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Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation . We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory...	Understanding how genetic variation between individuals determines variation in observable traits or disease risk is one of the core aims of genetics . It is known that genetic variation often affects gene regulatory DNA elements and directly causes variation in expression of nearby genes . This effect in turn cascades...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "gene", "regulation", "population", "genetics", "simulation", "and", "modeling", "regulator", "genes", "micrornas", "probability", "distribution", "mathematics", "non-coding", "rna", "gene", "types", "population", "biology", "research", "and", "analysis", "methods", "ge...	2017	Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data
Microparticles ( MPs ) are cell–cell communication vesicles derived from the cell surface plasma membrane , although they are not known to originate from cardiac ventricular muscle . In ventricular cardiomyocytes , the membrane deformation protein cardiac bridging integrator 1 ( cBIN1 or BIN1+13+17 ) creates transverse...	Microparticles are small vesicles generated from the cell surface membrane and externally released for communication with other cells . We now show that heart ventricular muscle cells , which form the main pumping chambers of the heart , release microparticles in both mouse and human . Ventricular microparticles arise ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "body", "fluids", "vesicles", "enzyme-linked", "immunoassays", "hela", "cells", "biological", "cultures", "membrane", "proteins", "immunoprecipitation", "cell", "cultures", "immunologic", "techniques", "cellula...	2017	The ESCRT-III pathway facilitates cardiomyocyte release of cBIN1-containing microparticles
Sleep loss causes profound cognitive impairments and increases the concentrations of adenosine and adenosine A1 receptors in specific regions of the brain . Time courses for performance impairment and recovery differ between acute and chronic sleep loss , but the physiological basis for these time courses is unknown . ...	Sleep loss is known to cause significant decrements in cognitive performance , but the physiological mechanisms responsible for this response are not well understood . Computational models have been developed to predict how individuals will cognitively perform under acute or chronic sleep loss , but they currently lack...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "physiology", "glycosylamines", "medicine", "and", "health", "sciences", "sleep", "deprivation", "cognitive", "neurology", "sleep", "mathematical", "models", "neuroscience", "homeostatic", "mechanisms", "physiological", "processes", "cognitive", "neuroscience", "rec...	2017	Modeling the adenosine system as a modulator of cognitive performance and sleep patterns during sleep restriction and recovery
Gene copy-number variations are widespread in natural populations , but investigating their phenotypic consequences requires contemporary duplications under selection . Such duplications have been found at the ace-1 locus ( encoding the organophosphate and carbamate insecticides’ target ) in the mosquito Anopheles gamb...	Mutations , whether they affect single nucleotides or large genomic regions , are responsible for the genetic variability that allows species to evolve in response to environmental changes . Duplication represents a class of mutation that results in polymorphism in the copy number of genes . Investigating the phenotypi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "animals", "invertebrate", "genomics", "developmental", "biology", "molecular", "biology", "techniques", "insect", "vectors", "research", "and", "analysis", "methods", "sequence", "analy...	2016	The ace-1 Locus Is Amplified in All Resistant Anopheles gambiae Mosquitoes: Fitness Consequences of Homogeneous and Heterogeneous Duplications
Transmission of malaria parasites relies on the formation of a specialized blood form called the gametocyte . Gametocytes of the human pathogen , Plasmodium falciparum , adopt a crescent shape . Their dramatic morphogenesis is driven by the assembly of a network of microtubules and an underpinning inner membrane comple...	Transmission of the malaria parasite from humans to mosquitoes relies on the formation of the specialised blood stage gametocyte . Plasmodium falciparum gametocytes mature over about 10 days , during which time they undergo a remarkable morphological transformation , eventually adopting a characteristic crescent shape ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "parasite", "groups", "microtubules", "vacuoles", "plasmodium", "gametocytes", "light", "microscopy", "parasitology", "germ", "cells", "membrane", "proteins", "apicomplexa", "microscopy", "cellular", "structures", "and", "organelles", "cytoskeleton", "research", "and", "a...	2017	Disrupting assembly of the inner membrane complex blocks Plasmodium falciparum sexual stage development
We propose a novel , closed-loop approach to tuning deep brain stimulation ( DBS ) for Parkinson’s disease ( PD ) . The approach , termed Phasic Burst Stimulation ( PhaBS ) , applies a burst of stimulus pulses over a range of phases predicted to disrupt pathological oscillations seen in PD . Stimulation parameters are ...	Deep brain stimulation ( DBS ) is effective at treating motor symptoms of patients with medication-refractory Parkinson’s disease ( PD ) . Currently , high frequency stimulation ( >100 Hz ) is tuned for each patient using a trial-and-error process . A systematic approach to tuning stimulation parameters based on patien...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "myoclonus", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "neurodegenerative", "diseases", "signal", "processing", "brain", "electrophysiology", "electrophysiology", "neuroscience", "surgical", "a...	2016	Phasic Burst Stimulation: A Closed-Loop Approach to Tuning Deep Brain Stimulation Parameters for Parkinson’s Disease
Many insect vectors of disease detect their hosts through olfactory cues , and thus it is of great interest to understand better how odors are encoded . However , little is known about the molecular underpinnings that support the unique function of coeloconic sensilla , an ancient and conserved class of sensilla that d...	Olfaction underlies the attraction of insect pests and vectors of disease to their plant and human hosts . In the genetic model insect Drosophila , the neuronal basis of odor coding has been extensively analyzed in the antenna , its major olfactory organ , but the molecular basis of odor coding has not . Additionally ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "molecular", "neuroscience", "medicine", "and", "health", "sciences", "neuroscience", "animals", "genome", "analysis", "gene", "types", "epidemiology", "insects", "disease", "vectors", "mutant", "genes", "arthropoda", "mosquitoes", "cellular", "neuroscien...	2014	An RNA-Seq Screen of the Drosophila Antenna Identifies a Transporter Necessary for Ammonia Detection
Investigating the relationship between brain structure and function is a central endeavor for neuroscience research . Yet , the mechanisms shaping this relationship largely remain to be elucidated and are highly debated . In particular , the existence and relative contributions of anatomical constraints and dynamical p...	By analogy with the road network , the human brain is defined both by its anatomy ( the ‘roads’ ) , that is , the way neurons are shaped , clustered together and connected to each others and its dynamics ( the ‘traffic’ ) : electrical and chemical signals of various types , shapes and strength constantly propagate thro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "computational", "biology", "biology", "anatomy", "and", "physiology" ]	2014	Relating Structure and Function in the Human Brain: Relative Contributions of Anatomy, Stationary Dynamics, and Non-stationarities
Derepression of transposable elements ( TEs ) in the course of epigenetic reprogramming of the mouse embryonic germline necessitates the existence of a robust defense that is comprised of PIWI/piRNA pathway and de novo DNA methylation machinery . To gain further insight into biogenesis and function of piRNAs , we studi...	Vast territories of animal genomes are populated by numerous types of mobile genetic elements ( or transposons ) that act predominantly as selfish parasites unconcerned with the impact of their activity on the well-being of the host . In response to the danger posed by transposons , organisms have evolved a defensive m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "genetics", "and", "genomics/animal", "genetics", "developmental", "biology/embryology", "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "genetics", "and", "genomics/gene", "expression", "molecular",...	2009	Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice
The causative agent of Legionnaires' disease , Legionella pneumophila , uses the Icm/Dot type IV secretion system ( T4SS ) to form in phagocytes a distinct “Legionella-containing vacuole” ( LCV ) , which intercepts endosomal and secretory vesicle trafficking . Proteomics revealed the presence of the small GTPase Ran an...	Legionella pneumophila is an environmental bacterium that grows within free-living amoebae and , upon inhalation , in human lung macrophages , thus causing the severe pneumonia Legionnaires' disease . Within amoebae or macrophages the bacteria form a distinct membrane-bound replication niche , the “Legionella-containin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Activation of Ran GTPase by a Legionella Effector Promotes Microtubule Polymerization, Pathogen Vacuole Motility and Infection
Orientation selectivity is the most striking feature of simple cell coding in V1 that has been shown to emerge from the reduction of higher-order correlations in natural images in a large variety of statistical image models . The most parsimonious one among these models is linear Independent Component Analysis ( ICA ) ...	Since the Nobel Prize winning work of Hubel and Wiesel it has been known that orientation selectivity is an important feature of simple cells in the primary visual cortex . The standard description of this stage of visual processing is that of a linear filter bank where each neuron responds to an oriented edge at a cer...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2009	Natural Image Coding in V1: How Much Use Is Orientation Selectivity?
