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Activation of the mammalian Notch receptor after ligand binding relies on a succession of events including metalloprotease-cleavage , endocytosis , monoubiquitination , and eventually processing by the gamma-secretase , giving rise to a soluble , transcriptionally active molecule . The Notch1 receptor was proposed to b...	The highly conserved signaling pathway involving the transmembrane receptor Notch is essential for development , and misregulation of this pathway is linked to many diseases . We previously proposed that the Notch1 receptor is monoubiquitinated during its activation . With the aim of identifying a deubiquinating enzyme...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "cell", "biology/membranes", "and", "sorting", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/transcription", "and", "translation" ]	2010	The Translation Initiation Factor 3f (eIF3f) Exhibits a Deubiquitinase Activity Regulating Notch Activation
The survival and persistence of Mycobacterium tuberculosis depends on its capacity to manipulate multiple host defense pathways , including the ability to actively inhibit the death by apoptosis of infected host cells . The genetic basis for this anti-apoptotic activity and its implication for mycobacterial virulence h...	The infection-induced suicide of host cells following invasion by intracellular pathogens is an ancient defense mechanism observed in multicellular organisms of both the animal and plant kingdoms . It is therefore not surprising that persistent pathogens of viral , bacterial , and protozoal origin have evolved to inhib...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "none", "in", "vitro", "immunology", "microbiology", "mus", "(mouse)", "eubacteria" ]	2007	Mycobacterium tuberculosis nuoG Is a Virulence Gene That Inhibits Apoptosis of Infected Host Cells
Intelligent organisms face a variety of tasks requiring the acquisition of expertise within a specific domain , including the ability to discriminate between a large number of similar patterns . From an energy-efficiency perspective , effective discrimination requires a prudent allocation of neural resources with more ...	One neural correlate of being an expert is more brain volume—and presumably more neurons and more synapses—devoted to processing the input patterns falling within one's field of expertise . As the number of neurons in the neocortex does not increase during the learning period that begins with novice abilities and ends ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Adaptive Synaptogenesis Constructs Neural Codes That Benefit Discrimination
The ecto-5’-nucleotidase CD73 plays an important role in the production of immune-suppressive adenosine in tumor micro-environment , and has become a validated drug target in oncology . Indeed , the anticancer immune response involves extracellular ATP to block cell proliferation through T-cell activation . However , i...	Nucleotidases play a central role in maintaining the nucleotide pool homeostasis and the only extracellular member of this family , CD73 , has become an attractive target in oncology because of its high expression level on immune and cancer cells . In the tumor microenvironment , CD73-generated adenosine prevents the p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "glycosylamines", "medicine", "and", "health", "sciences", "crystal", "structure", "enzymes", "immunology", "condensed", "matter", "physics", "enzymology", "molecular", "biology", "techniques", "crystallography", "enzyme", "inhibitors", "adenosine", "physical", "chemistry",...	2018	Identification of allosteric inhibitors of the ecto-5'-nucleotidase (CD73) targeting the dimer interface
Differentiated cells can be reprogrammed through the formation of heterokaryons and hybrid cells when fused with embryonic stem ( ES ) cells . Here , we provide evidence that conversion of human B-lymphocytes towards a multipotent state is initiated much more rapidly than previously thought , occurring in transient het...	One of the most pressing objectives of medical research today is the development of approaches to restore the function of tissues damaged by accident or disease . An important goal for this work is the isolation of stem cell populations to replace missing or nonfunctioning cells . Because problems of immune rejection a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/stem", "cells", "cell", "biology/developmental", "molecular", "mechanisms", "developmental", "biology/cell", "differentiation", "genetics", "and", "genomics/epigenetics", "cell", "biology/gene", "expression" ]	2008	Heterokaryon-Based Reprogramming of Human B Lymphocytes for Pluripotency Requires Oct4 but Not Sox2
Remodelling the methylome is a hallmark of mammalian development and cell differentiation . However , current knowledge of DNA methylation dynamics in human tissue specification and organ development largely stems from the extrapolation of studies in vitro and animal models . Here , we report on the DNA methylation lan...	Methylation of DNA is a key epigenetic mark . Adult tissues have highly distinct genome-wide DNA methylation signatures . How these signatures arise during human fetal development is largely unknown . Here , we studied DNA methylation profiles of four tissues ( amnion , muscle , adrenal , pancreas ) during first and se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	DNA Methylation Landscapes of Human Fetal Development
Injury to nerve axons induces diverse responses in neuronal cell bodies , some of which are influenced by the distance from the site of injury . This suggests that neurons have the capacity to estimate the distance of the injury site from their cell body . Recent work has shown that the molecular motor dynein transport...	Neurons have extremely long axonal processes that can reach lengths of up to 1 meter in human peripheral nerves . The neuronal cell body response to nerve injury is dependent on signals carried by molecular motors from the lesion site in the axon . The distance between the injury site and the cell body influences the t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/signaling", "networks", "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/neurobiology", "of", "disease", "and", "regeneration", "cell", "biology/cell", "signaling" ]	2009	Can Molecular Motors Drive Distance Measurements in Injured Neurons?
Memory CD8 T cells confer increased protection to immune hosts upon secondary viral , bacterial , and parasitic infections . The level of protection provided depends on the numbers , quality ( functional ability ) , and location of memory CD8 T cells present at the time of infection . While primary memory CD8 T cells c...	Following infection or vaccination , memory CD8 T cells persist at higher numbers and have enhanced functional abilities compared to naïve cells , providing immune hosts with increased protection from viral , bacterial , or parasitic infection . Protection provided by memory CD8 T cells depends on the numbers , quality...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phenotypic and Functional Alterations in Circulating Memory CD8 T Cells with Time after Primary Infection
Here we report the first quantitative analysis of spiking activity in human early visual cortex . We recorded multi-unit activity from two electrodes in area V2/V3 of a human patient implanted with depth electrodes as part of her treatment for epilepsy . We observed well-localized multi-unit receptive fields with tunin...	Our knowledge of the function of the early visual cortex is based largely on recordings of spiking activity from neurons in animal models , in particular the macaque monkey . Indirect measurements of neuronal activity in the human visual cortex have suggested many similarities with the macaque visual cortex , but to da...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "brain", "vertebrates", "social", "sciences", "electrophysiology", "neuroscience", "animals", "mammals", "signal", "filter...	2016	The Effects of Context and Attention on Spiking Activity in Human Early Visual Cortex
The molecular details underlying the time-dependent assembly of protein complexes in cellular networks , such as those that occur during differentiation , are largely unexplored . Focusing on the calcium-induced differentiation of primary human keratinocytes as a model system for a major cellular reorganization process...	A key challenge in cellular network biology is to understand how protein complexes are cell-type or condition-specific assembled and disassembled . Cell differentiation is a major cellular reorganization bringing about fundamental changes in the new differentiated cell type . As many genes are expressed throughout all ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dissecting the Calcium-Induced Differentiation of Human Primary Keratinocytes Stem Cells by Integrative and Structural Network Analyses
The genetically tractable model host Caenorhabditis elegans provides a valuable tool to dissect host-microbe interactions in vivo . Pseudomonas aeruginosa and Staphylococcus aureus utilize virulence factors involved in human disease to infect and kill C . elegans . Despite much progress , virtually nothing is known reg...	Pseudomonas aeruginosa and Staphylococcus aureus are bacteria that can form part of the human microbiota , but can also cause severe disease . Despite their great clinical importance , little is known about their interactions with the human host before disease onset , particularly regarding the molecules that host cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections" ]	2010	Distinct Pathogenesis and Host Responses during Infection of C. elegans by P. aeruginosa and S. aureus
The implementation of vector control interventions and potential introduction new tools requires baseline data to evaluate their direct and indirect effects . The objective of the study is to present the seroprevalence of dengue infection in a cohort of children 0 to 15 years old followed during 2015 to 2016 , the risk...	Dengue is a major public health problem in Latin America . Its transmission is highly heterogeneous , and its burden varies by geographic region , age group affected , serotype and other factors . While surveillance of dengue in the region has improved , several limitations remain , including under detection , misdiagn...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "chikungunya", "infection", "pathogens", "sociology", "tropical", "diseases", "microbiology", "social", "sciences", "viruses", "age", "grou...	2018	Dengue seroprevalence in a cohort of schoolchildren and their siblings in Yucatan, Mexico (2015-2016)
Many repair and recombination proteins play essential roles in telomere function and chromosome stability , notwithstanding the role of telomeres in “hiding” chromosome ends from DNA repair and recombination . Among these are XPF and ERCC1 , which form a structure-specific endonuclease known for its essential role in n...	Telomeres are the specialised nucleoprotein structures evolved to avoid progressive replicative shortening and recombinational instability of the ends of linear chromosomes . Notwithstanding this role of telomeres in “hiding” chromosome ends from DNA repair and recombination , many repair and recombination proteins pla...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/chromosome", "biology" ]	2009	ERCC1/XPF Protects Short Telomeres from Homologous Recombination in Arabidopsis thaliana
