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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Hypothalamic neurons are main regulators of energy homeostasis . Neuronal function essentially depends on plasma membrane-located gangliosides . The present work demonstrates that hypothalamic integration of metabolic signals requires neuronal expression of glucosylceramide synthase ( GCS; UDP-glucose:ceramide glucosyl...	Obesity is a growing health threat that affects nearly half a billion people worldwide , and its incidence rates in lower income countries are rising dramatically . As obesity is a major risk factor for type II diabetes and cardiovascular disease , significant effort has been put into the exploration of causes , preven...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurochemistry", "protein", "interactions", "neuroscience", "gene", "function", "animal", "models", "model", "organisms", "membrane", "receptor", "signaling", "membranes", "and", "sorting", "biology", "proteomics", "neuroendocrinology", "mouse", "biochemistry", "signal", ...	2013	Neuronal Expression of Glucosylceramide Synthase in Central Nervous System Regulates Body Weight and Energy Homeostasis
Neurons are equipped with homeostatic mechanisms that counteract long-term perturbations of their average activity and thereby keep neurons in a healthy and information-rich operating regime . While homeostasis is believed to be crucial for neural function , a systematic analysis of homeostatic control has largely been...	Despite their apparent robustness many biological system work best in controlled environments , the tightly regulated mammalian body temperature being a good example . Biological homeostatic control systems , not unlike those used in engineering , ensure that the right operating conditions are met . Similarly , neurons...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Stability of Neuronal Networks with Homeostatic Regulation
Residents of resource-poor tropical countries carry heavy burdens of concurrent parasitic infections , leading to high rates of morbidity and mortality . This study was undertaken to help identify the social and environmental determinants of multiple parasite infection in one such community . Residents of Kingwede , Ke...	Parasitic diseases such as malaria and schistosomiasis account for a large proportion of global morbidity and mortality by contributing to malnutrition , developmental delays , loss of productivity , negative birth outcomes , disfigurement , physical handicap and social stigma . We studied these two infections in a com...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "social", "epidemiology", "infectious", "diseases", "schistosomiasis", "public", "health", "and", "epidemiology", "tropical", "diseases", "(non-neglected)", "epidemiology", "environmental", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tro...	2012	Partnering Parasites: Evidence of Synergism between Heavy Schistosoma haematobium and Plasmodium Species Infections in Kenyan Children
Mycobacterium tuberculosis infection presents across a spectrum in humans , from latent infection to active tuberculosis . Among those with latent tuberculosis , it is now recognized that there is also a spectrum of infection and this likely contributes to the variable risk of reactivation tuberculosis . Here , functio...	Asymptomatic infection with Mycobacterium tuberculosis , often called latent tuberculosis , affects more than 2 billion people . Reactivation of latent infection to active TB occurs in only a minority of those infected , yet can lead to deadly disease and transmission . Here we show , using a non-human primate model , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "diagnostic", "radiology", "granulomas", "immunology", "vertebrates", "neuroscience", "animals", "mammals", "positron", "emis...	2016	PET CT Identifies Reactivation Risk in Cynomolgus Macaques with Latent M. tuberculosis
Virus-specific CD8+ T cells ( TCD8+ ) are initially triggered by peptide-MHC Class I complexes on the surface of professional antigen presenting cells ( pAPC ) . Peptide-MHC complexes are produced by two spatially distinct pathways during virus infection . Endogenous antigens synthesized within virus-infected pAPC are ...	Understanding the pathways by which protective immunity is mediated against viral pathogens is essential to allow the design of effective vaccines . No effective vaccine has been designed to activate killer cells of the immune system expressing CD8 , although CD8+ T cells are the most effective cells at modulating anti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immune", "evasion", "immunology/antigen", "processing", "and", "recognition", "immunology/immunity", "to", "infections", "virology/host", "antiviral", "responses" ]	2009	Viral Sequestration of Antigen Subverts Cross Presentation to CD8+ T Cells