The tumor-like growth of the metacestode larvae of the tapeworm E . multilocularis causes human alveolar echinococcosis , a severe disease mainly affecting the liver . The germinative cells , a population of adult stem cells , are crucial for the larval growth and development of the parasite within the hosts . Maintena...	Alveolar echinococcosis ( AE ) , caused by infection with the metacestode larvae of the tapeworm E . multilocularis , is a lethal disease in humans . A population of adult stem cells , called germinative cells , drive the cancer-like growth of the parasite within their host and are considered responsible for disease re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "phosphorylation", "vesicles", "atmospheric", "science", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "dna-binding", "proteins", "mitosis", "sequence", "motif", "analysis", "cellular", "structures", "and", "organelles", "rese...	2019	Impairing the maintenance of germinative cells in Echinococcus multilocularis by targeting Aurora kinase
Mammals evolved an endogenous timing system to coordinate their physiology and behaviour to the 24h period of the solar day . While it is well accepted that circadian rhythms are generated by intracellular transcriptional feedback loops , it is still debated which network motifs are necessary and sufficient for generat...	Circadian clocks are endogenous oscillators that drive daily rhythms in physiology , metabolism and behavior . The recent years have witnessed enormous progress in our understanding of the mechanistic and genetic basis of these clocks . While mathematical modelling has made important contributions to our current view o...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "synthetic", "genetic", "systems", "engineering", "and", "technology", "mechanisms", "of", "signal", "transduction", "gene", "regulation", "synthetic", "biology", "circadian", "oscillators", "network", "analysis", "chronobiology", "synthetic", "gene", "oscillators", "comp...	2016	Feedback Loops of the Mammalian Circadian Clock Constitute Repressilator
Type 2 diabetes is a leading cause of morbidity and mortality . While genetic variants have been found to influence the risk of type 2 diabetes mellitus , relatively few studies have focused on genes associated with glycated hemoglobin , an index of the mean blood glucose concentration of the preceding 8–12 weeks . Epi...	Type 2 diabetes is a leading cause of morbidity and mortality in both the developed and developing world . Because the main metabolic characteristic of diabetes is increased blood glucose concentration , we sought to uncover the genetic determinants of glycated hemoglobin , an index of the mean blood glucose concentrat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physiology/endocrinology", "genetics", "and", "genomics/complex", "traits", "diabetes", "and", "endocrinology/type", "2", "diabetes" ]	2008	Novel Association of HK1 with Glycated Hemoglobin in a Non-Diabetic Population: A Genome-Wide Evaluation of 14,618 Participants in the Women's Genome Health Study
The fungal disease chytridiomycosis , caused by Batrachochytrium dendrobatidis , is enigmatic because it occurs globally in both declining and apparently healthy ( non-declining ) amphibian populations . This distribution has fueled debate concerning whether , in sites where it has recently been found , the pathogen wa...	Amphibian species are facing a current global extinction crisis of unprecedented magnitude . The major factors causing their decline are the emerging disease chytridiomycosis and habitat destruction . Chytridiomycosis is caused by the aquatic fungus Batrachochytrium dendrobatidis and has been linked to species extincti...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/population", "genetics", "public", "health", "and", "epidemiology/infectious", "diseases", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2009	Rapid Global Expansion of the Fungal Disease Chytridiomycosis into Declining and Healthy Amphibian Populations
The understanding of G-protein coupled receptors ( GPCRs ) is undergoing a revolution due to increased information about their signaling and the experimental determination of structures for more than 25 receptors . The availability of at least one receptor structure for each of the GPCR classes , well separated in sequ...	G-protein coupled receptors ( GPCRs ) are a large superfamily of integral membrane proteins that share a characteristic 7 transmembrane helix fold . They detect various molecules outside of the cell and signal their presence to the inside of the cell . At least half of the 800 human GPCRs are potential drug targets , s...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "sequencing", "techniques", "crystal", "structure", "split-decomposition", "method", "condensed", "matter", "physics", "multiple", "alignment", "calculation", "protein", "structure", "prediction", "phylogenetic", "analysis", "protein", "structure", "sequence", "motif", "ana...	2016	Structure-Based Sequence Alignment of the Transmembrane Domains of All Human GPCRs: Phylogenetic, Structural and Functional Implications
Tumor microenvironmental stresses , such as hypoxia and lactic acidosis , play important roles in tumor progression . Although gene signatures reflecting the influence of these stresses are powerful approaches to link expression with phenotypes , they do not fully reflect the complexity of human cancers . Here , we des...	Gene signatures are a powerful tool to investigate biological processes in human cancer . However , it is clear that these gene signatures do not fully reflect the complexity of human cancer . Here we demonstrate how a latent factor model can improve the in vivo relevance of these pathway-associated gene signatures by ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/cancer", "genetics", "genetics", "and", "genomics/bioinformatics", "computational", "biology" ]	2010	Latent Factor Analysis to Discover Pathway-Associated Putative Segmental Aneuploidies in Human Cancers
The acquisition of neuraminidase ( NA ) inhibitor resistance by H5N1 influenza viruses has serious clinical implications , as this class of drugs can be an essential component of pandemic control measures . The continuous evolution of the highly pathogenic H5N1 influenza viruses results in the emergence of natural NA g...	Highly pathogenic avian H5N1 influenza viruses remain a potential pandemic threat . If vaccination is not available in the event of a pandemic , antiviral drugs such as neuraminidase ( NA ) inhibitors ( oseltamivir and zanamivir ) will be crucial for disease control . However , the emergence of NA inhibitor–resistant v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "infectious", "diseases/respiratory", "infections" ]	2010	Effect of Neuraminidase Inhibitor–Resistant Mutations on Pathogenicity of Clade 2.2 A/Turkey/15/06 (H5N1) Influenza Virus in Ferrets
Heterotaxy , a birth defect involving left-right patterning defects , and primary ciliary dyskinesia ( PCD ) , a sinopulmonary disease with dyskinetic/immotile cilia in the airway are seemingly disparate diseases . However , they have an overlapping genetic etiology involving mutations in cilia genes , a reflection of ...	Heterotaxy is a birth defect involving randomization of left-right body axis . Its genetic etiology is still poorly understood , but recent studies suggest mutations in genes causing primary ciliary dyskinesia ( PCD ) , a sinopulmonary disease , also can cause heterotaxy . Moreover , heterotaxy patients can show airway...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "children", "medicine", "and", "health", "sciences", "morpholino", "rna", "interference", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "vertebrates", "animals", "animal", "models", "osteichthyes", "age", "groups", "developmental", "bi...	2016	DNAH6 and Its Interactions with PCD Genes in Heterotaxy and Primary Ciliary Dyskinesia
Prior to a community-based efficacy trial of long-lasting insecticidal nets ( LLINs ) in the prevention of visceral leishmaniasis ( VL; also called kala-azar ) , a pilot study on preference of tools was held in endemic areas of India and Nepal in September 2005 . LLINs made of polyester and polyethylene were distribute...	Visceral leishmaniasis ( VL ) is a neglected , life-threatening , vector-borne disease . More than 90% of the reported VL cases occur in the Sudan and the Indian subcontinent , where it is considered a problem of great public health importance . To improve its control , which is currently mainly based on case detection...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health", "public", "health", "and", "epidemiology" ]	2007	Population Preference of Net Texture prior to Bed Net Trial in Kala-Azar–Endemic Areas
Neuronal differentiation often requires target-derived signals from the cells they innervate . These signals typically activate neural subtype-specific genes , but the gene regulatory mechanisms remain largely unknown . Highly restricted expression of the FMRFa neuropeptide in Drosophila Tv4 neurons requires target-der...	Nerve cells extend long processes that grow out to contact the target cells with which they communicate . When the nerve cell makes initial contact , the target cells send a retrograde signal back to the nerve cell . Such target-derived signals activate and maintain important genes that make the nerve cell functional ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Gene Regulatory Mechanisms Underlying the Spatial and Temporal Regulation of Target-Dependent Gene Expression in Drosophila Neurons
Differentiation between phenotypically neutral and disease-causing genetic variation remains an open and relevant problem . Among different types of variation , non-frameshifting insertions and deletions ( indels ) represent an understudied group with widespread phenotypic consequences . To address this challenge , we ...	An individual genome contains around ten thousand missense variants , hundreds of insertion/deletion variants , and dozens of protein truncating variants . Among them , non-frameshifting insertion and deletion variants exhibit diverse impact on protein sequence , encompassing alterations from a single residue to the de...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "statistics", "pervasive", "developmental", "disorders", "population", "genetics", "social", "sciences", "developmental", "psychology", "alleles", "mutation", "mathematics", "forecasting"...	2019	Pathogenicity and functional impact of non-frameshifting insertion/deletion variation in the human genome
Bacille Calmette–Guérin ( BCG ) is currently the only approved vaccine against tuberculosis ( TB ) and is administered in over 150 countries worldwide . Despite its widespread use , the vaccine has a variable protective efficacy of 0–80% , with the lowest efficacy rates in tropical regions where TB is most prevalent . ...	The current vaccine against tuberculosis ( TB ) , BCG , has variable efficacy ( 0–80% ) at protecting against infection . A large body of clinical and experimental evidence implicates host exposure to environmental mycobacteria ( EM ) as the cause of interference with BCG vaccine-induced immunity . We explore the mecha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "spleen", "immunology", "tropical", "diseases", "vaccines", "preventive", "medicine", "bacterial", "diseases", "vaccination", "and", "immunization", "bacteria", "public...	2016	Oral Tolerance to Environmental Mycobacteria Interferes with Intradermal, but Not Pulmonary, Immunization against Tuberculosis
The observed cooperation on the level of genes , cells , tissues , and individuals has been the object of intense study by evolutionary biologists , mainly because cooperation often flourishes in biological systems in apparent contradiction to the selfish goal of survival inherent in Darwinian evolution . In order to r...	The observed cooperation between genes , cells , tissues , and higher organisms represents a paradox for Darwinian evolution , because the individual success of cheating is rewarded before its long-term detrimental consequences are felt . The tension between cooperation and defection can be represented by a simple game...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "computational", "biology/population", "genetics" ]	2010	Critical Dynamics in the Evolution of Stochastic Strategies for the Iterated Prisoner's Dilemma