Vibrio parahaemolyticus is one of the human pathogenic vibrios . During the infection of mammalian cells , this pathogen exhibits cytotoxicity that is dependent on its type III secretion system ( T3SS1 ) . VepA , an effector protein secreted via the T3SS1 , plays a major role in the T3SS1-dependent cytotoxicity of V . ...	Vibrio parahaemolyticus is a bacterial pathogen that causes food-borne gastroenteritis and also wound infection and septicemia . It exhibits cytotoxicity that is dependent on its type III secretion system ( T3SS1 ) during the infection of mammalian cells . Although an effector VepA plays a major role in the cytotoxicit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "gram", "negative", "molecular", "cell", "biology", "cell", "biology", "genetic", "screens", "genetics", "microbial", "pathogens", "genetics", "and", "genomics", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2012	A Cytotoxic Type III Secretion Effector of Vibrio parahaemolyticus Targets Vacuolar H+-ATPase Subunit c and Ruptures Host Cell Lysosomes
Previous explanations of computations performed by recurrent networks have focused on symmetrically connected saturating neurons and their convergence toward attractors . Here we analyze the behavior of asymmetrical connected networks of linear threshold neurons , whose positive response is unbounded . We show that , f...	Biological systems are obviously able to process abstract information on the states of neuronal and molecular networks . However , the concepts and principles of such biological computation are poorly understood by comparison with technological computing . A key concept in models of biological computation has been the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Computation in Dynamically Bounded Asymmetric Systems
Molecular phylogenetics and phylogenomics are subject to noise from horizontal gene transfer ( HGT ) and bias from convergence in macromolecular compositions . Extensive variation in size , structure and base composition of alphaproteobacterial genomes has complicated their phylogenomics , sparking controversy over the...	If gene products work well in the networks of foreign cells , their genes may transfer horizontally between unrelated genomes . What factors dictate the ability to integrate into foreign networks ? Different RNAs and proteins must interact specifically in order to function well as a system . For example , tRNA function...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "macromolecular", "complex", "analysis", "sequence", "analysis", "systems", "biology", "organismal", "evolution", "genome", "evolution", "microbial", "evolution", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "microbiology", "b...	2014	tRNA Signatures Reveal a Polyphyletic Origin of SAR11 Strains among Alphaproteobacteria
Although psychological and computational models of time estimation have postulated the existence of neural representations tuned for specific durations , empirical evidence of this notion has been lacking . Here , using a functional magnetic resonance imaging ( fMRI ) adaptation paradigm , we show that the inferior par...	The human brain has the ability to estimate the passage of time , which allows us to perform complex cognitive tasks such as playing music , dancing , and understanding speech . Scientists have just begun to understand which brain areas become active when we estimate time . However , it still remains a mystery how exac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Time Adaptation Shows Duration Selectivity in the Human Parietal Cortex
While virus growth dynamics have been well-characterized in several infections , data are typically collected once the virus population becomes easily detectable . Earlier dynamics , however , remain less understood . We recently reported unusual early dynamics in an experimental system using adenovirus infection of hu...	We investigate in vitro adenovirus spread starting from the lowest infection multiplicities . This phase of virus dynamics remains poorly understood and is likely critical for ensuring that engineered oncolytic viruses successfully spread and destroy tumors . We find unexpectedly complex dynamics , which are analyzed w...	[ "Abstract", "Introduction", "Results", "Discussion", "and", "Conclusion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "antiviral", "immune", "response", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "cancer", "treatment", "immunology", "population", "dynamics", "microbiology", "enzymology", "oncolytic", "virus...	2017	Complex Dynamics of Virus Spread from Low Infection Multiplicities: Implications for the Spread of Oncolytic Viruses
Most bacteria live in colonies , where they often express different cell types . The ecological significance of these cell types and their evolutionary origin are often unknown . Here , we study the evolution of cell differentiation in the context of surface colonization . We particularly focus on the evolution of a ‘s...	In nature , most bacteria occur in surface-attached colonies . Inside these colonies , cells often express many different phenotypes . The significance of these phenotypes often remains unknown . We study the evolution of cell differentiation in the context of surface colonization . We particularly focus on the evoluti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "cell", "death", "cell", "motility", "organismal", "evolution", "decision", "making", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "neuroscience", "cell", "differentiation", "developmental", "biology", "cognition", "mi...	2016	Phenotypic Heterogeneity and the Evolution of Bacterial Life Cycles
Regulation of synaptic AMPA receptor levels is a major mechanism underlying homeostatic synaptic scaling . While in vitro studies have implicated several molecules in synaptic scaling , the in vivo mechanisms linking chronic changes in synaptic activity to alterations in AMPA receptor expression are not well understood...	Synaptic homeostasis increases or decreases synaptic strengths in order to stabilize neuronal firing in response to alterations in neuronal activity . Synaptic homeostasis plays an important role during neuronal development and may be deregulated in several neurological diseases . Neurons regulate glutamate neurotransm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "neurochemistry", "chemical", "compounds", "mechanisms", "of", "signal", "transduction", "caenorhabditis", "gene", "regulation", "neuroscience", "animals", "organic", "compounds", "dna", "transcription", "animal", "models", "caenorhabditis", "elegans", "mod...	2016	The CaM Kinase CMK-1 Mediates a Negative Feedback Mechanism Coupling the C. elegans Glutamate Receptor GLR-1 with Its Own Transcription
Living organisms need to maintain energetic homeostasis . For many species , this implies taking actions with delayed consequences . For example , humans may have to decide between foraging for high-calorie but hard-to-get , and low-calorie but easy-to-get food , under threat of starvation . Homeostatic principles pres...	Common decision-making models arise from firm axiomatic foundations but do not account for a variety of empirically observed choice patterns such as risk attitudes in the face of high-impact events . Here , we argue that one reason for this mismatch between theory and data lies in the neglect of basic biological princi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Maintaining Homeostasis by Decision-Making
Rhodnius nasutus , a vector of the etiological agent Trypanosoma cruzi , is one of the epidemiologically most relevant triatomine species of the Brazilian Caatinga , where it often colonizes rural peridomestic structures such as chicken coops and occasionally invades houses . Historical colonization and determination o...	Chagas disease is endemic to Latin America and the Caribbean and it is estimated that 6–7 million people are infected with the etiological agent Trypanosoma cruzi . Although new community-based ecosystem management ( ecohealth ) initiatives have been implemented , vector control based on insecticide-spraying of househo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "taxonomy", "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "population", "genetics", "animals", "genetic", "mapping", "animal", "models", "phylogenetics", "data", "management", "phylogenetic", "anal...	2018	Phylogeography and demographic history of the Chagas disease vector Rhodnius nasutus (Hemiptera: Reduviidae) in the Brazilian Caatinga biome
On its own , a single cell cannot exert more than a microscopic influence on its immediate surroundings . However , via strength in numbers and the expression of cooperative phenotypes , such cells can enormously impact their environments . Simple cooperative phenotypes appear to abound in the microbial world , but exp...	Cooperation is a fundamental and widespread phenomenon in nature , yet explaining the evolution of cooperation is difficult . Natural selection typically favors individuals that maximize their own reproduction , so how is it that many diverse organisms , from bacteria to humans , have evolved to help others at a cost t...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/pattern", "formation" ]	2010	Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation
Since 1999 a lineage of the pathogen Cryptococcus gattii has been infecting humans and other animals in Canada and the Pacific Northwest of the USA . It is now the largest outbreak of a life-threatening fungal infection in a healthy population in recorded history . The high virulence of outbreak strains is closely link...	How infections spread within the human population is an important question in forecasting potential epidemics . One way to investigate potential mechanisms is to test experimentally whether combinations of genes that confer high virulence are able to spread to less-virulent lineages . Here , we address this question in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Transmission of Hypervirulence Traits via Sexual Reproduction within and between Lineages of the Human Fungal Pathogen Cryptococcus gattii
Chagas disease ( CD ) affects over six million people and is a leading cause of cardiomyopathy in Latin America . Given recent migration trends , there is a large population at risk in the United States ( US ) . Early stage cardiac involvement from CD usually presents with conduction abnormalities on electrocardiogram ...	Chagas disease ( CD ) affects an estimated 300 , 000 people in the United States , but warning signs for the disease have not been closely studied . CD is usually acquired in Latin America , and can remain in the body for years or decades without producing any symptoms . However , in about 30% of patients , it can even...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "cardiomyopathies", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "biochemical", "analysis", "ethnicities", "north", "ame...	2017	Prevalence of Chagas Disease in a U.S. Population of Latin American Immigrants with Conduction Abnormalities on Electrocardiogram