As part of the Nucleotide Excision Repair ( NER ) process , the endonuclease XPG is involved in repair of helix-distorting DNA lesions , but the protein has also been implicated in several other DNA repair systems , complicating genotype-phenotype relationship in XPG patients . Defects in XPG can cause either the cance...	Accumulation of DNA damage has been implicated in aging . Many premature aging syndromes are due to defective DNA repair systems . The endonuclease XPG is involved in repair of helix-distorting DNA lesions , and XPG defects cause the cancer-prone condition xeroderma pigmentosum ( XP ) alone or combined with the severe ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "animal", "models", "physiological", "processes", "developmental", "biology", "model", "organisms", "organism", "development", "dna", "research", "and", "analysis", "methods", "mouse", "models", "aging", "biochemistry", "cell", "biology", "nucleic", "aci...	2014	Cell-Autonomous Progeroid Changes in Conditional Mouse Models for Repair Endonuclease XPG Deficiency
Voluntary motor commands produce two kinds of consequences . Initially , a sensory consequence is observed in terms of activity in our primary sensory organs ( e . g . , vision , proprioception ) . Subsequently , the brain evaluates the sensory feedback and produces a subjective measure of utility or usefulness of the ...	It is thought that motor adaptation relies on sensory prediction errors to form an estimate of the perturbation . Here , we present evidence that motor adaptation can be driven by both sensory and reward prediction errors . We found that learning from sensory prediction error altered the predicted consequences of motor...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "neuroscience" ]	2011	Learning from Sensory and Reward Prediction Errors during Motor Adaptation
miR-122 , a liver-specific microRNA , is one of the determinants for liver tropism of hepatitis C virus ( HCV ) infection . Although miR-122 is required for efficient propagation of HCV , we have previously shown that HCV replicates at a low rate in miR-122-deficient cells , suggesting that HCV-RNA is capable of propag...	A liver-specific microRNA , miR-122 , is one of the key determinants of hepatitis C virus ( HCV ) hepatotropism and is required for efficient propagation of HCV . On the other hand , chronic infection with HCV is often associated with extrahepatic manifestations ( EHMs ) , and a low level of HCV-RNA replication has bee...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "rna", "extraction", "microbiology", "cloning", "viruses", "mutation", "substitution", "mutation", "rna"...	2017	Characterization of miR-122-independent propagation of HCV
Clostridium difficile infection affects a significant number of hospitalized patients in the United States . Two homologous exotoxins , TcdA and TcdB , are the major virulence factors in C . difficile pathogenesis . The toxins are glucosyltransferases that inactivate Rho family-GTPases to disrupt host cellular function...	Clostridium difficile is a bacterial pathogen that causes nearly half a million infections each year in the United States . It infects the human colon and causes diarrhea , colitis and , in some cases , death . C . difficile infection is mediated by the action of two large homologous toxins , TcdA and TcdB . Disruption...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "toxins", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "enzymes", "biological", "cultures", "cell", "processes", "enzymology", "light", "microscopy", "toxicology", "toxic", "agents", "microsco...	2016	Clostridium difficile Toxin A Undergoes Clathrin-Independent, PACSIN2-Dependent Endocytosis
Ion channels catalyze ionic permeation across membranes via water-filled pores . To understand how changes in intracellular magnesium concentration regulate the influx of Mg2+ into cells , we examine early events in the relaxation of Mg2+ channel CorA toward its open state using massively-repeated molecular dynamics si...	This study shows how rapid wetting/dewetting transitions in the pores of ion channels participate in the control of biological ion permeation . Ion channels catalyze ionic permeation across non-polar membranes via water-filled pores . However , non-polar stretches or hydrophobic bottlenecks are present in the pores of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Hydrophobic Gating of Ion Permeation in Magnesium Channel CorA
