diverse , including diurn...	Controlled timing of all daily activity patterns is a highly adaptive trait that allows an animal to exploit its particular ecological environment . Environmental pressures such as light cycles , temperature cycles , food availability , and timing of predator activity selectively shape the activity patterns of differen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Mammalian Rest/Activity Patterns Explained by Physiologically Based Modeling
This study focused on Oeosophagostomum sp . , and more especially on O . bifurcum , as a parasite that can be lethal to humans and is widespread among humans and monkeys in endemic regions , but has not yet been documented in apes . Its epidemiology and the role played by non-human primates in its transmission are stil...	The disease caused by the nodular worm Oesophagostomum bifurcum can be lethal in humans and is thus of major human health significance in certain African regions . There are still gaps in the understanding of the epidemiology of the disease , including the role of non-human primates as reservoirs of the infection . We ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "ecology/conservation", "and", "restoration", "ecology", "ecology/behavioral", "ecology", "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Nodular Worm Infection in Wild Chimpanzees in Western Uganda: A Risk for Human Health?
In bacteria , replicative aging manifests as a difference in growth or survival between the two cells emerging from division . One cell can be regarded as an aging mother with a decreased potential for future survival and division , the other as a rejuvenated daughter . Here , we aimed at investigating some of the proc...	Bacteria were often considered to be potentially immortal and free of aging . This expectation was based on the idea that the two cells emerging from bacterial division are identical and thus also equally old . However , a number of recent studies followed individual bacterial cells over consecutive divisions and repor...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "deletion", "mutation", "medicine", "and", "health", "sciences", "microbial", "mutation", "cell", "division", "analysis", "engineering", "and", "technology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "physiological"...	2016	Genetic Manipulation of Glycogen Allocation Affects Replicative Lifespan in E. coli
VISA ( also known as MAVS , IPS-1 and Cardif ) is an essential adaptor protein in innate immune response to RNA virus . The protein level of VISA is delicately regulated before and after viral infection to ensure the optimal activation and timely termination of innate antiviral response . It has been reported that seve...	VISA is a central adaptor in innate immune response to RNA virus , which is down-regulated by multiple ubiquitination-dependent mechanisms . In this study , we found that the ER-associated protein iRhom2 promotes VISA stability by suppressing ER- and mitochondria-associated degradation pathways in early- and late-infec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "vesicular", "stomatitis", "virus", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "molecular", "probe", "techniques", "enzymes", "pathogens", "immunology...	2017	iRhom2 is essential for innate immunity to RNA virus by antagonizing ER- and mitochondria-associated degradation of VISA
Tick-borne relapsing fever in western North America is a zoonosis caused by the spirochete bacterium , Borrelia hermsii , which is transmitted by the bite of infected Ornithodoros hermsi ticks . The pathogen is maintained in natural cycles involving small rodent hosts such as chipmunks and tree squirrels , as well as t...	The model presented here provides valuable epidemiological information on tick-borne relapsing fever in western North America . The inference gleaned from these models represents areas where human infection with B . hermsii is likely to occur . The predicted distribution of O . hermsi and B . hermsii may allow health o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "ecological", "niches", "ixodes", "pathology", "and", "laboratory", "medicine", "atmospheric", "science", "pathogens", "california", "geographical"...	2017	Ecological niche modeling and distribution of Ornithodoros hermsi associated with tick-borne relapsing fever in western North America
The immunodominant lipopolysaccharide is a key antigenic factor for Gram-negative pathogens such as salmonellae where it plays key roles in host adaptation , virulence , immune evasion , and persistence . Variation in the lipopolysaccharide is also the major differentiating factor that is used to classify Salmonella in...	Bacterial pathogens frequently evolve mechanisms to vary the composition of their surface structures . The consequence is enhanced long-term survival by facilitating persistence and evasion of the host immune system . Salmonella sp . , cause severe infections in a range of mammalian hosts and guard themselves with a pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "gene", "identification", "and", "analysis", "gene", "expression", "genetics", "gene", "regulation", "molecular", "genetics", "salmonella", "biology", "genomics", "microbiology", "microbial", "pathogens", "bacterial", "pathogens", "dna", "transcr...	2013	Horizontally Acquired Glycosyltransferase Operons Drive Salmonellae Lipopolysaccharide Diversity