Experiments show that spike-triggered stimulation performed with Bidirectional Brain-Computer-Interfaces ( BBCI ) can artificially strengthen connections between separate neural sites in motor cortex ( MC ) . When spikes from a neuron recorded at one MC site trigger stimuli at a second target site after a fixed delay ,...	Recent developments in Bidirectional Brain-Computer Interfaces ( BBCI ) not only allow the reading out of neural activity from cortical neurons , but also the delivery of electrical signals . These drive neural dynamics and shape synaptic plasticity , thus opening the possibility of engineering novel neural circuits , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "synaptic", "plasticity", "bioassays", "and", "physiological", "analysis", "muscle", "electrophysiology"...	2017	Correlation-based model of artificially induced plasticity in motor cortex by a bidirectional brain-computer interface
Candida albicans yeast cells are found in the intestine of most humans , yet this opportunist can invade host tissues and cause life-threatening infections in susceptible individuals . To better understand the host factors that underlie susceptibility to candidiasis , we developed a new model to study antifungal innate...	Despite being a part of the normal flora of healthy individuals , Candida albicans is the most common fungal pathogen of humans and can cause infections that are associated with staggeringly high mortality rates . Here we devise a model for the study of the host immune response to C . albicans infection using the nemat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immunology", "microbiology", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "fungal", "diseases", "infectious", "diseases", "mycosis", "biology", "immunity", "innate", "immunity", "yeast", "and", "fungal", "models", "candida", "albic...	2011	Candida albicans Infection of Caenorhabditis elegans Induces Antifungal Immune Defenses
Leptospirosis causes significant morbidity and mortality worldwide; however , the role of the host immune response in disease progression and high case fatality ( >10–50% ) is poorly understood . We conducted a multi-parameter investigation of patients with acute leptospirosis to identify mechanisms associated with cas...	Leptospirosis causes over one million cases and nearly 60 , 000 deaths annually . Infection with the spirochetal bacterium results in a spectrum of symptoms , ranging from mild febrile illness to life-threatening pulmonary hemorrhage syndrome and acute kidney injury . Despite leptospirosis being a leading cause of zoon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "leptospira", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "immune", "cells", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "animals...	2016	Cathelicidin Insufficiency in Patients with Fatal Leptospirosis
The functional separation of ON and OFF pathways , one of the fundamental features of the visual system , starts in the retina . During postnatal development , some retinal ganglion cells ( RGCs ) whose dendrites arborize in both ON and OFF sublaminae of the inner plexiform layer transform into RGCs with dendrites that...	The developmental separation of ON and OFF pathways is one of the fundamental features of the visual system . In the mouse retina , some bi-stratified ON-OFF RGCs are refined into mono-stratified ON or OFF RGCs during the first postnatal month . However , the process by which the RGCs' physiological receptive field pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physiology/sensory", "systems", "physiology/neuronal", "signaling", "mechanisms", "computational", "biology/computational", "neuroscience", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment" ]	2010	Non-Centered Spike-Triggered Covariance Analysis Reveals Neurotrophin-3 as a Developmental Regulator of Receptive Field Properties of ON-OFF Retinal Ganglion Cells
RNA silencing is a highly conserved pathway in the network of interconnected defense responses that are activated during viral infection . As a counter-defense , many plant viruses encode proteins that block silencing , often also interfering with endogenous small RNA pathways . However , the mechanism of action of vir...	RNA silencing is an important antiviral defense in plants , and many plant viruses encode proteins that block RNA silencing . However , the mechanism of action of the viral suppressors is complex , and little is known about the role of host plant proteins in the process . Here we report the first example of a host prot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "virology/virulence", "factors", "and", "mechanisms", "molecular", "biology/mrna", "stability", "plant", "biology", "virology", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics...	2010	Two Plant Viral Suppressors of Silencing Require the Ethylene-Inducible Host Transcription Factor RAV2 to Block RNA Silencing
A large proportion of age-related hearing loss is caused by loss or damage to outer hair cells in the organ of Corti . The organ of Corti is the mechanosensory transducing apparatus in the inner ear and is composed of inner hair cells , outer hair cells , and highly specialized supporting cells . The mechanisms that re...	A large proportion of age-related hearing loss is caused by loss or damage to outer hair cells in the organ of Corti . The organ of Corti is a highly specialized structure in the inner ear that is composed of inner hair cells , outer hair cells , and associated supporting cells . Although we understand some of the mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "molecular", "neuroscience", "neurogenesis", "animal", "genetics", "genetic", "mutation", "anatomy", "and", "physiology", "neuroscience", "cell", "differentiation", "dna", "transcription", "animal", "models", "developmental", "biology", "model", "organisms", "...	2012	Differentiation of the Lateral Compartment of the Cochlea Requires a Temporally Restricted FGF20 Signal
Drug combinations for the treatment of leishmaniasis represent a promising and challenging chemotherapeutic strategy that has recently been implemented in different endemic areas . However , the vast majority of studies undertaken to date have ignored the potential risk that Leishmania parasites could develop resistanc...	Leishmania is a protozoan parasite that infects human macrophages to produce the neglected tropical disease known as leishmaniasis . Chemotherapy is currently the only treatment option for leishmaniasis . First-line therapies include pentavalent antimonials , except in some regions in the Indian subcontinent , the lipo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "leishmaniasis", "neglected", "tropical", "diseases", "parasitic", "diseases" ]	2012	Leishmania donovani Develops Resistance to Drug Combinations
A deterministic population dynamics model involving birth and death for a two-species system , comprising a wild-type and more resistant species competing via logistic growth , is subjected to two distinct stress environments designed to mimic those that would typically be induced by temporal variation in the concentra...	The possibilities of lower antibiotic dosages and treatment times , as demanded by antibiotic stewardship programmes have been investigated with complex mathematical models to account for , for example , the presence of an immune host . At the same time , microbial experiments are getting better at mimicking real setup...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "drugs", "immunology", "microbiology", "antibiotic", "resistance", "probability", "distribution", "mathematics", "pharmaceutics", "antibiotics", "pharmacology", "populati...	2017	Exploiting ecology in drug pulse sequences in favour of population reduction
Transfer RNAs ( tRNAs ) are ancient molecules that are central to translation . Since they probably carry evolutionary signatures that were left behind when the living world diversified , we reconstructed phylogenies directly from the sequence and structure of tRNA using well-established phylogenetic methods . The tree...	The origins of the three major cellular lineages of life—Archaea , Bacteria , and Eukarya—and of viruses have been shrouded in mystery . In this study , we focus on transfer RNA , an ancient nucleic acid molecule that takes center stage in the process of protein biosynthesis and can be found everywhere in life . In a p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/rna", "structure", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/evolutionary", "modeling", "evolutionary", "biology/bioinformatics", "computational", "biology", "evolutionary", "biology" ]	2008	Evolutionary Patterns in the Sequence and Structure of Transfer RNA: Early Origins of Archaea and Viruses
The polymerization of actin in filaments generates forces that play a pivotal role in many cellular processes . We introduce a novel technique to determine the force-velocity relation when a few independent anchored filaments grow between magnetic colloidal particles . When a magnetic field is applied , the colloidal p...	Actin self-assembles into filaments , and this produces forces that deform cell membranes in a large number of motile processes . While physical measurements have been performed of the force produced by growth of either a single filament or a large intricate array of filaments organized in an active macroscopic gel , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "biochemistry/macromolecular", "assemblies", "and", "machines", "biochemistry/experimental", "biophysical", "methods", "cell", "biology/cytoskeleton" ]	2011	Force-Velocity Measurements of a Few Growing Actin Filaments
Plants continuously extend their root and shoot systems through the action of meristems at their growing tips . By regulating which meristems are active , plants adjust their body plans to suit local environmental conditions . The transport network of the phytohormone auxin has been proposed to mediate this systemic gr...	Plants can adapt their form to suit the environment in which they are growing . For example , genetically identical plants can develop as a single unbranched stem or as a highly ramified bush . This broad developmental potential is possible because the shoot system is produced continuously by growing tips , known as sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "plant", "science", "plant", "biology", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2013	Strigolactone Can Promote or Inhibit Shoot Branching by Triggering Rapid Depletion of the Auxin Efflux Protein PIN1 from the Plasma Membrane
African trypanosomes thrive in the bloodstream and tissue spaces of a wide range of mammalian hosts . Infections of cattle cause an enormous socio-economic burden in sub-Saharan Africa . A hallmark of the trypanosome lifestyle is the flagellate’s incessant motion . This work details the cell motility behavior of the fo...	African trypanosomes are protist flagellates that are successful parasites in a wide spectrum of hosts . These include humans , where they cause the deadly sleeping sickness , and livestock , where they cause nagana . Nagana has a tremendous negative impact in wide regions of sub-Saharan Africa . The motility of these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "swimming", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "flagellar", "motility", "biological", "locomotion", "biomechanics", "parasitic", "protozoans", "viscosity", "protozoans",...	2016	Species-Specific Adaptations of Trypanosome Morphology and Motility to the Mammalian Host