Adequate predictions of mosquito-borne disease risk require an understanding of the relevant drivers governing mosquito populations . Since previous studies have focused mainly on the role of temperature , here we assessed the effects of other important ecological variables ( predation , nutrient availability , presenc...	Human actions have strongly altered ecosystems worldwide , through climate change , eutrophication , and biodiversity loss . The consequences of these global changes for mosquito populations could have important implications for mosquito-borne infections . Previous studies have focused on the effects of temperature fro...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "death", "rates", "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "plant", "cell", "biology", "chloroplasts", "pigments", "animals", "developmental", "biology", "plant", "science", "pupae", "materials", "science",...	2018	Eutrophication and predator presence overrule the effects of temperature on mosquito survival and development
For any organism , population size , and fluctuations thereof , are of primary importance in determining the forces driving its evolution . This is particularly true for viruses—rapidly evolving entities that form populations with transient and explosive expansions alternating with phases of migration , resulting in st...	Infecting viruses progress within multi-cellular hosts via two distinct mechanisms: cell-to-cell proximal contamination and long-distance migration to remote organs through the vasculature . In distant susceptible organs , it seems logical that the number of initially infected cells , the number of viral genomes enteri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "transmission", "and", "infection", "plant", "biology", "population", "dynamics", "population", "genetics", "microbiology", "host-pathogen", "interaction", "plant", "science", "effective", "population", "size", "plant", "pathology", "population", "biology", "vira...	2012	Circulating Virus Load Determines the Size of Bottlenecks in Viral Populations Progressing within a Host
Acute respiratory distress syndrome ( ARDS ) is the leading cause of death in critical care medicine . The syndrome is typified by an exaggerated inflammatory response within the lungs . ARDS has been reported in many species , including dogs . We have previously reported a fatal familial juvenile respiratory disease a...	Acute respiratory distress syndrome ( ARDS ) is characterized by life-threatening impairment of pulmonary gas exchange and leads to substantial mortality in man . Spontaneous ARDS has also been described in dogs including a familial fatal ARDS-like syndrome in young Dalmatian dogs . The main clinical signs include prog...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "respiratory", "failure", "membrane", "staining", "vertebrates", "dogs", "animals", "mammals", "lungs", "pulmonology", "respiratory", "system", "genome", "analysis", "mammalian", "genomics", "research", "and", "analysis", "method...	2017	ANLN truncation causes a familial fatal acute respiratory distress syndrome in Dalmatian dogs
Toxoplasma gondii resides in an intracellular compartment ( parasitophorous vacuole ) that excludes transmembrane molecules required for endosome - lysosome recruitment . Thus , the parasite survives by avoiding lysosomal degradation . However , autophagy can re-route the parasitophorous vacuole to the lysosomes and ca...	Toxoplasma gondii resides in a parasitophorous vacuole that excludes transmembrane proteins required for recruitment of endosomes and lysosomes and thus , does not follow the path of classical lysosomal degradation . However , the non-fusogenic nature of the vacuole can be reverted when autophagy , a pathway to lysosom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Toxoplasma gondii-Induced Activation of EGFR Prevents Autophagy Protein-Mediated Killing of the Parasite
The ontogeny of large-scale functional organization of the human brain is not well understood . Here we use network analysis of intrinsic functional connectivity to characterize the organization of brain networks in 23 children ( ages 7–9 y ) and 22 young-adults ( ages 19–22 y ) . Comparison of network properties , inc...	The disruption of normal brain organization in humans is believed to underlie a number of behavioral conditions , such as autism spectrum disorders ( ASD ) and attention-deficit/hyperactivity disorder ( ADHD ) . To gain insight into how normal brain organization develops , we mapped functional brain connectivity in chi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neurodevelopment", "neuroscience/cognitive", "neuroscience", "radiology", "and", "medical", "imaging/magnetic", "resonance", "imaging", "computational", "biology/computational", "neuroscience" ]	2009	Development of Large-Scale Functional Brain Networks in Children