Regulatory interactions buffer development against genetic and environmental perturbations , but adaptation requires phenotypes to change . We investigated the relationship between robustness and evolvability within the gene regulatory network underlying development of the larval skeleton in the sea urchin Strongylocen...	Animal development is highly stereotypic in the face of changing environmental conditions and individual genetic differences . At the same time , developmental processes can evolve rapidly , suggesting that selectable genetic variation is hidden beneath this apparent stability . To better understand the relationship be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Impact of Gene Expression Variation on the Robustness and Evolvability of a Developmental Gene Regulatory Network
Central nervous system ( CNS ) infections are important diseases in both children and adults worldwide . The spectrum of infections is broad , encompassing bacterial/aseptic meningitis and encephalitis . Viruses are regarded as the most common causes of encephalitis and aseptic meningitis . Better understanding of the ...	Central nervous system ( CNS ) infections are important diseases worldwide . The spectrum of infections is broad , encompassing bacterial/aseptic meningitis and encephalitis . Viruses are regarded as the most common causes of encephalitis and aseptic meningitis . Better understanding of the causes of the diseases is of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "microbiology", "molecular", "biology" ]	2014	Viral Aetiology of Central Nervous System Infections in Adults Admitted to a Tertiary Referral Hospital in Southern Vietnam over 12 Years
Single amino acid substitutions in the voltage-gated sodium channel associated with pyrethroid resistance constitute one of the main causative factors of knockdown resistance in insects . The kdr gene has been observed in several mosquito species; however , point mutations in the para gene of Aedes aegypti populations ...	The use of pyrethroids with high killing activity has accelerated the development of pyrethroid resistance in vector mosquitoes . The knockdown resistance ( kdr ) allele contains a single amino acid substitution in the voltage-gated sodium channel and is one of the main causative factors of pyrethroid resistance in ins...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "disease", "control", "infectious", "diseases", "vector-borne", "diseases", "medicine", "and", "health", "sciences" ]	2014	Co-occurrence of Point Mutations in the Voltage-Gated Sodium Channel of Pyrethroid-Resistant Aedes aegypti Populations in Myanmar
Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock . Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs . Recently , NGS appr...	The majority of human pathogens are of animal origin , i . e . zoonoses; both domestic and wild animals act as host reservoirs . Epidemiological surveys of wildlife may help to predict , prevent and control putative episodes of emerging zoonoses . Microbial diversity and their interactions at both the individual and po...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife
Entomopathogenic nematodes ( EPNs ) are unique parasites due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection . It is widely believed that EPNs rely on their bacterial partners for killing hosts . Here we disproved this theory by demonstrating that the in ...	Steinernema carpocapsae belongs to a special group of insect-parasitic nematodes known as entomopathogenic nematodes ( EPNs ) . These differ from other insect parasites in at least two ways; first they kill their hosts quickly ( within 2–3 days ) , and second they associate with bacteria to facilitate their parasitic l...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "parasitic", "diseases", "toxicology", "toxic", "agents", "nematode", "infections", "developmental", "biology", "genome", "analysis", "venoms", "genomics", "proteins", "gene...	2017	Activated entomopathogenic nematode infective juveniles release lethal venom proteins
Poly-ubiquitination of target proteins typically marks them for destruction via the proteasome and provides an essential mechanism for the dynamic control of protein levels . The E1 ubiquitin-activating enzyme lies at the apex of the ubiquitination cascade , and its activity is necessary for all subsequent steps in the...	Proteins that control an organism's development must first be turned on at the proper time and place , and then turned off when they are no longer needed . One of the “off” signals occurs through the attachment of a small protein , known as ubiquitin , to the target protein , which typically leads to the destruction of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "genetics", "and", "genomics/gene", "function", "developmental", "biology" ]	2008	E1 Ubiquitin-Activating Enzyme UBA-1 Plays Multiple Roles throughout C. elegans Development
Global trade and the movement of people accelerate biological invasions by spreading species worldwide . Biosecurity measures seek to allow trade and passenger movements while preventing incursions that could lead to the establishment of unwanted pests , pathogens , and weeds . However , few data exist to evaluate whet...	When people and goods move around the world , they spread nonnative species—including pathogens that can cause disease—leading to huge economic impacts . Many countries try to limit pathogen arrivals by screening goods and people before they enter . But are these biosecurity measures effective ? Pathogens are hard to d...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "forestry", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "trees", "microbiology", "plant", "science", "crops", "plant", "pathology", "plants", "fungal", "pathogens", "mycology", "crop", "science", "medical", "micr...	2018	Import volumes and biosecurity interventions shape the arrival rate of fungal pathogens
The timing of flowering initiation is a fundamental trait for the adaptation of annual plants to different environments . Large amounts of intraspecific quantitative variation have been described for it among natural accessions of many species , but the molecular and evolutionary mechanisms underlying this genetic vari...	In many plant species , the timing of flowering initiation shows abundant quantitative variation among natural varieties , which reflects the importance of this trait for adaptation to different environments . Currently , a major goal in plant biology is to determine the molecular and evolutionary bases of this natural...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2013	The Flowering Repressor SVP Underlies a Novel Arabidopsis thaliana QTL Interacting with the Genetic Background
The rapid and robust synthesis of polymers of adenosine diphosphate ( ADP ) -ribose ( PAR ) chains , primarily catalyzed by poly ( ADP-ribose ) polymerase 1 ( PARP1 ) , is crucial for cellular responses to DNA damage . However , the precise mechanisms through which PARP1 is activated and PAR is robustly synthesized are...	Maintaining genome integrity is crucial for all organisms , and failure to do so can lead to fatal diseases such as cancer . Exposure to challenging environments can induce DNA strand breaks or other lesions; thus , rapid and appropriate DNA damage responses ( DDRs ) need to be in place to detect and repair the damage ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "classical", "mechanics", "gene", "regulation", "dna", "damage", "stem", "cells", "immunoprecipitation", "damage", "mechanics", "dna", "epigenetics", "chromatin", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "animal", "cells", "proteins", ...	2016	Sam68 Is Required for DNA Damage Responses via Regulating Poly(ADP-ribosyl)ation
The kinetochore is the macromolecular complex that assembles onto centromeric DNA and orchestrates the segregation of duplicated chromosomes . More than 60 components make up the budding yeast kinetochore , including inner kinetochore proteins that bind to centromeric chromatin and outer proteins that directly interact...	The flawless execution of cell division is essential to the survival of all organisms . The loss or gain of a single chromosome , the state called aneuploidy , is a hallmark of cancer cells and is the leading cause of spontaneous miscarriages and hereditary birth defects . Segregation is mediated by the kinetochore , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	The Mub1/Ubr2 Ubiquitin Ligase Complex Regulates the Conserved Dsn1 Kinetochore Protein
In Grenada , West Indies , rabies is endemic , and is thought to be maintained in a wildlife host , the small Indian mongoose ( Herpestes auropunctatus ) with occasional spillover into other hosts . Therefore , the present study was undertaken to improve understanding of rabies epidemiology in Grenada and to inform rab...	Rabies , a fatal disease of animals and humans has been endemic in Grenada , West Indies , since the early 1900s . The small Indian mongoose , an introduced animal , is the most likely rabies reservoir , with spillover into domestic animals and humans . To control rabies , large numbers of mongooses were killed in the ...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "epidemiology", "virology", "molecular", "evolution", "biology", "and", "life", "sciences", "microbiology", "evolutionary", "biology", "veterinary", "science" ]	2014	The Phylogeography of Rabies in Grenada, West Indies, and Implications for Control
Plant Resistance ( R ) proteins play an integral role in defense against pathogen infection . A unique gain-of-function mutation in the R gene SNC1 , snc1 , results in constitutive activation of plant immune pathways and enhanced resistance against pathogen infection . We previously found that mutations in MOS4 suppres...	Plants have evolved sophisticated mechanisms to sense and respond to pathogen infection . One robust defense response is mediated by Resistance ( R ) proteins that recognize specific pathogen-derived effector molecules and initiate signaling cascades in the infected cells to impede pathogen growth . By using mutants wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology" ]	2009	Two Prp19-Like U-Box Proteins in the MOS4-Associated Complex Play Redundant Roles in Plant Innate Immunity
VDJ rearrangement and somatic hypermutation work together to produce antibody-coding B cell receptor ( BCR ) sequences for a remarkable diversity of antigens . It is now possible to sequence these BCRs in high throughput; analysis of these sequences is bringing new insight into how antibodies develop , in particular fo...	The binding properties of antibodies are determined by the sequences of their corresponding B cell receptors ( BCRs ) . These BCR sequences are created in “draft” form by VDJ recombination , which randomly selects and deletes from the ends of V , D , and J genes , then joins them together with additional random nucleot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Consistency of VDJ Rearrangement and Substitution Parameters Enables Accurate B Cell Receptor Sequence Annotation
Burkholderia pseudomallei is a Gram-negative bacterium that infects macrophages and other cell types and causes melioidosis . The interaction of B . pseudomallei with the inflammasome and the role of pyroptosis , IL-1β , and IL-18 during melioidosis have not been investigated in detail . Here we show that the Nod-like ...	The disease melioidosis is caused by the intracellular bacterium Burkholderia pseudomallei , a potential bioterrorism agent . Here we examined the interaction of B . pseudomallei with the inflammasome , an important innate immune pathway that regulates at least two host responses protective against infections: 1 ) secr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "inflammation", "emerging", "infectious", "diseases", "immunity", "innate", "immunity", "immune", "defense", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "burkholderia", "infection" ]	2011	Inflammasome-dependent Pyroptosis and IL-18 Protect against Burkholderia pseudomallei Lung Infection while IL-1β Is Deleterious
Epidemics and pandemics of cholera , a severe diarrheal disease , have occurred since the early 19th century and waves of epidemic disease continue today . Cholera epidemics are caused by individual , genetically monomorphic lineages of Vibrio cholerae: the ongoing seventh pandemic , which has spread globally since 196...	Cholera is a life-threatening , diarrheal disease caused by the bacterium Vibrio cholerae . After a long interregnum of decades without epidemics , the seventh cholera pandemic spread globally since 1961 , causing considerable morbidity and mortality . Our analysis of published and newly sequenced genomes provides deta...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Role of China in the Global Spread of the Current Cholera Pandemic