Recent evidence supports the involvement of inducible , highly diverse lectin-like recognition molecules in snail hemocyte-mediated responses to larval Schistosoma mansoni . Because host lectins likely are involved in initial parasite recognition , we sought to identify specific carbohydrate structures ( glycans ) shar...	Early larval stages of the human blood fluke Schistosoma mansoni face many barriers in their attempt to establish successful infections within their snail host , Biomphalaria spp . The snail's internal defense system represents one such barrier , which includes lectin-like recognition receptors and circulating hemocyte...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology", "biology", "molecular", "cell", "biology" ]	2012	Glycotope Sharing between Snail Hemolymph and Larval Schistosomes: Larval Transformation Products Alter Shared Glycan Patterns of Plasma Proteins
The role of Activation-Induced Cytidine Deaminase ( AID ) in somatic hypermutation and polyclonal antibody affinity maturation has not been shown for polyclonal responses in humans . We investigated whether AID induction in human B cells following H1N1pdm09 vaccination correlated with in-vivo antibody affinity maturati...	Antibody affinity maturation is a key aspect of an effective immune response to vaccines , likely to have an impact on clinical outcome following exposure to pathogens . Activation-Induced Cytidine Deaminase ( AID ) in B cells is a key enzyme involved in antibody class switching and somatic hypermutation , required for...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "humoral", "immunity", "medicine", "viral", "vaccines", "influenza", "immunology", "microbiology", "vaccines", "vaccination", "infectious", "diseases", "biology", "immune", "response", "clinical", "immunology", "immunity", "virology", "viral", "diseases" ]	2012	AID Activity in B Cells Strongly Correlates with Polyclonal Antibody Affinity Maturation in-vivo Following Pandemic 2009-H1N1 Vaccination in Humans
Devil facial tumour disease ( DFTD ) is a fatal , transmissible malignancy that threatens the world's largest marsupial carnivore , the Tasmanian devil , with extinction . First recognised in 1996 , DFTD has had a catastrophic effect on wild devil numbers , and intense research efforts to understand and contain the dis...	The world's largest carnivorous marsupial , the Tasmanian devil , is threatened with extinction due to the emergence of devil facial tumour disease ( DFTD ) , a fatal transmissible tumour . Critical loss of genetic diversity has rendered the devil vulnerable to transmission of tumour cells by grafting or transplanting ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "cytogenetics", "genetics", "and", "genomics" ]	2012	Genomic Restructuring in the Tasmanian Devil Facial Tumour: Chromosome Painting and Gene Mapping Provide Clues to Evolution of a Transmissible Tumour
We aimed to identify genetic variants associated with cortical bone thickness ( CBT ) and bone mineral density ( BMD ) by performing two separate genome-wide association study ( GWAS ) meta-analyses for CBT in 3 cohorts comprising 5 , 878 European subjects and for BMD in 5 cohorts comprising 5 , 672 individuals . We th...	Bone traits are highly dependent on genetic factors . To date , numerous genetic loci for bone mineral density ( BMD ) and only one locus for osteoporotic fracture have been previously identified to be genome-wide significant . Cortical bone has been reported to be an important determinant of bone strength; so far , no...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "endocrinology", "genetics", "and", "genomics", "diabetes", "and", "endocrinology", "metabolic", "disorders", "clinical", "genetics" ]	2012	WNT16 Influences Bone Mineral Density, Cortical Bone Thickness, Bone Strength, and Osteoporotic Fracture Risk
The interaction of proteins at cellular interfaces is critical for many biological processes , from intercellular signaling to cell adhesion . For example , the selectin family of adhesion receptors plays a critical role in trafficking during inflammation and immunosurveillance . Quantitative measurements of binding ra...	The binding of a receptor on one cell to a ligand on another is a process of broad biological interest , important to cell adhesion and signaling . Interactions between cell surfaces can be called “two-dimensional” because the reactive groups on interacting molecular pairs are constrained to move 100 nm or less in the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/biomacromolecule-ligand", "interactions", "cell", "biology/cell", "adhesion", "biophysics/theory", "and", "simulation" ]	2009	Nano-motion Dynamics are Determined by Surface-Tethered Selectin Mechanokinetics and Bond Formation
A steady increase in knowledge of the molecular and antigenic structure of the gp120 and gp41 HIV-1 envelope glycoproteins ( Env ) is yielding important new insights for vaccine design , but it has been difficult to translate this information to an immunogen that elicits broadly neutralizing antibodies . To help bridge...	Neutralizing antibodies block infection of cells and thus are considered important to elicit with vaccines . A central problem in HIV-1 vaccine design is that HIV-1 is extremely variable and employs a number of strategies to avoid being recognized by antibodies . Despite this , a subset of infected individuals mounts p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/structural", "genomics", "microbiology/immunity", "to", "infections", "virology/vaccines", "computational", "biology/comparative", "sequence", "analysis", "immunology/immune", "response", "computational", "biology/evolutionary", "modeling", "infectious", "diseases/hiv", ...	2010	Genetic Signatures in the Envelope Glycoproteins of HIV-1 that Associate with Broadly Neutralizing Antibodies
Selective routing of information between cortical areas is required in order to combine different sources of information according to cognitive demand . Recent experiments have suggested that alpha band activity originating from the pulvinar coordinates this inter-areal cortical communication . Using a computer model w...	Cortical oscillations have been linked to the process of communication between two brain areas . Here we investigated how a third area could control communication between two other brain areas . We find that the phase of a slower alpha-band oscillation is able to influence the power of faster gamma oscillations . By ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Models", "&", "methods" ]	[ "cognitive", "science", "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "brain", "social", "sciences", "electrophysiology", "neuroscience", "cognitive", "psychology", "gamma", "spectrometry", "extraction", "techniques", "crystallogr...	2017	Top-down control of cortical gamma-band communication via pulvinar induced phase shifts in the alpha rhythm
Recent advances in next-generation sequencing and computational technologies have enabled routine analysis of large-scale single-cell ribonucleic acid sequencing ( scRNA-seq ) data . However , scRNA-seq technologies have suffered from several technical challenges , including low mean expression levels in most genes and...	Single-cell RNA sequencing ( scRNA-seq ) can reveal complex and rare cell populations , uncover gene regulatory relationships , track the trajectories of distinct cell lineages in development , and identify cell-cell variabilities in human diseases and therapeutics . Although experimental methods for scRNA-seq are incr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "clinical", "research", "design", "engineering", "and", "technology", "statistics", "gene", "regulation", "computational", "biology", "cancers", "and", "neoplasms", "biomarkers", "oncology", "research", "design", ...	2019	A component overlapping attribute clustering (COAC) algorithm for single-cell RNA sequencing data analysis and potential pathobiological implications
Rural populations in the Gran Chaco region have large prevalence rates of Trypanosoma cruzi infection and very limited access to diagnosis and treatment . We implemented an innovative strategy to bridge these gaps in 13 rural villages of Pampa del Indio held under sustained vector surveillance and control . The non-ran...	Less than 1% of patients infected with Trypanosoma cruzi have access to parasiticidal treatment with the two available drugs , including millions of patients in the early chronic phase who would greatly benefit from treatment . Furthermore , rural populations living under poor and marginalized conditions usually have l...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "health", "care", "health", "care", "providers", "protozoans", "pharmaceutics", "neglected", "tropical", "d...	2017	Improving access to Chagas disease diagnosis and etiologic treatment in remote rural communities of the Argentine Chaco through strengthened primary health care and broad social participation
Interleukin ( IL ) -22 , an immune cell-derived cytokine whose receptor expression is restricted to non-immune cells ( e . g . epithelial cells ) , can be anti-inflammatory and pro-inflammatory . Mice infected with the tapeworm Hymenolepis diminuta are protected from dinitrobenzene sulphonic acid ( DNBS ) -induced coli...	Interleukin ( IL ) -22 , produced by innate and adaptive immune cells , plays a complex role in immunity; under specific conditions , targeting this cytokine could treat inflammatory diseases . The hygiene hypothesis suggests infection with helminth parasites could ameliorate inflammation . Here we show that IL-22 is r...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "helminths", "immunology", "parasitic", "diseases", "animals", "nematode", "infections", "colitis", "developmental", "biology", "gastroenterology", ...	2016	IL-22 Restrains Tapeworm-Mediated Protection against Experimental Colitis via Regulation of IL-25 Expression
Treponema pallidum infection evokes vigorous immune responses , resulting in tissue damage . Several studies have demonstrated that IL-17 may be involved in the pathogenesis of syphilis . However , the role of Th17 response in neurosyphilis remains unclear . In this study , Th17 in peripheral blood from 103 neurosyphil...	Syphilis , caused by the bacterium Treponema pallidum , can progress to affect the central nervous system ( CNS ) and cause damage in the brain and spinal cord , which is called neurosyphilis . While many neurosyphilis patients may not have any symptoms , some patients develop severe symptoms which can be life-threaten...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacterial", "diseases", "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "medicine", "and", "health", "sciences", "neurology" ]	2014	Increased Interleukin-17 in Peripheral Blood and Cerebrospinal Fluid of Neurosyphilis Patients
Cerebral malaria claims the lives of over 600 , 000 African children every year . To better understand the pathogenesis of this devastating disease , we compared the cellular dynamics in the cortical microvasculature between two infection models , Plasmodium berghei ANKA ( PbA ) infected CBA/CaJ mice , which develop ex...	Malaria remains one of the most serious health problems globally , but our understanding of the biology of the Plasmodium parasite and the pathogenesis of severe disease is still limited . Human cerebral malaria ( HCM ) , a severe neurological complication characterized by rapid progression from headache to convulsions...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "apicomplexa", "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "biology", "and", "life", "sciences", "cerebral", "malaria", "malaria", "tropical", "diseases", "parasitic", "diseases", "parasitology" ]	2014	Experimental Cerebral Malaria Pathogenesis—Hemodynamics at the Blood Brain Barrier