The phenotypic heterogeneity that characterizes human cancers reflects the enormous genetic complexity of the oncogenic process . This complexity can also be seen in mouse models where it is frequently observed that in addition to the initiating genetic alteration , the resulting tumor harbors additional , somatically ...	The diversity of human cancers reflects the variety of genetic changes that cause tumors to emerge and progress . Even for mice engineered with a specific cancer-causing mutation , the resulting tumors are often divergent , reflecting different additional mutations . We wanted to investigate how activities that work to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/cancer", "genetics", "genetics", "and", "genomics/gene", "expression" ]	2009	A Role for E2F Activities in Determining the Fate of Myc-Induced Lymphomagenesis
Proteasomes recognize and degrade poly-ubiquitinylated proteins . In infectious disease , cells activated by interferons ( IFNs ) express three unique catalytic subunits β1i/LMP2 , β2i/MECL-1 and β5i/LMP7 forming an alternative proteasome isoform , the immunoproteasome ( IP ) . The in vivo function of IPs in pathogen-i...	The proteasome recognizes and degrades protein substrates tagged with poly-ubiquitin chains . Immune cells and cells activated by inflammatory cytokines/interferons express immunoproteasomes ( IPs ) that are characterized by unique catalytic subunits with increased substrate turnover . In infectious disease , the funct...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "immunology", "microbiology", "histology", "adaptive", "immunity", "animal", "models", "of", "infection", "inflammation", "major", "histocompatibility", "complex", "proteins", "biology", "immune", "response", "biochemistry", "protein", "chemistry", "antigen", "processing", ...	2011	Impairment of Immunoproteasome Function by β5i/LMP7 Subunit Deficiency Results in Severe Enterovirus Myocarditis
Circadian clocks are ubiquitous in eukaryotic organisms where they are used to anticipate regularly occurring diurnal and seasonal environmental changes . Nevertheless , little is known regarding pathways connecting the core clock to its output pathways . Here , we report that the HAD family phosphatase CSP-6 is requir...	Though molecules and components in the core circadian oscillator are well studied in Neurospora , the mechanisms through which output pathways are coupled with core components are less well understood . In this study we investigated a HAD phosphatase , CSP-6; loss-of-function Δcsp-6 strains are overtly arrhythmic but h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "luciferase", "enzymes", "gene", "regulation", "regulatory", "proteins", "enzymology", "dna-binding", "proteins", "light", "electromagnetic", "radiation", "phosphatases", "circadian", "oscillators", "transcription", "factors", "chronobiology", "proteins", "...	2018	A HAD family phosphatase CSP-6 regulates the circadian output pathway in Neurospora crassa
The importance of a mesoscopic description level of the brain has now been well established . Rate based models are widely used , but have limitations . Recently , several extremely efficient population-level methods have been proposed that go beyond the characterization of a population in terms of a single variable . ...	A group of slow , noisy and unreliable cells collectively implement our mental faculties , and how they do this is still one of the big scientific questions of our time . Mechanistic explanations of our cognitive skills , be it locomotion , object handling , language comprehension or thinking in general—whatever that m...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results/Discussion" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "statistics", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "systems", "science", "mathematics", "population", "biology", "research", "an...	2019	Computational geometry for modeling neural populations: From visualization to simulation
A fundamental assumption , common to the vast majority of high-throughput transcriptome analyses , is that the expression of most genes is unchanged among samples and that total cellular RNA remains constant . As the number of analyzed experimental systems increases however , different independent studies demonstrate t...	We present a complete statistical model for the analysis of RNA-seq data from a population of cells using external RNA spike-ins and a maximum-likelihood method for genome-wide estimation of transcripts per cell . The model includes biological variability of cellular transcript number and sampling noise . We derive an ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cdna", "libraries", "sequencing", "techniques", "statistics", "rna", "extraction", "fungi", "mathematics", "forms", "of", "dna", "dna", "libraries", "molecular", "biology", "techniques", "dna", "rna", "sequencing", "cell", "enumeration", "techniques", "cellular", "st...	2019	A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