In this investigation , machine-enhanced techniques were applied to bring about scientific insights to identify a minimum set of phenotypic/functional memory-related biomarkers for post-vaccination follow-up upon yellow fever ( YF ) vaccination . For this purpose , memory status of circulating T-cells ( Naïve/early-eff...	In this study , a set of immunological biomarkers was studied in order to understand protection upon vaccination with yellow fever ( 17DD-YF ) vaccine . For this purpose , the immunological memory statuses of circulating T- and B-cells along with the plasmatic molecules ( cytokine profile ) were monitored before and at...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "immunology", "biomarkers", "neuroscience", "learning", "and", "memory", "preventive", "medicine", "cognition", "memory", "cytotoxic", "t", "cells", "vaccination", "a...	2018	Multi-parameter approach to evaluate the timing of memory status after 17DD-YF primary vaccination
Genome instability is regarded as a hallmark of cancer . Human tumors frequently carry clonally expanded mutations in their mitochondrial DNA ( mtDNA ) , some of which may drive cancer progression and metastasis . The high prevalence of clonal mutations in tumor mtDNA has commonly led to the assumption that the mitocho...	Mitochondria are the intracellular organelles responsible for energy production in eukaryotic cells . They are unique in that they contain their own DNA ( mtDNA ) , which encodes genes important for mitochondrial function and is the cell's only genetic material stored outside the nucleus . Mutations in both nuclear and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutagenesis", "cancer", "genetics", "genetic", "mutation", "mutation", "types", "genetics", "biology", "evolutionary", "biology", "genomic", "evolution", "genetics", "and", "genomics", "mutational", "hypotheses" ]	2012	Decreased Mitochondrial DNA Mutagenesis in Human Colorectal Cancer
A basic organizational principle of the primate visual system is that it maps the visual environment repeatedly and retinotopically onto cortex . Simple algebraic models can be used to describe the projection from visual space to cortical space not only for V1 , but also for the complex of areas V1 , V2 and V3 . Typica...	Cortical areas V1 , V2 and V3 each contain a complete and orderly representation of the visual environment , and their detailed layout is often studied . Here we discuss and compare algebraic mapping functions providing a transformation from visual field to cortical maps . Such algebraic models allow prediction of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physiology/sensory", "systems", "neuroscience/sensory", "systems", "computational", "biology/systems", "biology", "computational", "biology/computational", "neuroscience", "neuroscience/natural", "and", "synthetic", "vision" ]	2010	Modeling Magnification and Anisotropy in the Primate Foveal Confluence
Marine sediments are frequently covered by mats of the filamentous Beggiatoa and other large nitrate-storing bacteria that oxidize hydrogen sulfide using either oxygen or nitrate , which they store in intracellular vacuoles . Despite their conspicuous metabolic properties and their biogeochemical importance , little is...	In 1888 Winogradsky proposed the concept of chemolithotrophy—growth using inorganic compounds as an energy source—after studying the sulfur bacterium Beggiatoa . These filamentous bacteria and related organisms inhabit the surface of marine and freshwater sediments , where they oxidize hydrogen sulfide using either oxy...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "eubacteria", "microbiology" ]	2007	Insights into the Genome of Large Sulfur Bacteria Revealed by Analysis of Single Filaments
A growing body of evidence supports the notion that variation in gene regulation plays a crucial role in both speciation and adaptation . However , a comprehensive functional understanding of the mechanisms underlying regulatory evolution remains elusive . In primates , one of the crucial missing pieces of information ...	The way in which a genome folds affects the regulation of gene expression . This is often due to loops in the three-dimensional structure that bring linearly distant genes and regulatory elements into close proximity . Most studies examining three-dimensional structure genome-wide are limited to a single species . In t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "gene", "regulation", "vertebrates", "animals", "mammals", "primates", "chromosome", "mapping", "epigenetics", "mammalian", "genomics", "molecular", "biology", "techniques", "chromatin", "structural", "genomics", "research", "and", "analysis", "methods", "gene", "mapping"...	2019	Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates
Type III Secretion Systems ( T3SS ) are complex bacterial structures that provide gram-negative pathogens with a unique virulence mechanism whereby they grow a needle-like structure in order to inject bacterial effector proteins into the cytoplasm of a host cell . Numerous experiments have been performed to understand ...	The Type III Secretion System ( T3SS ) is a molecular needle that allows pathogenic bacteria ( e . g . Salmonella ) to inject proteins into host cells and control their behavior . Two mechanisms have been proposed to explain how bacteria regulate the length of the T3SS needle , but to date neither of these mechanisms h...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "mathematical", "models", "simulation", "and", "modeling", "membrane", "proteins", "bacterial", "diseases", "mathematics", "statistics", "(mathematics)", "o...	2016	Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System
Leprosy is a leading cause of preventable disability worldwide . Delay in diagnosis of patients augments the transmission of infection , and allows progression of disease and more severe disability . Delays in diagnosis greater than ten years have been reported in Brazil . To reduce this delay , it is important to iden...	Leprosy is caused by a bacterium that affects people’s nerves , giving rise to deformities . Leprosy largely affects the poor , and many people around the world are disabled due to leprosy . The deformities that the disease causes are largely preventable through early detection of the disease . In countries such as Bra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "medical", "doctors", "salaries", "disabilities", "demography", "tropical", "diseases", "geographical", "locations", "social", "sciences", "health", "care", "bacterial", "diseases", "research", "design", "health", "care", "provid...	2016	Factors Contributing to the Delay in Diagnosis and Continued Transmission of Leprosy in Brazil – An Explorative, Quantitative, Questionnaire Based Study
Both yaws and trachoma are endemic in the Pacific . Mass treatment with azithromycin is the mainstay of the WHO strategy for both the eradication of yaws and the elimination of trachoma as a public health problem , but the dose recommended for trachoma is lower than that for yaws . In countries where both diseases are ...	Yaws is a neglected tropical disease caused by a bacterium closely related to the agent of syphilis . Mass treatment is recommended by WHO for the control of both yaws and the blinding eye disease trachoma , but the dose used for trachoma is lower ( 20 mg/kg versus 30 mg/kg ) . We have previously shown that a single ro...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "solomon", "islands", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "treponematoses", "bacterial", "diseases", "age", "groups", "signs", "and", "sy...	2016	Prevalence of Active and Latent Yaws in the Solomon Islands 18 Months after Azithromycin Mass Drug Administration for Trachoma
Merkel cell polyomavirus ( MCV or MCPyV ) is the first human polyomavirus to be definitively linked to cancer . The mechanisms of MCV-induced oncogenesis and much of MCV biology are largely unexplored . In this study , we demonstrate that bromodomain protein 4 ( Brd4 ) interacts with MCV large T antigen ( LT ) and play...	MCV is a novel human polyomavirus that has recently been discovered in Merkel cell carcinoma ( MCC ) , a rare but highly aggressive skin cancer . Several independent studies have confirmed that MCV is present in ∼80% of MCC tumors . However , very little is known about how the interaction between MCV and its human host...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "biochemistry", "infectious", "diseases", "biology", "microbiology", "molecular", "cell", "biology", "proteomics" ]	2012	Bromodomain Protein Brd4 Plays a Key Role in Merkel Cell Polyomavirus DNA Replication
In the past decade , over 50 genome-scale metabolic reconstructions have been built for a variety of single- and multi- cellular organisms . These reconstructions have enabled a host of computational methods to be leveraged for systems-analysis of metabolism , leading to greater understanding of observed phenotypes . T...	Over the past decade , the increasing availability of fully sequenced genomes , functional genomics databases , and a broad existing scientific literature on metabolism have been leveraged towards the generation of genome-scale metabolic reconstructions for a wide variety of organisms . A major hurdle in the field , ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/metabolic", "networks", "computational", "biology", "computational", "biology/systems", "biology" ]	2011	Reconciliation of Genome-Scale Metabolic Reconstructions for Comparative Systems Analysis