HLA-B27 exerts protective effects in hepatitis C virus ( HCV ) and human immunodeficiency virus ( HIV ) infections . While the immunological and virological features of HLA-B27-mediated protection are not fully understood , there is growing evidence that the presentation of specific immunodominant HLA-B*27-restricted...	HLA-B27 has a protective effect in hepatitis C virus ( HCV ) infection which could be linked to a single highly immunodominant HLA-B27-restricted CD8+ T-cell epitope . However , the immunological mechanisms determining this protective effect are poorly understood . In this study , we analyzed multiple immunological d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "adaptive", "immunity", "immune", "cells", "major", "histocompatibility", "complex", "antigen", "processing", "and", "recognition", "immunity", "immune", "activation", "antigen-presenting", "cells", "t", "cells", "immunology", "biology" ]	2012	Rapid Antigen Processing and Presentation of a Protective and Immunodominant HLA-B*27-restricted Hepatitis C Virus-specific CD8+ T-cell Epitope
The hippocampus is the main locus of episodic memory formation and the neurons there encode the spatial map of the environment . Hippocampal place cells represent location , but their role in the learning of preferential location remains unclear . The hippocampus may encode locations independently from the stimuli and ...	Episodic memories relate positive or negative experiences to environmental context . The neurophysiological mechanisms of this connection , however , remain unknown . Hippocampal place cells represent location , but it is unclear if they encode only the spatial representation of the environment or if they are also proc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "action", "potentials", "neurochemistry", "medicine", "and", "health", "sciences", "optogenetics", "dopaminergics", "membrane", "potential", "electrophysiology", "light", "neuroscience", "electromagnetic", "radiation", "luminescent", "proteins", "animal", "behavior", "yellow"...	2017	Place field assembly distribution encodes preferred locations
Trypanosomatid protozoan parasites lack a functional heme biosynthetic pathway , so must acquire heme from the environment to survive . However , the molecular pathway responsible for heme acquisition by these organisms is unknown . Here we show that L . amazonensis LHR1 , a homolog of the C . elegans plasma membrane h...	The biological activity of many proteins and enzymes requires heme , a large organic ring containing one iron atom at the center . It has been known for several decades that trypanosomatid protozoa lack several enzymes in the heme biosynthetic pathway . Therefore , unlike mammalian cells that can synthesize heme , thes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	Heme Uptake by Leishmania amazonensis Is Mediated by the Transmembrane Protein LHR1
The macrophage is the primary host cell for the fungal pathogen Histoplasma capsulatum during mammalian infections , yet little is known about fungal genes required for intracellular replication in the host . Since the ability to scavenge iron from the host is important for the virulence of most pathogens , we investig...	Fungal infections are a growing public health threat , particularly for immunocompromised individuals such as people with AIDS , organ transplant recipients , and cancer patients . Present antifungal therapies are often highly toxic and resistance to these therapies continues to rise . Histoplasma capsulatum is a patho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "microbiology/microbial", "physiology", "and", "metabolism", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2008	Histoplasma Requires SID1, a Member of an Iron-Regulated Siderophore Gene Cluster, for Host Colonization
Host genetic variations play an important role in several pathogenic diseases , and we have previously provided strong evidences that these genetic variations contribute significantly to differences in susceptibility and clinical outcomes of invasive Group A Streptococcus ( GAS ) infections , including sepsis and necro...	GAS bacteria are major human pathogens that are responsible for millions of infections worldwide , including severe and deadly NSTIs . Several studies have identified numerous GAS secreted virulence factors including proteases , DNases , and superantigens , which mediate several pathologic features of GAS NSTIs . Howev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dermatology", "medicine", "and", "health", "sciences", "quantitative", "trait", "loci", "biopsy", "gene", "regulation", "population", "genetics", "surgical", "and", "invasive", "medical", "procedures", "animal", "models", "model", "organisms", "skin", "infections", "...	2016	Genetic Architecture of Group A Streptococcal Necrotizing Soft Tissue Infections in the Mouse
The recent whole-genome scan for breast cancer has revealed the FGFR2 ( fibroblast growth factor receptor 2 ) gene as a locus associated with a small , but highly significant , increase in the risk of developing breast cancer . Using fine-scale genetic mapping of the region , it has been possible to narrow the causativ...	Recently , a number of whole-genome association studies have identified genes that predispose individuals to common diseases such as cancer . The challenge now is to understand how the identified risk loci contribute to disease , since the majority of these loci are located within introns ( which are discarded after tr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics" ]	2008	Allele-Specific Up-Regulation of FGFR2 Increases Susceptibility to Breast Cancer
Chromosome 3p21–22 harbors two clusters of chemokine receptor genes , several of which serve as major or minor coreceptors of HIV-1 . Although the genetic association of CCR5 and CCR2 variants with HIV-1 pathogenesis is well known , the role of variation in other nearby chemokine receptor genes remain unresolved . We g...	Human chemokine receptors are cell surface proteins that may be utilized by HIV-1 for entry into host cells . DNA variation in the HIV-1 major coreceptor CCR5 affects HIV-1 infection and progression . This study comprehensively assesses the role of genetic variation of multiple chemokine receptor genes clustered in the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "genetic", "association", "studies", "hiv", "genetics", "biology", "human", "genetics", "viral", "diseases", "genetics", "and", "genomics" ]	2011	Role of Exonic Variation in Chemokine Receptor Genes on AIDS: CCRL2 F167Y Association with Pneumocystis Pneumonia
Numerous problems encountered in computational biology can be formulated as optimization problems . In this context , optimization of drug release characteristics or dosing schedules for anticancer agents has become a prominent area not only for the development of new drugs , but also for established drugs . However , ...	Mathematical models of the disease processes are widely used in computational biology to quantitatively describe the time course of disease progression and are often linked to pharmacokinetic–pharmacodynamic models in order to evaluate the effect of drug treatment on disease . Once the models are built from observed in...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "urology", "medicine", "and", "health", "sciences", "drug", "absorption", "cancer", "treatment", "sorption", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumors", "surgical", "and", "invasive", "medical", "procedures", "hormones", "castration", "oncology", ...	2018	Optimal dynamic control approach in a multi-objective therapeutic scenario: Application to drug delivery in the treatment of prostate cancer
Enveloped viruses need to fuse with a host cell membrane in order to deliver their genome into the host cell . While some viruses fuse with the plasma membrane , many viruses are endocytosed prior to fusion . Specific cues in the endosomal microenvironment induce conformational changes in the viral fusion proteins lead...	Enveloped viruses need to fuse with a host cell membrane in order to deliver their genome into the host cell . In the present study we investigated the entry of coronaviruses ( CoVs ) . CoVs are important pathogens of animals and man with high zoonotic potential as demonstrated by the emergence of SARS- and MERS-CoVs ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "viral", "attachment", "viral", "entry", "coronaviruses", "feline", "coronavirus", "host", "cells", "rna", "viruses", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "medica...	2014	Coronavirus Cell Entry Occurs through the Endo-/Lysosomal Pathway in a Proteolysis-Dependent Manner
Dendritic cells ( DC ) , including those of the skin , act as sentinels for intruding microorganisms . In the epidermis , DC ( termed Langerhans cells , LC ) are sessile and screen their microenvironment through occasional movements of their dendrites . The spatio-temporal orchestration of antigen encounter by dermal D...	Cutaneous Leishmaniasis is a difficult-to-treat disease affecting millions of people worldwide . Hence , there is high demand for the development of vaccines against Leishmania parasites , begging for a better understanding of immune responses against this pathogen . Dendritic cells , as part of the innate immune syste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2008	Migratory Dermal Dendritic Cells Act as Rapid Sensors of Protozoan Parasites
Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts . In one , mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other . In the...	Rhizobia are an important group of bacteria that can enter into mutually beneficial symbiotic interactions with legume plants to fix atmospheric nitrogen . However , in order to do so , a complex dialog involving the exchange of chemical and molecular signals must occur between partners . Some species of beneficial rhi...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "plant", "microbiology", "microbial", "evolution", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2013	Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum
Because topical therapy is easy and usually painless , it is an attractive first-line option for the treatment of localized cutaneous leishmaniasis ( LCL ) . Promising ointments are in the final stages of development . One main objective was to help optimize the treatment modalities of human LCL with WR279396 , a topic...	When initiating the cutaneous disease named cutaneous leishmaniasis ( CL ) , Leishmania parasites develop within the parasitophorous vacuoles of phagocytes residing in and/or recruited to the dermis , a process leading to more or less chronic dermis and epidermis-damaging inflammatory processes . Topical treatment of C...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2007	Optimization of Topical Therapy for Leishmania major Localized Cutaneous Leishmaniasis Using a Reliable C57BL/6 Model
The spinal cord participates in the execution of skilled movements by translating high-level cerebral motor representations into musculotopic commands . Yet , the extent to which motor skill acquisition relies on intrinsic spinal cord processes remains unknown . To date , attempts to address this question were limited ...	When we acquire a new motor skill—for example , learning how to play a musical instrument—new synaptic connections are induced in a distributed network of brain areas . There is ample evidence from human neuroimaging studies for this high plasticity of the brain , but what about the spinal cord , the main link between ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Simultaneous Brain–Cervical Cord fMRI Reveals Intrinsic Spinal Cord Plasticity during Motor Sequence Learning