Protein aggregation is a process in which identical proteins self-associate into imperfectly ordered macroscopic entities . Such aggregates are generally classified as amorphous , lacking any long-range order , or highly ordered fibrils . Protein fibrils can be composed of native globular molecules , such as the hemogl...	Protein aggregation is a process by which identical proteins self-associate into imperfectly ordered macroscopic entities . Such aggregates are associated with several pathological conditions in humans , including Alzheimer disease , Parkinson disease , and diabetes type II . Furthermore , protein aggregation is a majo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "neurological", "disorders", "biophysics" ]	2008	Bacterial Inclusion Bodies Contain Amyloid-Like Structure
Cross-sectional studies have associated short telomere length with smoking , body weight , physical activity , and possibly alcohol intake; however , whether these associations are due to confounding is unknown . We tested these hypotheses in 4 , 576 individuals from the general population cross-sectionally , and with ...	Human chromosomes are capped by protective ends called telomeres . These ends are shortened during renewal of tissue and eventually become critically short , causing cells to become senescent or die . It is widely believed that lifestyle features such as smoking , obesity , physical inactivity , and possibly alcohol in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "medicine", "clinical", "epidemiology", "cardiovascular", "disease", "epidemiology", "epidemiology", "cancer", "epidemiology", "lifecourse", "epidemiology", "genetic", "epidemiology", "clinical", "genetics" ]	2014	Telomere Shortening Unrelated to Smoking, Body Weight, Physical Activity, and Alcohol Intake: 4,576 General Population Individuals with Repeat Measurements 10 Years Apart
Given prior evidence that an affected woman conveys a higher risk of ovarian cancer to her sister than to her mother , we hypothesized that there exists an X-linked variant evidenced by transmission to a woman from her paternal grandmother via her father . We ascertained 3 , 499 grandmother/granddaughter pairs from the...	Our article uses the largest familial study of ovarian cancer to argue that there exists an ovarian cancer susceptibility gene on the X-chromosome acting independently of BRCA1 and BRCA2 . This observation implies that there may be many cases of seemingly sporadic ovarian cancer that are actually inherited; for example...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "urology", "medicine", "and", "health", "sciences", "breast", "tumors", "reproductive", "system", "genetic", "dominance", "dominant", "traits", "cancer", "risk", "factors", "cancers", "and", "neoplasms", "genitourinary", "tract", "tumors", "oncology", "x-linked", "tra...	2018	Paternal lineage early onset hereditary ovarian cancers: A Familial Ovarian Cancer Registry study
The efficient coding hypothesis predicts that sensory neurons adjust their coding resources to optimally represent the stimulus statistics of their environment . To test this prediction in the moth olfactory system , we have developed a stimulation protocol that mimics the natural temporal structure within a turbulent ...	Sensory neural systems of living organisms encode the representation of their environment with remarkable efficiency . We study the dynamic coding of naturalistic olfactory stimulation by pheromone-specific antennal neurons . The analysis reveals that the representation is optimal from several complementary information...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "moths", "and", "butterflies", "neuroscience", "animals", "mathematics", "odorants", "materials", "science", "computational", "neuroscience", "zoology", "coding", "mechanisms", "statistical", "distributions", "insect", "pheromones", "animal", "cells", "olfa...	2018	Moth olfactory receptor neurons adjust their encoding efficiency to temporal statistics of pheromone fluctuations
Methylation of histone H3K36 in higher eukaryotes is mediated by multiple methyltransferases . Set2-related H3K36 methyltransferases are targeted to genes by association with RNA Polymerase II and are involved in preventing aberrant transcription initiation within the body of genes . The targeting and roles of the NSD ...	Germ cells transmit the genome from one generation to the next . The identity and immortality of germ cells are crucial for the perpetuation of species , yet the mechanisms that regulate these properties remain elusive . In C . elegans , a histone methyltransferase MES-4 is required for survival of the primordial germ ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "developmental", "biology", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics", "developmental", "biology/dev...	2010	The Histone H3K36 Methyltransferase MES-4 Acts Epigenetically to Transmit the Memory of Germline Gene Expression to Progeny
Advances in computational metabolic optimization are required to realize the full potential of new in vivo metabolic engineering technologies by bridging the gap between computational design and strain development . We present Redirector , a new Flux Balance Analysis-based framework for identifying engineering targets ...	A deeper understanding of biological processes , along with methods in synthetic biology , is driving the frontier of metabolic engineering . In particular , a better representation of cell metabolism will enable the engineering of bacterial strains that can act as factories for valuable biochemical products , from med...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "computer", "science", "operations", "research", "computer", "modeling", "social", "and", "behavioral", "sciences", "metabolic", "pathways", "mathematical", "optimization", "biology", "computational", "biology", "metabolic", "networks", "metabolism", "econom...	2013	Redirector: Designing Cell Factories by Reconstructing the Metabolic Objective
The persistence of latently infected cells in patients under combinatory antiretroviral therapy ( cART ) is a major hurdle to HIV-1 eradication . Strategies to purge these reservoirs are needed and activation of viral gene expression in latently infected cells is one promising strategy . Bromodomain and Extraterminal (...	Persistence of latently infected cells during cART is a major hurdle for HIV-1 eradication . A widely proposed strategy to purge these reservoirs involves the reactivation of latent proviruses . The low levels of active P-TEFb and the cytoplasmic sequestration of NF-κB in resting infected cells largely contribute to ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An In-Depth Comparison of Latency-Reversing Agent Combinations in Various In Vitro and Ex Vivo HIV-1 Latency Models Identified Bryostatin-1+JQ1 and Ingenol-B+JQ1 to Potently Reactivate Viral Gene Expression
The most powerful genome-scale framework to model metabolism , flux balance analysis ( FBA ) , is an evolutionary optimality model . It hypothesizes selection upon a proposed optimality criterion in order to predict the set of internal fluxes that would maximize fitness . Here we present a direct test of the optimality...	The most common method of modeling genome-scale metabolism , flux balance analysis , involves using known stoichiometry to define feasible metabolic states and then choosing between these states by proposing that evolution has selected a metabolic flux that optimizes fitness . But does evolution optimize metabolism , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "metabolism", "population", "genetics", "metabolic", "networks", "microbiology", "escherichia", "coli", "biological", "systems", "engineering", "prokaryotic", "models", "model", "organisms", "microbial", "evolution", "population", "biology", "bioengineering", "...	2013	The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
Bacterial cells are typically surrounded by an net-like macromolecule called the cell wall constructed from the heteropolymer peptidoglycan ( PG ) . Biogenesis of this matrix is the target of penicillin and related beta-lactams . These drugs inhibit the transpeptidase activity of PG synthases called penicillin-binding ...	Penicillin and related beta-lactams are one of our oldest and most effective classes of antibiotics . These drugs target enzymes called penicillin-binding proteins ( PBPs ) that build the essential cell wall that surrounds bacterial cells . Beta-lactams have long been used as chemical and genetic probes to uncover the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "cell", "walls", "transfer", "rna", "cellular", "stress", "responses", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "drugs", "cell", "processes", "microbiology", "non-coding", "rna", "antibiotics", "genetic", ...	2017	The mecillinam resistome reveals a role for peptidoglycan endopeptidases in stimulating cell wall synthesis in Escherichia coli
Immunoglobulin A ( IgA ) secretion by plasma cells in the immune system is critical for protecting the host from environmental and microbial infections . However , the molecular mechanisms underlying the generation of IgA+ plasma cells remain poorly understood . Here , we report that the B cell–expressed tetraspanin CD...	Antibody , or immunoglobulin ( Ig ) , production by plasma cells in the immune system is important for protecting the host from microbial infections . IgA is the most abundant antibody isotype produced in the body . However , the molecular mechanisms underlying the generation of IgA–producing plasma cells remain poorly...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "immunology/immunity", "to", "infections", "immunology/immune", "response" ]	2009	The Tetraspanin Protein CD37 Regulates IgA Responses and Anti-Fungal Immunity
Antibiotic-resistance of hospital-acquired infections is a major public health issue . The worldwide emergence and diffusion of extended-spectrum β-lactamase ( ESBL ) -producing Enterobacteriaceae , including Escherichia coli ( ESBL-EC ) and Klebsiella pneumoniae ( ESBL-KP ) , is of particular concern . Preventing thei...	Tracing extended-spectrum β-lactamase ( ESBL ) dissemination in hospitals is an important step in the fight against the spread of multi-drug resistant bacteria . Indeed , understanding ESBL spreading dynamics will help identify efficient control interventions . In the i-Bird study , patients and hospital staff from a F...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "medical", "personnel", "pathogens", "drugs", "microbiology", "species", "delimitation", "health", "care", "antibiotic", "resistance", "health", "care", "providers", ...	2019	Close proximity interactions support transmission of ESBL-K. pneumoniae but not ESBL-E. coli in healthcare settings
Distinguishing the somatic mutations responsible for cancer ( driver mutations ) from random , passenger mutations is a key challenge in cancer genomics . Driver mutations generally target cellular signaling and regulatory pathways consisting of multiple genes . This heterogeneity complicates the identification of driv...	Cancer is a disease driven largely by the accumulation of somatic mutations during the lifetime of an individual . The declining costs of genome sequencing now permit the measurement of somatic mutations in hundreds of cancer genomes . A key challenge is to distinguish driver mutations responsible for cancer from rando...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "algorithms", "computer", "science", "biology", "genomics", "computational", "biology" ]	2013	Simultaneous Identification of Multiple Driver Pathways in Cancer
Two billion people are latently infected with Mycobacterium tuberculosis ( Mtb ) . Mtb-infected macrophages are likely to be sequestered inside the hypoxic environments of the granuloma and differentiate into lipid-loaded macrophages that contain triacylglycerol ( TAG ) -filled lipid droplets which may provide a fatty ...	Two billion people are latently infected with Mycobacterium tuberculosis ( Mtb ) . Cure and possible eradication of tuberculosis are limited by the lack of availability of any drug that can kill dormant Mtb . Understanding of the processes critical for dormancy and a reliable dormancy model suitable for high throughput...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biology", "microbiology", "molecular", "cell", "biology" ]	2011	Mycobacterium tuberculosis Uses Host Triacylglycerol to Accumulate Lipid Droplets and Acquires a Dormancy-Like Phenotype in Lipid-Loaded Macrophages