Achieving a complete understanding of cellular signal transduction requires deciphering the relation between structural and biochemical features of a signaling system and the shape of the signal-response relationship it embeds . Using explicit analytical expressions and numerical simulations , we present here this rela...	Two-component phosphorelays constitute the key signaling pathways in all prokaryotes , lower eukaryotes , and plants , where they underline diverse physiological responses such as virulence , cell-cycle progression and sporulation . Despite such prevalence , our understanding of the dynamics and function of these syste...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell
Nucleosomes , basic units of chromatin , are known to show spontaneous DNA unwrapping dynamics that are crucial for transcriptional activation , but its structural details are yet to be elucidated . Here , employing a coarse-grained molecular model that captures residue-level structural details up to histone tails , we...	Nucleosomes , folding units of chromatin , wrap DNA about 1 . 75 turns and provide bottlenecks for transcription . Recent experiments showed that nucleosomes are not rigid but dynamic , showing spontaneous and partial unwrapping which is thus important for transcriptional activation . Experimentally , however , one can...	[ "Abstract", "Introduction", "Methods", "Results/Discussions" ]	[]	2015	Partial Unwrapping and Histone Tail Dynamics in Nucleosome Revealed by Coarse-Grained Molecular Simulations
Metabolomics is a relatively new “omics” platform , which analyzes a discrete set of metabolites detected in bio-fluids or tissue samples of organisms . It has been used in a diverse array of studies to detect biomarkers and to determine activity rates for pathways based on changes due to disease or drugs . Recent impr...	Metabolomics is an experimental approach that analyzes differences in metabolite levels detected in experimental samples . It has been used in the literature to understand the changes in metabolism with respect to diseases or drugs . Unlike transcriptomics or proteomics , which analyze gene and protein expression level...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "algorithms", "computer", "science", "biology", "computational", "biology", "metabolic", "networks" ]	2013	ADEMA: An Algorithm to Determine Expected Metabolite Level Alterations Using Mutual Information
Alzheimer’s disease ( AD ) is the most prevalent form of dementia in the elderly . β-amyloid ( Aβ ) accumulation in the brain is thought to be a primary event leading to eventual cognitive and motor dysfunction in AD . Aβ has been shown to promote neuronal hyperactivity , which is consistent with enhanced seizure activ...	Alzheimer’s disease ( AD ) is the most prevalent form of dementia in the elderly population . While it is established that β-amyloid ( Aβ ) peptide accumulation is a primary even leading to AD , there is little known about how Aβ induces progressive neurodegeneration and decline in cognitive and motor function . Recent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Linking Aβ42-Induced Hyperexcitability to Neurodegeneration, Learning and Motor Deficits, and a Shorter Lifespan in an Alzheimer’s Model
Cone photoreceptors and horizontal cells ( HCs ) have a reciprocal synapse that underlies lateral inhibition and establishes the antagonistic center-surround organization of the visual system . Cones transmit to HCs through an excitatory synapse and HCs feed back to cones through an inhibitory synapse . Here we report ...	Visual images are projected by the lens of the eye onto a sheet of photoreceptor cells in the retina called rods and cones . Like the pixels in a digital camera , each photoreceptor generates an electrical response proportional to the local light intensity . Each photoreceptor then initiates a chemical signal that is t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "visual", "system", "molecular", "neuroscience", "cellular", "neuroscience", "ion", "channels", "neurophysiology", "central", "nervous", "system", "synapses", "signaling", "pathways", "biology", "sensory", "systems", "neurotransmitters", "biophysics", "neuroscience" ]	2011	A Positive Feedback Synapse from Retinal Horizontal Cells to Cone Photoreceptors
In the neocortex , the coexistence of temporally locked excitation and inhibition governs complex network activity underlying cognitive functions , and is believed to be altered in several brain diseases . Here we show that this equilibrium can be unlocked by increased activity of layer 5 pyramidal neurons of the mouse...	The proper activity of cortical neurons ( the brain cells responsible for memory and consciousness ) relies on the precise integration of excitatory and inhibitory inputs . The excitation and inhibition ( E/I ) ratio has to remain constant both in time and strength to prevent neurological and psychiatric diseases . Fas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "calcium", "imaging", "biochemistry", "signal", "transduction", "molecular", "neuroscience", "specimen", "preparation", "and", "treatment", "neurochemistry", "mechanical", "treatment", "of", "specimens", "specimen", "disruption", "cell", "biology", "neural", "networks", "...	2014	Non-associative Potentiation of Perisomatic Inhibition Alters the Temporal Coding of Neocortical Layer 5 Pyramidal Neurons