Clostridium difficile is the most common cause of antibiotic-associated nosocomial infection in the United States . C . difficile secretes two homologous toxins , TcdA and TcdB , which are responsible for the symptoms of C . difficile associated disease . The mechanism of toxin action includes an autoprocessing event w...	Clostridium difficile is an anaerobic spore-forming bacterium that infects the human colon and causes diarrhea , pseudomembranous colitis , and toxic megacolon . Most people that develop disease symptoms have undergone antibiotic treatment , which alters the normal gut flora and allows C . difficile to flourish . C . d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2012	Clostridium difficile Toxin B Causes Epithelial Cell Necrosis through an Autoprocessing-Independent Mechanism
Heart valve anomalies are some of the most common congenital heart defects , yet neither the genetic nor the epigenetic forces guiding heart valve development are well understood . When functioning normally , mature heart valves prevent intracardiac retrograde blood flow; before valves develop , there is considerable r...	The growth and development of vertebrates are critically dependent on efficient cardiac output to drive blood circulation . An essential step of heart development is the formation of heart valves , whose leaflets are made through a complex set of cellular rearrangements of endothelial cells . Endothelial cells experien...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cardiovascular", "disorders/hemodynamics", "developmental", "biology/morphogenesis", "and", "cell", "biology" ]	2009	Reversing Blood Flows Act through klf2a to Ensure Normal Valvulogenesis in the Developing Heart
Despite recent interest in reconstructing neuronal networks , complete wiring diagrams on the level of individual synapses remain scarce and the insights into function they can provide remain unclear . Even for Caenorhabditis elegans , whose neuronal network is relatively small and stereotypical from animal to animal ,...	Connectomics , the generation and analysis of neuronal connectivity data , stands to revolutionize neurobiology just as genomics has revolutionized molecular biology . Indeed , since neuronal networks are the physical substrates upon which neural functions are carried out , their structural properties are intertwined w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/motor", "systems", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2011	Structural Properties of the Caenorhabditis elegans Neuronal Network
Close interpersonal contact likely drives spatial clustering of cases of cholera and diarrhea , but spatial clustering of risk factors may also drive this pattern . Few studies have focused specifically on how exposures for disease cluster at small spatial scales . Improving our understanding of the micro-scale cluster...	While clustering of cholera incidence had been previously described , the relative role of similar risk behaviors versus transmission dynamics is not well understood . We explored how risk factors for cholera clustered at the sub-community scale , and found significant more correlation in risk behaviors among spatially...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "tropical", "diseases", "condensed", "matter", "physics", "geographical", "locations", "health", "care", "bacterial", "diseases", "physiological", "processes", ...	2016	Micro-scale Spatial Clustering of Cholera Risk Factors in Urban Bangladesh
RNA–directed DNA methylation ( RdDM ) is an epigenetic control mechanism driven by small interfering RNAs ( siRNAs ) that influence gene function . In plants , little is known of the involvement of the RdDM pathway in regulating traits related to immune responses . In a genetic screen designed to reveal factors regulat...	The influence of epigenetic regulation in controlling the adaptive responses of living organisms to changes in the environment is becoming a common theme in biology . RNA–directed DNA methylation ( RdDM ) is an epigenetic control mechanism driven by a subset of noncoding small interfering RNAs ( siRNAs ) that influence...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "model", "organisms", "plant", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2011	The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity
Quantifying epidemiological dynamics is crucial for understanding and forecasting the spread of an epidemic . The coalescent and the birth-death model are used interchangeably to infer epidemiological parameters from the genealogical relationships of the pathogen population under study , which in turn are inferred from...	The control or prediction of an epidemic outbreak requires the quantification of the parameters of transmission and recovery . These parameters can be inferred from phylogenetic relationships among the pathogen strains isolated from infected individuals . The coalescent and the birth-death process are two mathematical ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phylogenetics", "plant", "science", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "epidemiology", "plant", "pathology", "biology", "and", "life", "sciences", "population", "biology", "evolutionary", "biology", "evolutionary", "systemat...	2014	Inference of Epidemiological Dynamics Based on Simulated Phylogenies Using Birth-Death and Coalescent Models
Asexual spores ( conidia ) are the infectious propagules of many pathogenic fungi , and the capacity to sense the host environment and trigger conidial germination is a key pathogenicity determinant . Germination of conidia requires the de novo establishment of a polarised growth axis and consequent germ tube extension...	Many fungal infections are initiated by the entry of dormant fungal spores into their host . Once inside the host these dormant spores must reactivate ( germinate ) for the infection to proceed . Productive infections necessitate that the fungus grow and divide within the host , which makes understanding the mechanisms...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology", "yeast", "and", "fungi", "microbiology", "genetics", "and", "genomics" ]	2007	A p21-Activated Kinase Is Required for Conidial Germination in Penicillium marneffei
Arthropod-borne viruses ( arboviruses ) are among the most common agents of human febrile illness worldwide and the most important emerging pathogens , causing multiple notable epidemics of human disease over recent decades . Despite the public health relevance , little is know about the geographic distribution , relat...	Over recent decades , the variety and quantity of diseases caused by viruses transmitted to humans by mosquitoes and other arthropods ( also known as arboviruses ) have increased around the world . One difficulty in studying these diseases is the fact that the symptoms are often non-descript , with patients reporting s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "virology/emerging", "viral", "diseases" ]	2010	Arboviral Etiologies of Acute Febrile Illnesses in Western South America, 2000–2007
It is important that bacterium can coordinately deliver several effectors into host cells to disturb the cellular progress during infection , however , the precise role of effectors in host cell cytosol remains to be resolved . In this study , we identified a new bacterial virulence effector from pathogenic Edwardsiell...	Thioredoxin ( Trx ) is universally conserved thiol-oxidoreductase that regulates numerous cellular pathways under thiol-based redox control in both prokaryotic and eukaryotic organisms . Despite its central importance , the mechanism of bacterial Trx recognizes its target proteins in host cellular signaling remains unk...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "fish", "viral", "transmission", "and", "infection", "redox", "signaling", "hela", "cells", "molecular", "probe", "techniques", "biological", "cultures", "immunoblotting", "vertebrates", "microbiology", "animals", "animal", "models", "osteichthyes", "de...	2019	The Edwardsiella piscicida thioredoxin-like protein inhibits ASK1-MAPKs signaling cascades to promote pathogenesis during infection
The loop-mediated isothermal amplification ( LAMP ) assay , with its advantages of simplicity , rapidity and cost effectiveness , has evolved as one of the most sensitive and specific methods for the detection of a broad range of pathogenic microorganisms including African trypanosomes . While many LAMP-based assays ar...	Human African trypanosomiasis or sleeping sickness is a fatal disease ( if untreated ) spread by bloodsucking tsetse flies . Trypanosome parasites first enter the blood and lymph and eventually invade the brain . In rural clinical settings , diagnosis still relies on the detection of these microbes in blood and cerebro...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biology" ]	2011	Using Detergent to Enhance Detection Sensitivity of African Trypanosomes in Human CSF and Blood by Loop-Mediated Isothermal Amplification (LAMP)
The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions , but such gene–environment interactions are poorly understood . Recently developed approaches that treat transcript abundances of thousands of genes as quantitative traits offer the opportunity to broadly ch...	Individuals frequently encounter different environmental conditions , and the physiological and behavioral responses to these conditions can depend on an individual's genetic makeup . This phenomenon is known as gene–environment interaction . For example , individuals who are infected with the Plasmodium falciparum par...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "genetics", "and", "genomics" ]	2008	Gene–Environment Interaction in Yeast Gene Expression
Sfl1p and Sfl2p are two homologous heat shock factor-type transcriptional regulators that antagonistically control morphogenesis in Candida albicans , while being required for full pathogenesis and virulence . To understand how Sfl1p and Sfl2p exert their function , we combined genome-wide location and expression analy...	Candida albicans can switch from a harmless colonizer of body organs to a life-threatening invasive pathogen . This switch is linked to the ability of C . albicans to undergo a yeast-to-filament shift induced by various cues , including temperature . Sfl1p and Sfl2p are two transcription factors required for C . albica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "cellular", "stress", "responses", "genetic", "networks", "microbiology", "fungal", "physiology", "dna", "transcription", "genome", "analysis", "tools", "model", "organisms", "mycology", "gene", "expression", "microbial", "pathogens", ...	2013	A Comprehensive Functional Portrait of Two Heat Shock Factor-Type Transcriptional Regulators Involved in Candida albicans Morphogenesis and Virulence