Theiler's virus , a picornavirus , persists for life in the central nervous system of mouse and causes a demyelinating disease that is a model for multiple sclerosis . The virus infects neurons first but persists in white matter glial cells , mainly oligodendrocytes and macrophages . The mechanism , by which the virus ...	Theiler's virus persists in the central nervous system of mice and causes a chronic disease that resembles multiple sclerosis , a common demyelinating disease of humans . The virus infects neurons for one to two weeks , but later on it persists in the white matter , in oligodendrocytes and also in macrophages . Oligode...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "neurological", "disorders", "virology", "mus", "(mouse)", "neuroscience", "animals" ]	2007	The Role of Myelin in Theiler's Virus Persistence in the Central Nervous System
A complete theory of cognitive architecture ( i . e . , the basic processes and modes of composition that together constitute cognitive behaviour ) must explain the systematicity property—why our cognitive capacities are organized into particular groups of capacities , rather than some other , arbitrary collection . Th...	John , your greengrocer , arranges apples and oranges in order of price . Being on a budget , you choose the fruit to the left , because it is always cheaper . Last week it was apples; this week it's oranges . Your ability to choose the fruit on the left , be it apples or oranges , is an example of systematicity: a pro...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "psychology", "social", "and", "behavioral", "sciences", "mathematics", "cognitive", "psychology", "biology", "computational", "biology", "neuroscience" ]	2011	Categorial Compositionality II: Universal Constructions and a General Theory of (Quasi-)Systematicity in Human Cognition
HIV infection has a profound effect on “bystander” cells causing metabolic co-morbidities . This may be mediated by exosomes secreted by HIV-infected cells and containing viral factors . Here we show that exosomes containing HIV-1 protein Nef ( exNef ) are rapidly taken up by macrophages releasing Nef into the cell int...	HIV infects only a limited repertoire of cells expressing HIV receptors . Nevertheless , co-morbidities of HIV infection , such as atherosclerosis , dementia , renal impairment , myocardial pathology , abnormal haematopoiesis and others , involve dysfunction of cells that can not be infected by HIV . These co-morbiditi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "vesicles", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "rna", "viru...	2019	Exosomes containing HIV protein Nef reorganize lipid rafts potentiating inflammatory response in bystander cells
Lipoprotein-associated phospholipase A2 ( Lp-PLA2 ) is an emerging risk factor and therapeutic target for cardiovascular disease . The activity and mass of this enzyme are heritable traits , but major genetic determinants have not been explored in a systematic , genome-wide fashion . We carried out a genome-wide associ...	Blood levels of lipoprotein-associated phospholipase A2 ( Lp-PLA2 ) show a strong association with atherosclerosis in humans . This enzyme is made by certain cells of the immune system , associates with lipoproteins ( HDL and LDL ) , and is thought to be involved in inflammation . Studies have shown that Lp-PLA2 is a g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits" ]	2010	Genome-Wide Association Study of Lp-PLA2 Activity and Mass in the Framingham Heart Study
The N-terminal domains of the herpesvirus large tegument proteins encode a conserved cysteine protease with ubiquitin- and NEDD8-specific deconjugase activity . The proteins are expressed during the productive virus cycle and are incorporated into infectious virus particles , being delivered to the target cells upon pr...	The N-terminal domains of the herpesvirus large tegument proteins encode a conserved cysteine protease with ubiquitin- and NEDD8-specific deconjugase activity that was shown to regulate different aspects of the virus life cycle including virus replication , the assembly of infectious virus particles and the host innate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hela", "cells", "enzymes", "pathogens", "biological", "cultures", "enzymology", "microbiology", "cloning", "viruses", "immunoprecipitation", "dna", "viruses", "signalosomes", "cell", ...	2018	Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome
Shugoshin-1 ( Sgo1 ) protects the integrity of the centromeres , and H2A phosphorylation is critical for this process . The mitotic checkpoint kinase Bub1 , phosphorylates H2A and ensures fidelity of chromosome segregation and chromosome number . Oncogenic KSHV induces genetic alterations through chromosomal instabilit...	KSHV is a known oncogenic herpes virus associated with human malignancies and lymphoproliferative disorders , which includes Kaposi’s sarcoma , Primary effusion lymphoma , and Multicentric Castleman’s disease . KSHV disrupts the G1 and G2/M checkpoints through multiple pathways . Whether KSHV can directly interfere wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "chromosome", "structure", "and", "function", "centromeres", "cell", "cycle", "and", "cell", "division", "cell", "processes", "departures", "from", "diploidy", "mitosis", "immunoprecipitation", "research", "and", "analysis", "methods", "aneuploidy", "...	2018	Shugoshin 1 is dislocated by KSHV-encoded LANA inducing aneuploidy
Cytoplasmic RNA localization is a key biological strategy for establishing polarity in a variety of organisms and cell types . However , the mechanisms that control directionality during asymmetric RNA transport are not yet clear . To gain insight into this crucial process , we have analyzed the molecular machinery dir...	Like traffic on highways , molecular cargos are transported within cells on tracks that are collectively referred to as cytoskeletal networks . RNA molecules are one such cargo , and in many species , the localization of RNAs in egg cells or oocytes is essential for establishing the first asymmetries that are necessary...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "biology", "molecular", "cell", "biology" ]	2013	Directional Transport Is Mediated by a Dynein-Dependent Step in an RNA Localization Pathway
The principles by which networks of neurons compute , and how spike-timing dependent plasticity ( STDP ) of synaptic weights generates and maintains their computational function , are unknown . Preceding work has shown that soft winner-take-all ( WTA ) circuits , where pyramidal neurons inhibit each other via interneur...	How do neurons learn to extract information from their inputs , and perform meaningful computations ? Neurons receive inputs as continuous streams of action potentials or “spikes” that arrive at thousands of synapses . The strength of these synapses - the synaptic weight - undergoes constant modification . It has been ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "circuit", "models", "developmental", "neuroscience", "synaptic", "plasticity", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience" ]	2013	Bayesian Computation Emerges in Generic Cortical Microcircuits through Spike-Timing-Dependent Plasticity
Triatomines are hematophagous arthropod vectors of Trypanosoma cruzi , the causative agent of Chagas Disease . Panstrongylus lignarius , also known as Panstrongylus herreri , is considered one of the most versatile triatomines because it can parasitize different hosts , it is found in different habitats and countries ,...	This work describes an in-depth salivary and fat body transcriptome from the triatomine P . lignarius , the main vector of Chagas disease in Peru . Following “de novo” assembly of over 160 million reads , 11 thousand coding sequences were obtained , 9 , 013 of which were submitted to GenBank . Those over expressed in t...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "and", "discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "protein", "metabolism", "animals", "animal", "models", "amino", "acid", "sequence", "analysis", "genome", "analysis", "experimental", "organism", "systems", "insect", "vectors", "triatoma", "digestive", "system"...	2018	An insight into the salivary gland and fat body transcriptome of Panstrongylus lignarius (Hemiptera: Heteroptera), the main vector of Chagas disease in Peru
Species within the human pathogenic Cryptococcus species complex are major threats to public health , causing approximately 1 million annual infections globally . Cryptococcus amylolentus is the most closely known related species of the pathogenic Cryptococcus species complex , and it is non-pathogenic . Additionally ,...	This manuscript explores the evolution of the genomic regions encoding the mating type loci of basidiomycetous fungi . Typically , the mating system is tetrapolar , meaning that it is composed of 2 unlinked mating type ( MAT ) loci ( P/R and HD ) that are located on different chromosomes . However , species with bipola...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "chromosome", "structure", "and", "function", "centromeres", "pathogens", "microbiology", "fungi", "genetic", "elements", "translocations", ...	2017	Fungal genome and mating system transitions facilitated by chromosomal translocations involving intercentromeric recombination
Food allergy is usually difficult to diagnose in early life , and the inability to diagnose patients with atopic diseases at an early age may lead to severe complications . Numerous studies have suggested an association between the infant gut microbiome and development of allergy . In this work , we investigated the ca...	Deep learning has become a powerful methodology to derive knowledge from the vast amount of data available from biomedical studies . However , successful applications of deep learning models to clinical studies remain challenging due to the complexity of biological data generated from the new experimental platforms as ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Experiments", "Results", "and", "discussion", "Conclusion" ]	[ "learning", "medicine", "and", "health", "sciences", "microbiome", "markov", "models", "immunology", "microbiology", "social", "sciences", "neuroscience", "learning", "and", "memory", "allergic", "diseases", "clinical", "medicine", "cognitive", "psychology", "mathematics"...	2019	Utilizing longitudinal microbiome taxonomic profiles to predict food allergy via Long Short-Term Memory networks
During long-term cystic fibrosis lung infections , Pseudomonas aeruginosa undergoes genetic adaptation resulting in progressively increased persistence and the generation of adaptive colony morphotypes . This includes small colony variants ( SCVs ) , auto-aggregative , hyper-adherent cells whose appearance correlates w...	During long-term chronic infections of cystic fibrosis patients , Pseudomonas aeruginosa adapts to the lung environment , generating various different morphotypes including small colony variants ( SCVs ) , small , strongly adherent colonies whose appearance correlates with persistence of infection . The SCV morphology ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology", "infectious", "diseases/respiratory", "infections" ]	2010	YfiBNR Mediates Cyclic di-GMP Dependent Small Colony Variant Formation and Persistence in Pseudomonas aeruginosa
A novel , swine-origin influenza H1N1 virus ( H1N1pdm ) caused the first pandemic of the 21st century . This pandemic , although efficient in transmission , is mild in virulence . This atypical mild pandemic season has raised concerns regarding the potential of this virus to acquire additional virulence markers either ...	The 19th century experienced three major influenza pandemics: the Spanish flu of 1918 ( H1N1 ) , the Asian flu of 1957 ( H2N2 ) and the Hong Kong flu of 1968 ( H3N2 ) . These pandemics were introduced into the human population through the accumulation of avian and human influenza genes ( genetic reassortment ) , creati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "virology/virus", "evolution", "and", "symbiosis", "virology/animal", "models", "of", "infection", "virology/emerging", "viral", "diseases", "virology" ]	2010	Variations in the Hemagglutinin of the 2009 H1N1 Pandemic Virus: Potential for Strains with Altered Virulence Phenotype?