FUS/TLS is a nucleic acid binding protein that , when mutated , can cause a subset of familial amyotrophic lateral sclerosis ( fALS ) . Although FUS/TLS is normally located predominantly in the nucleus , the pathogenic mutant forms of FUS/TLS traffic to , and form inclusions in , the cytoplasm of affected spinal motor ...	Of all the thousand natural shocks that flesh is heir to , one of the most devastating is amyotrophic lateral sclerosis ( ALS ) , commonly known as Lou Gehrig's Disease . This disorder , which comes in both inherited and random forms , is characterized by degeneration of spinal motor neurons , leading to paralysis and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurodegenerative", "diseases", "amyotrophic", "lateral", "sclerosis", "microbiology", "neuroscience", "model", "organisms", "huntington", "disease", "motor", "neuron", "diseases", "biology", "dementia", "genetic", "screens", "neurology", "neuromuscular", "dise...	2011	A Yeast Model of FUS/TLS-Dependent Cytotoxicity
A standardized test for the serodiagnosis of human cystic echinococcosis ( CE ) is still needed , because of the low specificity and sensitivity of the currently available commercial tools and the lack of proper evaluation of the existing recombinant antigens . In a previous work , we defined the new ELISA-B2t diagnost...	Cystic echinococcosis ( CE ) is a widespread zoonotic disease . Its complex clinical presentation precludes a “one-size-fits-all” approach to clinical management , particularly with regard to serodiagnosis . While CE is often detected incidentally by imaging , imaging findings may be inconclusive . Therefore , there is...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "test", "evaluation", "diagnostic", "medicine", "emerging", "infectious", "diseases", "immunology", "biology", "immunologic", "techniques", "microbiology", "parasitology" ]	2012	Improved Serodiagnosis of Cystic Echinococcosis Using the New Recombinant 2B2t Antigen
Homoploid hybrid speciation is the formation of a new hybrid species without change in chromosome number . So far , there has been a lack of direct molecular evidence for hybridization generating novel traits directly involved in animal speciation . Heliconius butterflies exhibit bright aposematic color patterns that a...	Hybrid speciation challenges our view of biodiversity as a branching tree and is considered rare or absent in animals . A possible route by which it may occur is establishment of a novel “magic trait , ” influencing both ecological adaptation and mating preference , via hybridization . We provide , to our knowledge , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "biology/animal", "genetics" ]	2010	Genetic Evidence for Hybrid Trait Speciation in Heliconius Butterflies
A central goal of sensory neuroscience is to construct models that can explain neural responses to natural stimuli . As a consequence , sensory models are often tested by comparing neural responses to natural stimuli with model responses to those stimuli . One challenge is that distinct model features are often correla...	Modeling neural responses to natural stimuli is a core goal of sensory neuroscience . A standard way to test sensory models is to predict responses to natural stimuli . One challenge with this approach is that different features are often correlated across natural stimuli , making their contributions hard to tease apar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "auditory", "cortex", "acoustics", "medicine", "and", "health", "sciences", "statistical", "noise", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "engineering", "and", "technology", "statistics", "signal", "processing", "matched", "filters",...	2018	Neural responses to natural and model-matched stimuli reveal distinct computations in primary and nonprimary auditory cortex
Using a phenome-wide association study ( PheWAS ) approach , we comprehensively tested genetic variants for association with phenotypes available for 70 , 061 study participants in the Population Architecture using Genomics and Epidemiology ( PAGE ) network . Our aim was to better characterize the genetic architecture ...	In phenome-wide association studies ( PheWAS ) all potential genetic variants in a dataset are systematically tested for association with all available phenotypes and traits that have been measured in study participants . By investigating the relationship between genetic variation and a diversity of phenotypes , there ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "analysis", "tools", "genomics", "genetic", "networks", "genetic", "polymorphism", "genome", "scans", "population", "genetics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2013	Phenome-Wide Association Study (PheWAS) for Detection of Pleiotropy within the Population Architecture using Genomics and Epidemiology (PAGE) Network

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