Protein domain motion is often implicated in biological electron transfer , but the general significance of motion is not clear . Motion has been implicated in the transfer of electrons from human cytochrome P450 reductase ( CPR ) to all microsomal cytochrome P450s ( CYPs ) . Our hypothesis is that tight coupling of mo...	Enzymes are proteins that catalyze a large array of chemical reactions , often in partnership with other enzymes . We understand in detail the chemical mechanisms of many of these reactions; however , the importance of the physical movements of enzymes during catalysis ( or protein dynamics ) is , increasingly , becomi...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biology", "biophysics" ]	2011	Coupled Motions Direct Electrons along Human Microsomal P450 Chains
A key challenge in movement ecology is to understand how animals move in nature . Previous studies have predicted that animals should perform a special class of random walks , called Lévy walk , to obtain more targets . However , some empirical studies did not support this hypothesis , and the relationship between sear...	Moving agents should efficiently search for targets ( e . g . , food , prey , or specific locations ) when lacking information about the location of the targets . For this random search problem , the Lévy walk hypothesis claims that Lévy walk movement patterns ( i . e . , each step length follows a distribution that is...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Lévy Walks Suboptimal under Predation Risk
Many pathogens , particularly those that require their host for survival , have devised mechanisms to subvert the host immune response in order to survive and replicate intracellularly . Legionella pneumophila , the causative agent of Legionnaires' disease , promotes intracellular growth by translocating proteins into ...	Translation inhibition is a common virulence mechanism used by a number of pathogens ( e . g . Diphtheria Toxin , Shiga Toxin and Pseudomonas Exotoxin A ) . It has been a mystery how host cells mount a pathogen-specific response and clear infection under conditions where protein synthesis is blocked by pathogens . Usin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "immunology", "microbiology", "molecular", "cell", "biology" ]	2014	The Frustrated Host Response to Legionella pneumophila Is Bypassed by MyD88-Dependent Translation of Pro-inflammatory Cytokines
About 85% of the maize genome consists of highly repetitive sequences that are interspersed by low-copy , gene-coding sequences . The maize community has dealt with this genomic complexity by the construction of an integrated genetic and physical map ( iMap ) , but this resource alone was not sufficient for ensuring th...	The maize genome contains abundant repeats interspersed by low-copy , gene-coding sequences that make it a challenge to sequence; consequently , current BAC sequence assemblies average 11 contigs per clone . The iMap deals with such complexity by the judicious integration of IBM genetic and B73 physical maps , but the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "genetics", "and", "genomics/chromosome", "biology" ]	2009	A Single Molecule Scaffold for the Maize Genome
Understanding the medical effect of an ever-growing number of human variants detected is a long term challenge in genetic counseling . Functional assays , based on in vitro or in vivo evaluations of the variant effects , provide essential information , but they require robust statistical validation , as well as adapted...	Human genetics has entered a new age with the advent of next generation sequencing . However , this great advance also comes with new concerns . Currently , the extensive use of multi-gene panels , whole exome and whole genome sequencing , is generating an ever-growing number of new DNA sequence variations detected in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "decision", "making", "gene", "regulation", "pathogens", "microbiology", "cloning", "neuroscience", "plasmid", "construction", "mutation", "probability", "distribution", "mathematics", ...	2016	Functional Assessment of Genetic Variants with Outcomes Adapted to Clinical Decision-Making
Escherichia coli ( E . coli ) bacteria govern their trajectories by switching between running and tumbling modes as a function of the nutrient concentration they experienced in the past . At short time one observes a drift of the bacterial population , while at long time one observes accumulation in high-nutrient regio...	The chemotaxis of Escherichia coli is a prototypical model of navigational strategy . The bacterium maneuvers by switching between near-straight motion , termed runs , and tumbles which reorient its direction . To reach regions of high nutrient concentration , the run-durations are modulated according to the nutrient c...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "physics", "statistical", "mechanics", "theoretical", "biology", "biophysics", "theory", "biology", "computational", "biology", "biophysics", "simulations", "biophysics" ]	2011	Chemotaxis when Bacteria Remember: Drift versus Diffusion
Gene expression signatures that are predictive of therapeutic response or prognosis are increasingly useful in clinical care; however , mechanistic ( and intuitive ) interpretation of expression arrays remains an unmet challenge . Additionally , there is surprisingly little gene overlap among distinct clinically valida...	Clinical utilization of multi-gene expression signatures that are predictive of therapeutic response has been steadily increasing , however , interpretation of such results remains challenging because multi-gene signatures , generated from analyzing different patient cohorts , tend to be equally predictive but contain ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "medicine", "genomics", "biology", "computational", "biology", "cancers", "and", "neoplasms", "genetics", "and", "genomics" ]	2012	Single Sample Expression-Anchored Mechanisms Predict Survival in Head and Neck Cancer
Ribosome profiling produces snapshots of the locations of actively translating ribosomes on messenger RNAs . These snapshots can be used to make inferences about translation dynamics . Recent ribosome profiling studies in yeast , however , have reached contradictory conclusions regarding the average translation rate of...	Ribosome profiling measures the precise locations of millions of actively translating ribosomes on mRNAs . In theory , the frequency with which ribosomes are observed positioned over each type of codon can be used to quantify the speed with which each codon is translated . In practice , ribosome profiling experiments i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast
Although more than 20 genetic susceptibility loci have been reported for type 2 diabetes ( T2D ) , most reported variants have small to moderate effects and account for only a small proportion of the heritability of T2D , suggesting that the majority of inter-person genetic variation in this disease remains to be deter...	Type 2 diabetes , a complex disease affecting more than a billion people worldwide , is believed to be caused by both environmental and genetic factors . Although some studies have shown that certain genes may make some people more susceptible to type 2 diabetes than others , the genes reported to date have only a smal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics" ]	2010	Identification of New Genetic Risk Variants for Type 2 Diabetes
Studies in fission yeast have previously identified evolutionarily conserved shelterin and Stn1-Ten1 complexes , and established Rad3ATR/Tel1ATM-dependent phosphorylation of the shelterin subunit Ccq1 at Thr93 as the critical post-translational modification for telomerase recruitment to telomeres . Furthermore , shelte...	Stable maintenance of telomeres is critical to maintain a stable genome and to prevent accumulation of undesired mutations that may lead to formation of tumors . Telomere dysfunction can also lead to premature aging due to depletion of the stem cell population , highlighting the importance of understanding the regulato...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Fission Yeast Shelterin Regulates DNA Polymerases and Rad3ATR Kinase to Limit Telomere Extension
There is increasing consensus that males are more vulnerable than females to infection by several pathogens . However , the underlying mechanism needs further investigation . Here , it was showed that knockdown of androgen receptor ( AR ) expression or pre-treatment with 5α-dihydrotestosterone , the AR agonist , led to...	Although KS incidence is higher in males , which correlates with higher seroprevalence and viral DNA levels in the blood , little is known whether male sex steroids contribute to this disparity . In the present study , we have confirmed the role of both AR and its ligand in promoting KSHV primary infection in target ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "293t", "cells", "biological", "cultures", "cell", "processes", "microbiology", "plasmid", "construction", "viruses", "dna", "vir...	2017	Male hormones activate EphA2 to facilitate Kaposi’s sarcoma-associated herpesvirus infection: Implications for gender disparity in Kaposi’s sarcoma
A non-targeted metabolomics-based approach is presented that enables the study of pathways in response to drug action with the aim of defining the mode of action of trypanocides . Eflornithine , a polyamine pathway inhibitor , and nifurtimox , whose mode of action involves its metabolic activation , are currently used ...	Understanding drug mode of action is of fundamental importance . Of the five drugs in use against human African trypanosomiasis ( HAT ) , convincing evidence on a specific mode of action has been proposed only for the polyamine pathway inhibitor eflornithine . Eflornithine is currently used with nifurtimox as first lin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biology" ]	2012	Untargeted Metabolomics Reveals a Lack Of Synergy between Nifurtimox and Eflornithine against Trypanosoma brucei
Synaptic long-term potentiation ( LTP ) at spinal neurons directly communicating pain-specific inputs from the periphery to the brain has been proposed to serve as a trigger for pain hypersensitivity in pathological states . Previous studies have functionally implicated the NMDA receptor-NO pathway and the downstream s...	Pain is an important physiological function that protects our body from harm . Pain-sensing neurons , called nociceptors , transduce harmful stimuli into electrical signals and transmit this information to the brain via the spinal cord . When nociceptors are persistently activated , such as after injury , the connectio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "neuroscience" ]	2012	Presynaptically Localized Cyclic GMP-Dependent Protein Kinase 1 Is a Key Determinant of Spinal Synaptic Potentiation and Pain Hypersensitivity
The gut-to-brain axis exhibits significant control over motivated behavior . However , mechanisms supporting this communication are poorly understood . We reveal that a gut-based bariatric surgery chronically elevates systemic bile acids and attenuates cocaine-induced elevations in accumbal dopamine . Notably , this su...	Communication between the gut and the brain is increasingly being appreciated as influencing motivated behavior . The gut can influence brain function through secreted hormones traveling through the blood and entering the brain . We utilize a weight-loss surgery designed to elevate one class of circulating hormones , b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biliary", "system", "alkaloids", "medicine", "and", "health", "sciences", "liver", "body", "fluids", "chemical", "compounds", "gallbladder", "bile", "vertebrates", "mice", "animals", "mammals", "biological", "locomotion", "surgical", "and", "invasive", "medical", "pr...	2018	Bile diversion, a bariatric surgery, and bile acid signaling reduce central cocaine reward