Disturbances of lipoprotein metabolism are recognized as indicators of cardiometabolic disease risk . Lipoprotein size and composition , measured in a lipoprotein profile , are considered to be disease risk markers . However , the measured profile is a collective result of complex metabolic interactions , which complic...	Lipids such as triglycerides and cholesterol are important building blocks and energy suppliers for the body . However , because lipids are hydrophobic they require a matrix to circulate in the bloodstream . This function is fulfilled by lipoproteins . Altered lipoprotein metabolism is known to be associated with disea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biochemistry", "physiological", "processes", "physiology", "biology", "and", "life", "sciences", "computational", "biology", "metabolism", "energy", "metabolism" ]	2014	A Computational Model for the Analysis of Lipoprotein Distributions in the Mouse: Translating FPLC Profiles to Lipoprotein Metabolism
Small RNA pathways act at the front line of defence against transposable elements across the Eukaryota . In animals , Piwi interacting small RNAs ( piRNAs ) are a crucial arm of this defence . However , the evolutionary relationships among piRNAs and other small RNA pathways targeting transposable elements are poorly r...	Transposable elements are segments of DNA that have the ability to copy themselves independently of the host genome and thus pose a severe threat to the integrity of the genome . Organisms have evolved mechanisms to restrict the spread of transposable elements , with small RNA molecules being one of the most important ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ancient and Novel Small RNA Pathways Compensate for the Loss of piRNAs in Multiple Independent Nematode Lineages
Protein structure modeling by homology requires an accurate sequence alignment between the query protein and its structural template . However , sequence alignment methods based on dynamic programming ( DP ) are typically unable to generate accurate alignments for remote sequence homologs , thus limiting the applicabil...	It has been suggested that , for nearly every protein sequence , there is already a protein with a similar structure in current protein structure databases . However , with poor or undetectable sequence relationships , it is expected that accurate alignments and models cannot be generated . Here we show that this is no...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "structure", "prediction", "genomics", "biology", "computational", "biology" ]	2011	Using Structure to Explore the Sequence Alignment Space of Remote Homologs
Complement C1q is a soluble protein capable of initiating components of the classical pathway in host defence system . In earlier qualitative studies , C1q has been implicated in the pathogenesis of Erythema Nodosum Leprosum ( ENL ) . However , little is known about the role of this complement in ENL reaction . In the ...	Erythema nodosum leprosum ( ENL ) is a painful inflammatory reaction which occurs in patients with lepromatous and borderline lepromatous leprosy . The diagnosis of ENL is mainly based on clinical signs and symptoms and there is no definitive laboratory diagnosis . The causes of ENL are not fully understood but immune-...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "complement", "system", "medicine", "and", "health", "sciences", "innate", "immune", "system", "body", "fluids", "immune", "physiology", "cytokines", "biopsy", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "surgical", "and", "inva...	2018	Complement C1q expression in Erythema nodosum leprosum
Aspergillus fumigatus is a common mould whose spores are a component of the normal airborne flora . Immune dysfunction permits developmental growth of inhaled spores in the human lung causing aspergillosis , a significant threat to human health in the form of allergic , and life-threatening invasive infections . The su...	Airborne spores of the fungus Aspergillus fumigatus are present in significant quantities worldwide and are responsible for a range of illnesses from allergy to deadly invasive lung infection . A number of fungal properties are likely required for germination and growth of the fungus in the host , and now that the geno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "respiratory", "medicine/respiratory", "infections", "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/fungal", "infections", "microbiology/medical", "microbiology" ]	2008	Sub-Telomere Directed Gene Expression during Initiation of Invasive Aspergillosis
Herpesviridae is a diverse family of large and complex pathogens whose genomes are extremely difficult to sequence . This is particularly true for clinical samples , and if the virus , host , or both genomes are being sequenced for the first time . Although herpesviruses are known to occasionally integrate in host geno...	Herpesviridae is a family of DNA viruses that have characteristically large and complex genomes . This defining feature is also responsible for bioinformatic challenges that complicate herpesvirus genomics , and why an endogenous herpesvirus remains elusive . Given that several species of herpesvirus are clinically rel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "genomics", "genome", "evolution", "microbial", "evolution", "virology", "genetics", "biology", "and", "life", "sciences", "microbiology", "computational", "biology", "evolutionary", "biology", "evolutionary", "genetics", "viral", "evolution" ]	2014	The First Endogenous Herpesvirus, Identified in the Tarsier Genome, and Novel Sequences from Primate Rhadinoviruses and Lymphocryptoviruses
To determine the incidence of congenital toxoplasmosis in Colombian newborns from 19 hospital or maternal child health services from seven different cities of five natural geographic regions ( Caribbean , Central , Andean , Amazonia and Eastern ) . We collected 15 , 333 samples from umbilical cord blood between the per...	Congenital toxoplasmosis can result in permanent sequel as blindness or neurological damage in children and it seems to be more severe in South America than in other continents . There is a lack of information about this frequency in Colombia , where no control program is established , although it is a recognized cause...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "pediatric", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "neonatalology", "neglected", "tropical", "diseases", "pediatrics", "and", "child", "health", "parasitic", ...	2011	First Colombian Multicentric Newborn Screening for Congenital Toxoplasmosis
Insect immune systems can recognize specific pathogens and prime offspring immunity . High specificity of immune priming can be achieved when insect females transfer immune elicitors into developing oocytes . The molecular mechanism behind this transfer has been a mystery . Here , we establish that the egg-yolk protein...	Insects lack antibodies , the carriers of immunological memory that vertebrate mothers can transfer to their offspring . Yet , it has been shown that an insect mother facing pathogens can prime her offspring’s immune system . To date , it has remained enigmatic how insects achieve specific trans-generational immune pri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Transfer of Immunity from Mother to Offspring Is Mediated via Egg-Yolk Protein Vitellogenin
Natural genetic variation in Arabidopsis thaliana exists for many traits and often reflects acclimation to local environments . Studying natural variation has proven valuable in the characterization of phenotypic traits and , in particular , in identifying genetic factors controlling these traits . It has been previous...	The habitat of the plant model species Arabidopsis thaliana can be found throughout the Northern hemisphere . As a consequence , individual populations have acclimated to a great diversity of environmental conditions . This is reflected by a wealth of natural genetic variation in many phenotypic traits . We utilized th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology/plant-environment", "interactions", "molecular", "biology/chromatin", "structure", "genetics", "and", "genomics/gene", "discovery", "molecular", "biology/histone", "modification", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/chromosome", ...	2009	PHYTOCHROME B and HISTONE DEACETYLASE 6 Control Light-Induced Chromatin Compaction in Arabidopsis thaliana
L . monocytogenes is a facultative intracellular bacterium responsible for listeriosis . It is able to invade , survive and replicate in phagocytic and non-phagocytic cells . The infectious process at the cellular level has been extensively studied and many virulence factors have been identified . Yet , the role of Inl...	L . monocytogenes is a food-born pathogen responsible for listeriosis , a severe illness with a high mortality rate , which mainly affects immunocompromised patients and pregnant women . The bacterium is a facultative intracellular pathogen able to invade , survive and multiply in large variety of cells . Although the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "gram", "positive" ]	2011	Recruitment of the Major Vault Protein by InlK: A Listeria monocytogenes Strategy to Avoid Autophagy
Several essential biochemical processes are situated in mitochondria . The metabolic transformation of mitochondria in distinct lineages of eukaryotes created proteomes ranging from thousands of proteins to what appear to be a much simpler scenario . In the case of Entamoeba histolytica , tiny mitochondria known as mit...	All eukaryotic organisms have mitochondria , organelles cordoned by a double membrane , which are descendants of an ancestral bacterial endosymbiont . Nowadays , mitochondria are fully integrated into the context of diverse cellular processes and serve in providing energy , iron-containing prosthetic groups and some of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "microbiology/parasitology" ]	2010	The Essentials of Protein Import in the Degenerate Mitochondrion of Entamoeba histolytica
Small-World Networks ( SWNs ) represent a fundamental model for the comprehension of many complex man-made and biological networks . In the central nervous system , SWN models have been shown to fit well both anatomical and functional maps at the macroscopic level . However , the functional microscopic level , where th...	Cell assemblies ( sequences of neuronal activations ) , seem to represent a functional unit of information processing . However , it remains unclear how groups of neurons may organize their activity during information processing , working as a sole functional unit . One prominent principle in complex network theory is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "circuit", "models", "algorithms", "computer", "science", "stochastic", "processes", "computer", "modeling", "mathematics", "neural", "networks", "computational", "neuroscience", "sensory", "systems", "biology", "computerized", "simulations", "neuroscience", "markov", "mode...	2013	Neuronal Functional Connection Graphs among Multiple Areas of the Rat Somatosensory System during Spontaneous and Evoked Activities
Double strand breaks ( DSB ) in the DNA backbone are the most lethal type of defect induced in the cell nucleus by chemical and radiation treatments of cancer . However , little is known about the outcomes of damage in nucleosomal DNA , and on its effects on damage repair . We performed microsecond-long molecular dynam...	Cancer therapy involves generation of damage to DNA by various means , ranging from chemicals to ionizing radiation . The most lethal form of damage is the breaking of the DNA molecule , especially effective when the rupture occurs simultaneously on both sides of the DNA double helix , in what is called a double-strand...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "molecular", "dynamics", "classical", "mechanics", "dna-binding", "proteins", "mechanical", "stress", "dna", "damage", "mathematics", "algebra", "epigenetics", "dna", "dna", "structure", "chromatin", "chromosome", "biology", "proteins", "gene", "expression", "chemistry", ...	2018	Mechanical evolution of DNA double-strand breaks in the nucleosome
Despite intensive breeding efforts , potato late blight , caused by the oomycete pathogen Phytophthora infestans , remains a threat to potato production worldwide because newly evolved pathogen strains have consistently overcome major resistance genes . The potato RB gene , derived from the wild species Solanum bulboca...	The potato late blight pathogen , Phytophthora infestans , is able to rapidly evolve to overcome resistance genes . The pathogen accomplishes this by secreting an arsenal of proteins , termed effectors , that function to modify host cells . Although hundreds of candidate effectors have been identified in P . infestans ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "plant", "pathology", "biology" ]	2012	Molecular Determinants of Resistance Activation and Suppression by Phytophthora infestans Effector IPI-O
Leptospirosis is the most common zoonotic disease worldwide . The diagnostic performance of a serological test for human leptospirosis is mainly influenced by the antigen used in the test assay . An ideal serological test should cover all serovars of pathogenic leptospires with high sensitivity and specificity and use ...	Leptospirosis is an infectious disease that is transmitted from animals to humans . It is associated with a broad range of clinical presentations , and diagnostic tests with high diagnostic accuracy are required in order to enable accurate diagnosis . Leptospirosis is diagnosed by detecting DNA of the pathogen or antib...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "bacteriophages", "pathogens", "tropical", "diseases", "microbiology", "cloning", "genomic", "library", "construction", "viruses", "bacteria...	2019	Discovery of Leptospira spp. seroreactive peptides using ORFeome phage display
Modulation of host cell function is vital for intracellular pathogens to survive and replicate within host cells . Most commonly , these pathogens utilize specialized secretion systems to inject substrates ( also called effector proteins ) that function as toxins within host cells . Since it would be detrimental for an...	A key attribute of many pathogens is their ability to survive and replicate within eukaryotic host cells . One such pathogen , Legionella pneumophila , is able to grow within macrophages in the lungs , thereby causing a form of pneumonia called Legionnaires’ Disease . L . pneumophila causes disease by translocating sev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Spatiotemporal Regulation of a Legionella pneumophila T4SS Substrate by the Metaeffector SidJ
Streptococcus gordonii and Streptococcus sanguinis are primary colonizers of the tooth surface . Although generally non-pathogenic in the oral environment , they are a frequent cause of infective endocarditis . Both streptococcal species express a serine-rich repeat surface adhesin that mediates attachment to sialylate...	Infective endocarditis ( IE ) is a life-threatening infection of heart valves , and streptococci that normally reside in the mouth are a leading cause of this disease . Some oral streptococcal species express a protein on their surface that enables attachment to glycan ( sugar ) modifications on saliva proteins , an in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "blood", "cells", "bacteriology", "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "sialic", "acids", "cardiovascular", "anatomy", "pathogens", "microbiology", "carbohydrates", "organic", "...	2019	Recognition of specific sialoglycan structures by oral streptococci impacts the severity of endocardial infection
During infection with human immunodeficiency virus ( HIV ) , immune pressure from cytotoxic T-lymphocytes ( CTLs ) selects for viral mutants that confer escape from CTL recognition . These escape variants can be transmitted between individuals where , depending upon their cost to viral fitness and the CTL responses mad...	HIV evolves so quickly that it can be seen to adapt within one infected person . Evolutionary escape from immunity is particularly well-described . Escape variants transmit to new hosts , where they may revert . We present a mathematical model of three processes: within-host evolution of escape mutants , transmission o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "immunology/genetics", "of", "the", "immune", "system", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/sexually", "transmitted", "diseases", "mathematics/statistics", "immunology/immunity", ...	2010	Modelling the Evolution and Spread of HIV Immune Escape Mutants
Experiments involving mosquito mark-release-recapture ( MRR ) design are helpful to determine abundance , survival and even recruitment of mosquito populations in the field . Obstacles in mosquito MRR protocols include marking limitations due to small individual size , short lifespan , low efficiency in capturing devic...	Mosquito-borne diseases such as dengue and malaria impose a global burden with recurrent outbreaks . Recently , emergence of arboviral diseases caused by Zika and chikungunya viruses has also become a global concern . Knowledge about the ecology of mosquito populations under natural conditions may provide significant a...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "pathogens", "experimental", "design", "microbiology", "animals", "alphaviruses", "simulation", "and", "modeling", "viruses", "researc...	2017	Novel inference models for estimation of abundance, survivorship and recruitment in mosquito populations using mark-release-recapture data
We analyze evolutionary dynamics on graphs , where the nodes represent individuals of a population . The links of a node describe which other individuals can be displaced by the offspring of the individual on that node . Amplifiers of selection are graphs for which the fixation probability is increased for advantageous...	Evolutionary dynamics describes the spread of individuals with different features within a population . This spreading process can be strongly influenced by the population structure—if a highly successful individual can only displace a few neighbors , it may take more time to spread than an individual that can displace...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Most Undirected Random Graphs Are Amplifiers of Selection for Birth-Death Dynamics, but Suppressors of Selection for Death-Birth Dynamics
Konzo ( caused by consumption of improperly processed cassava , Manihot esculenta ) and neurolathyrism ( caused by prolonged overconsumption of grass pea , Lathyrus sativus ) are two distinct non-infectious upper motor neurone diseases with identical clinical symptoms of spastic paraparesis of the legs . They affect ma...	The irreversible crippling diseases konzo and neurolathyrism with identical clinical symptoms occur among poor subsistence farmers in Africa and Asia . The victims are mostly illiterate and among the poorest section of the population who can only afford the cheapest food in a monotonous diet: bitter cassava roots ( Man...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "science", "policy" ]	2012	Research on Motor Neuron Diseases Konzo and Neurolathyrism: Trends from 1990 to 2010
The evolution of drug resistance is an important process that affects clinical outcomes . Resistance to fluconazole , the most widely used antifungal , is often associated with acquired aneuploidy . Here we provide a longitudinal study of the prevalence and dynamics of gross chromosomal rearrangements , including aneup...	C . albicans , the most prevalent human fungal pathogen , acquires resistance to fluconazole by genetic alterations that often include changes in the number of chromosomes or chromosome arms ( aneuploidy ) . Here we demonstrate that chromosomal rearrangements resulting in increased gene dosage are the predominant means...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "...	2009	Acquisition of Aneuploidy Provides Increased Fitness during the Evolution of Antifungal Drug Resistance
Yaws is a non-venereal treponemal infection caused by Treponema pallidum ssp . pertenue . The WHO has launched a worldwide control programme , which aims to eradicate yaws by 2020 . The development of a rapid diagnostic test ( RDT ) for serological diagnosis in the isolated communities affected by yaws is a key require...	Yaws is a bacterial infection closely related to syphilis . The WHO has launched a worldwide campaign to eradicate yaws by 2020 . If this goal is to be achieved , programme managers and clinical staff will need access to a rapid diagnostic test ( RDT ) for yaws that can be used in the remote communities where the disea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "clinical", "medicine", "diagnostic", "medicine", "tropical", "diseases" ]	2014	Evaluation of a Rapid Diagnostic Test for Yaws Infection in a Community Surveillance Setting
Interacting-particle reaction dynamics ( iPRD ) combines the simulation of dynamical trajectories of interacting particles as in molecular dynamics ( MD ) simulations with reaction kinetics , in which particles appear , disappear , or change their type and interactions based on a set of reaction rules . This combinatio...	Biological cells are not well-mixed reaction containers . Cellular signaling strongly depends on crowding , space exclusion , association and dissociation of proteins and other macromolecules . These are often confined to complex geometries and cell compartments . Understanding the mechanisms is challenging , as experi...	[ "Abstract", "Introduction", "interacting-particle", "reaction", "dynamics", "(iPRD)", "Design", "and", "implementation", "Results", "Availability", "and", "future", "directions" ]	[ "medicine", "and", "health", "sciences", "molecular", "dynamics", "membrane", "potential", "electrophysiology", "simulation", "and", "modeling", "materials", "science", "macromolecules", "reaction", "dynamics", "research", "and", "analysis", "methods", "physical", "chemis...	2019	ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics
The KIX domain of CBP is a transcriptional coactivator . Concomitant binding to the activation domain of proto-oncogene protein c-Myb and the transactivation domain of the trithorax group protein mixed lineage leukemia ( MLL ) transcription factor lead to the biologically active ternary MLL∶KIX∶c-Myb complex which play...	CBP ( CREB-binding protein ) is a transcriptional regulator of RNA polymerase II-mediated transcription . KIX is a domain of CBP . KIX binding to the activation domain of proto-oncogene protein c-Myb and the transactivation domain of the trithorax group protein mixed lineage leukemia ( MLL ) transcription factor forms ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "physics", "computational", "chemistry", "chemistry", "biology", "computational", "biology", "biophysics" ]	2012	Conformational Control of the Binding of the Transactivation Domain of the MLL Protein and c-Myb to the KIX Domain of CREB
In Drosophila melanogaster , the male-specific lethal ( MSL ) complex plays a key role in dosage compensation by stimulating expression of male X-chromosome genes . It consists of MSL proteins and two long noncoding RNAs , roX1 and roX2 , that are required for spreading of the complex on the chromosome and are redundan...	In humans and fruit flies , females and males have different sets of sex chromosomes . This causes gene dosage differences that must be compensated for by adjusting the expression of most genes located on the X-chromosome . Long non-coding RNAs are central in this compensation and in fruit flies this is mediated by two...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "dosage", "compensation", "invertebrates", "molecular", "probe", "techniques", "gene", "regulation", "animals", "long", "non-coding", "rnas", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "e...	2018	RNA-on-X 1 and 2 in Drosophila melanogaster fulfill separate functions in dosage compensation
Gene expression actualizes the organismal phenotypes encoded within the genome in an environment-dependent manner . Among all encoded phenotypes , cell population growth rate ( fitness ) is perhaps the most important , since it determines how well-adapted a genotype is in various environments . Traditional biological m...	It is common belief that the properties of cells depend on their environment and on the genes they carry . Yet , many cases exist where individual cells in the same environment behave very differently , despite sharing the same genes . This creates a problem when we try to explain the behavior of a cell population base...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "synthetic", "biology", "biology", "computational", "biology" ]	2012	Mapping the Environmental Fitness Landscape of a Synthetic Gene Circuit
The term epistasis refers to interactions between multiple genetic loci . Genetic epistasis is important in regulating biological function and is considered to explain part of the ‘missing heritability , ’ which involves marginal genetic effects that cannot be accounted for in genome-wide association studies . Thus , t...	A new mixed-model was recently developed for mapping DNA regions that are associated with variations in observable traits , known as quantitative trait loci . This model incorporates multiple polygenic covariance genetic structures and has been used to successfully predict yield in hybrid rice . However , quantitativel...	[ "Abstract", "Introduction", "Design", "and", "Implementation", "Results", "Performance", "Analysis", "and", "Discussion", "Availability", "and", "Future", "Directions" ]	[ "genome-wide", "association", "studies", "quantitative", "trait", "loci", "quantitative", "traits", "epistasis", "optimization", "cereal", "crops", "rice", "model", "organisms", "mathematics", "genome", "analysis", "crops", "plants", "research", "and", "analysis", "meth...	2016	PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies
The transcriptional network and protein regulators that govern T helper 17 ( Th17 ) cell differentiation have been studied extensively using advanced genomic approaches . For a better understanding of these biological processes , we have moved a step forward , from gene- to protein-level characterization of Th17 cells ...	T helper 17 ( Th17 ) cells and induced regulatory T ( iTreg ) cells are two subsets of T helper cells differentiated from naïve cells that play important roles in autoimmune diseases , immune homeostasis , and tumor immunity . The differentiation process is achieved by changes in numerous proteins , including transcrip...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "methods", "and", "resources", "immune", "cells", "forkhead", "box", "gene", "regulation", "regulatory", "proteins", "immunology", "dna-binding", "proteins", "cell", "differentiation", "developmental", "biology"...	2018	Quantitative proteomic characterization and comparison of T helper 17 and induced regulatory T cells
The human nasal microbiota is highly variable and dynamic often enclosing major pathogens such as Staphylococcus aureus . The potential roles of bacteriocins or other mechanisms allowing certain bacterial clones to prevail in this nutrient-poor habitat have hardly been studied . Of 89 nasal Staphylococcus isolates , un...	The complex and dynamic microbial communities of human body surfaces are of utmost importance for human body functions in health and diseases . Human microbiomes contribute to metabolic processes , instruct the immune system , and often include antibiotic-resistant pathogens , responsible for the majority of severe bac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "toxins", "microbiome", "pathology", "and", "laboratory", "medicine", "face", "nose", "pathogens", "drugs", "microbiology", "staphylococcus", "aureus", "toxicology", "toxic", "agents", "pharmacology", "bacteria", ...	2016	High Frequency and Diversity of Antimicrobial Activities Produced by Nasal Staphylococcus Strains against Bacterial Competitors
Synaptic vesicle fusion is mediated by SNARE proteins forming in between synaptic vesicle ( v-SNARE ) and plasma membrane ( t-SNARE ) , one of which is Syntaxin-1A . Although exocytosis mainly occurs at active zones , Syntaxin-1A appears to cover the entire neuronal membrane . By using STED super-resolution light micro...	For the communication between two nerve cells , a synaptic vesicle containing neurotransmitters has to fuse with the neuronal membrane at a specific fusion site , releasing its signaling molecules . The vesicle fusion is mediated by a specific family of proteins ( SNAREs ) that are located on the vesicle as well as on ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Dynamical Organization of Syntaxin-1A at the Presynaptic Active Zone
Speed-accuracy tradeoff ( SAT ) is an adaptive process balancing urgency and caution when making decisions . Computational cognitive theories , known as “evidence accumulation models” , have explained SATs via a manipulation of the amount of evidence necessary to trigger response selection . New light has been shed on ...	In everyday life we constantly balance urgency against caution when making decisions – known as the speed-accuracy tradeoff . Traditionally , computational cognitive theories called “evidence accumulation models” have explained the speed accuracy tradeoff as changes in the amount of evidence necessary to trigger the se...	[ "Abstract", "Introduction", "Results", "Models", "Discussion", "Summary", "Conclusions" ]	[ "psychology", "cognitive", "psychology", "social", "sciences", "human", "performance", "behavior", "biology", "and", "life", "sciences", "neuropsychology", "cognitive", "science", "neuroscience" ]	2014	Brain and Behavior in Decision-Making
Several rodent-associated Bartonella species are human pathogens but little is known about their epidemiology . We trapped rodents and shrews around human habitations at two sites in Kenya ( rural Asembo and urban Kibera ) to determine the prevalence of Bartonella infection . Bartonella were detected by culture in five...	Bartonella are bacteria that infect many different mammal species and can cause illness in people . Several Bartonella species carried by rodents cause disease in humans but little is known about their distribution or the importance of bartonellosis as a cause of human illness . Data from Africa are particularly scarce...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Prevalence and Diversity of Small Mammal-Associated Bartonella Species in Rural and Urban Kenya
Early detection of several skin-related neglected tropical diseases ( skin NTDs ) –including leprosy , Buruli ulcer , yaws , and scabies- may be achieved through school surveys , but such an approach has seldom been tested systematically on a large scale in endemic countries . Additionally , a better understanding of t...	Integration of neglected tropical diseases ( NTDs ) into the public health agenda has been a priority in global health for the last decade . A common feature shared by several NTDs is skin involvement . Conditions within this group of NTDs have now been classified as skin NTDs to promote wider NTD integration . Several...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dermatology", "schoolchildren", "children", "medicine", "and", "health", "sciences", "education", "sociology", "tropical", "diseases", "social", "sciences", "bacterial", "diseases", "age", "groups", "neglected", "tropical", "diseases", "educational", "status", "fungal", ...	2018	Skin disease prevalence study in schoolchildren in rural Côte d'Ivoire: Implications for integration of neglected skin diseases (skin NTDs)
We have investigated the potential of the GTP synthesis pathways as chemotherapeutic targets in the human pathogen Cryptococcus neoformans , a common cause of fatal fungal meningoencephalitis . We find that de novo GTP biosynthesis , but not the alternate salvage pathway , is critical to cryptococcal dissemination and ...	The fungal pathogen Cryptococcus neoformans is responsible for up to a million deaths annually , and the currently available antifungal medicines used to combat this infection are limited and patently inadequate . We have investigated the GTP biosynthesis pathway as a new drug target , a pathway that has been a chemoth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "enzymes", "microbiology", "host-pathogen", "interaction", "nucleotides", "emerging", "infectious", "diseases", "enzyme", "kinetics", "mycology", "metabolic", "pathways", "microbial", "pathogens", "biology", "pathogenesis", "fungal", "biochemistry", "biochemistry", "enzyme", ...	2012	De novo GTP Biosynthesis Is Critical for Virulence of the Fungal Pathogen Cryptococcus neoformans

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