The -function and the -function are phenomenological models that are widely used in the context of timing interceptive actions and collision avoidance , respectively . Both models were previously considered to be unrelated to each other: is a decreasing function that provides an estimation of time-to-contact ( ttc ) in...	In 1957 , Sir Fred Hoyle published a science fiction novel in which he described humanity's encounter with an extraterrestrial life form . It came in the shape of a huge black cloud which approached the earth . Hoyle proposed a formula ( “” ) for computing the remaining time until contact ( “ttc” ) of the cloud with th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "signal", "processing", "neuroscience", "signal", "filtering", "cognitive", "neuroscience", "behavioral", "neuroscience", "mathematics", "computational", "neuroscience", "circuit", "models", "biology", "differential", "equations", "visual", "system", "calculus", "psychophysic...	2012	Unifying Time to Contact Estimation and Collision Avoidance across Species
The small GTPase Rab27a has been shown to control membrane trafficking and microvesicle transport pathways , in particular the secretion of exosomes . In the liver , high expression of Rab27a correlates with the development of hepatocellular carcinoma . We discovered that low abundance of Rab27a resulted in decreased h...	Eukaryotic cells constantly expel a variety of small vesicles that are loaded with proteins , nucleic acids and other small compounds that were produced inside the cell . One particular kind of vesicle is called exosome . Exosomes are initially located in multivesicular compartments inside cells and are docked at the c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Supporting Role for GTPase Rab27a in Hepatitis C Virus RNA Replication through a Novel miR-122-Mediated Effect
In order to control malaria , it is important to understand the genetic structure of the parasites in each endemic area . Plasmodium vivax is widely distributed in the tropical to temperate regions of Asia and South America , but effective strategies for its elimination have yet to be designed . In South Korea , for ex...	Vivax malaria is widely prevalent , mainly in Asia and South America with 390 million reported cases in 2009 . Worldwide , in the same year , 2 . 85 billion people were at risk . Plasmodium vivax is prevalent not only in tropical and subtropical areas but also in temperate areas where there are no mosquitoes in cold se...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "ecology", "epidemiology", "global", "health", "genetics", "biology", "population", "biology", "public", "health", "genetics", "and", "genomics" ]	2012	Population Structure and Transmission Dynamics of Plasmodium vivax in the Republic of Korea Based on Microsatellite DNA Analysis
Patients infected by Plasmodium vivax or Plasmodium ovale suffer repeated clinical attacks without primaquine therapy against latent stages in liver . Primaquine causes seriously threatening acute hemolytic anemia in patients having inherited glucose-6-phosphate dehydrogenase ( G6PD ) deficiency . Access to safe primaq...	G6PD is an enzyme that chemically protects us from otherwise toxic substances , like some chemotherapeutic agents . About 8% of people exposed to malaria have an inherited disorder that impairs G6PD activity , leaving them vulnerable to harm by an important therapy against malaria , primaquine . This drug alone prevent...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "plasmodium", "drugs", "tropical", "diseases", "parasitic", "diseases", "anemia", "parasitic", "protozoans", "parasitology", "organisms", "apicomplexa", "protozoans", "red...	2016	Assessment of Point-of-Care Diagnostics for G6PD Deficiency in Malaria Endemic Rural Eastern Indonesia
The blood-feeding hookworm Necator americanus infects hundreds of millions of people worldwide . In order to elucidate fundamental molecular biological aspects of this hookworm , the transcriptome of the adult stage of Necator americanus was explored using next-generation sequencing and bioinformatic analyses . A total...	The blood-feeding hookworm Necator americanus infects hundreds of millions of people . To elucidate fundamental molecular biological aspects of this hookworm , the transcriptome of adult Necator americanus was studied using next-generation sequencing and in silico analyses . Contigs ( n = 19 , 997 ) were assembled from...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics", "computational", "biology/transcriptional", "regulation" ]	2010	Massively Parallel Sequencing and Analysis of the Necator americanus Transcriptome
Different synonymous codons are favored by natural selection for translation efficiency and accuracy in different organisms . The rules governing the identities of favored codons in different organisms remain obscure . In fact , it is not known whether such rules exist or whether favored codons are chosen randomly in e...	Codon bias is a long recognized and long studied biological phenomenon . Yet several basic questions regarding codon usage remain unresolved . Here , we address one such basic open question: the identity of the codons that are favoured by selection for translation accuracy and efficiency varies greatly and , at first g...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "molecular", "biology/translation", "mechanisms", "microbiology/microbial", "evolution", "and", ...	2009	General Rules for Optimal Codon Choice
Spontaneous waves in the developing retina are essential in the formation of the retinotopic mapping in the visual system . From experiments in rabbits , it is known that the earliest type of retinal waves ( stage I ) is nucleated spontaneously , propagates at a speed of 451±91 μm/sec and relies on gap junction couplin...	Retinal waves are a prominent example of spontaneous activity that is observed in neuronal systems of many different species during development . Spatio-temporally correlated bursts travel across the retina at a few hundred μm/sec to facilitate the maturation of the underlying neuronal circuits . Even at the earliest s...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "action", "potentials", "nervous", "system", "membrane", "potential", "ocular", "anatomy", "condensed", "matter", "physics", "junctional", "complexes", "electrophysiology", "neuroscience", "gap", "junctions", ...	2019	Gap junctions set the speed and nucleation rate of stage I retinal waves
The lysin LysGH15 , which is derived from the staphylococcal phage GH15 , demonstrates a wide lytic spectrum and strong lytic activity against methicillin-resistant Staphylococcus aureus ( MRSA ) . Here , we find that the lytic activity of the full-length LysGH15 and its CHAP domain is dependent on calcium ions . To el...	The staphylococcal phage lysin LysGH15 demonstrates great potential against methicillin-resistant Staphylococcus aureus ( MRSA ) . Here , we report that the lytic activity of LysGH15 and its CHAP domain is dependent on calcium ions . To elucidate the molecular mechanism , we determined the structures of three individua...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gram", "positive", "bacteria", "staphylococcus", "medical", "microbiology", "microbial", "pathogens", "microbial", "control", "biology", "and", "life", "sciences", "microbiology", "bacterial", "pathogens" ]	2014	Structural and Biochemical Characterization Reveals LysGH15 as an Unprecedented “EF-Hand-Like” Calcium-Binding Phage Lysin
Buruli ulcer ( BU ) vaccine design faces similar challenges to those observed during development of prophylactic tuberculosis treatments . Multiple BU vaccine candidates , based upon Mycobacterium bovis BCG , altered Mycobacterium ulcerans ( MU ) cells , recombinant MU DNA , or MU protein prime-boosts , have shown prom...	Mycobacterium ulcerans ( MU ) infection causes a highly disfiguring , necrotic skin disease known as Buruli ulcer ( BU ) . Antibiotic treatments have low efficacy if the infection is diagnosed after ulceration begins , leading to frequent dependence on surgical removal of infected tissues . A prophylactic vaccine for B...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "immunology", "tropical", "diseases", "vaccines", "preventive", "medicine", "bacterial", "diseases", "neglected", "tropical", "diseases", "vaccination", "and", "immuniz...	2016	Overexpression of a Mycobacterium ulcerans Ag85B-EsxH Fusion Protein in Recombinant BCG Improves Experimental Buruli Ulcer Vaccine Efficacy
Duplications of genes encoding highly connected and essential proteins are selected against in several species but not in human , where duplicated genes encode highly connected proteins . To understand when and how gene duplicability changed in evolution , we compare gene and network properties in four species ( Escher...	Gene copy number is often tightly controlled because it directly affects the gene dosage . In several species , including yeast , worm , and fly , genes that have a single gene copy ( singleton genes ) encode proteins with several connections in the protein interaction network ( hubs ) as well as essential proteins . S...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "genomics", "cancer", "genetics", "genome", "evolution", "genetics", "biology", "computational", "biology", "comparative", "genomics", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2011	Modification of Gene Duplicability during the Evolution of Protein Interaction Network
Wild and domesticated Atlantic salmon males display large variation for sea age at sexual maturation , which varies between 1–5 years . Previous studies have uncovered a genetic predisposition for variation of age at maturity with moderate heritability , thus suggesting a polygenic or complex nature of this trait . The...	For most species the factors that contribute to the genetic predisposition for age at maturity are currently unknown . In salmon aquaculture early maturation is negative for the growth , disease resistance and flesh quality . In addition , using populations of salmon selected to mature late may limit the genetic impact...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The vgll3 Locus Controls Age at Maturity in Wild and Domesticated Atlantic Salmon (Salmo salar L.) Males
Biologically inspired deep convolutional neural networks ( CNNs ) , trained for computer vision tasks , have been found to predict cortical responses with remarkable accuracy . However , the internal operations of these models remain poorly understood , and the factors that account for their success are unknown . Here ...	How does visual cortex compute behaviorally relevant properties of the local environment from sensory inputs ? For decades , computational models have been able to explain only the earliest stages of biological vision , but recent advances in deep neural networks have yielded a breakthrough in the modeling of high-leve...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "engineering", "and", "technology", "applied", "mathematics", "brain", "social", "sciences", "neuroscience", "magnetic", "resonance"...	2018	Computational mechanisms underlying cortical responses to the affordance properties of visual scenes

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