An increasing risk of Schistosoma mansoni infection has been observed around Lake Victoria , western Kenya since the 1970s . Understanding local transmission dynamics of schistosomiasis is crucial in curtailing increased risk of infection . We carried out a cross sectional study on a population of 310 children from eig...	It is estimated that more than ten percent of the world's population is at risk of schistosome transmission , with over 90% of infections occurring in sub-Saharan Africa . In Kenya , schistosomiasis remains a major public health concern particularly around Lake Victoria . The objective of this study was to identify the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "helminth", "infections", "medicine", "and", "health", "sciences", "schistosomiasis", "infectious", "disease", "epidemiology", "epidemiology", "neglected", "tropical", "diseases", "tropical", "diseases", "parasitic", "diseases" ]	2014	Risk Factors and Spatial Distribution of Schistosoma mansoni Infection among Primary School Children in Mbita District, Western Kenya
Drosophila Lnk is the single ancestral orthologue of a highly conserved family of structurally-related intracellular adaptor proteins , the SH2B proteins . As adaptors , they lack catalytic activity but contain several protein–protein interaction domains , thus playing a critical role in signal transduction from recept...	Many human populations are experiencing increased life expectancy , and as populations age the incidence of age-related diseases becomes more prevalent . The identification of single gene mutations that extend lifespan in invertebrate model organisms has revealed that several cellular signaling pathways , including the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/aging" ]	2010	Regulation of Lifespan, Metabolism, and Stress Responses by the Drosophila SH2B Protein, Lnk
In most eukaryotes , including the majority of fungi , expression of sterol biosynthesis genes is regulated by Sterol-Regulatory Element Binding Proteins ( SREBPs ) , which are basic helix-loop-helix transcription activators . However , in yeasts such as Saccharomyces cerevisiae and Candida albicans sterol synthesis is...	All but a few eukaryotes die without oxygen and respond dynamically to changes in the level of oxygen available to them . One ancient oxygen-requiring biochemical pathway in eukaryotes is the pathway for the biosynthesis of sterols , leading to cholesterol in animals and ergosterol in fungi . Mutations in this pathway ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome", "expression", "analysis", "mycology", "fungi", "functional", "genomics", "molecular", "cell", "biology", "genome", "evolution", "fungal", "evolution", "comparative", "genomics", "biology", "genomics", "evolutionary", "biology", "microbiology" ]	2014	Zinc Finger Transcription Factors Displaced SREBP Proteins as the Major Sterol Regulators during Saccharomycotina Evolution
Because of evolutionary pressures imposed through episodic colonization by retroviruses , many mammals express factors , such as TRIM5α and APOBEC3 proteins , that directly restrict retroviral replication . TRIM5 and APOBEC restriction factors are most often studied in the context of modern primate lentiviruses , but i...	Retroviruses integrate their genomes into host-cell DNA as an essential part of their replication cycle . If a retrovirus is integrated into a cell that becomes a germ line cell such as a sperm or an egg , then it may be inherited as an ‘endogenous’ retrovirus . In fact , endogenous retroviruses are extraordinarily com...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "antiviral", "responses" ]	2008	Evidence for Restriction of Ancient Primate Gammaretroviruses by APOBEC3 but Not TRIM5α Proteins
Neuroinvasive larvae of the worldwide occurring zoonotic roundworms Toxocara canis and T . cati may induce neurotoxocarosis ( NT ) in humans , provoking a variety of symptoms including cognitive deficits as well as neurological dysfunctions . An association with neuropsychological disorders has been discussed . Similar...	The worldwide occurring zoonotic roundworms Toxocara canis and T . cati may cause the so-called neurotoxocarosis ( NT ) in humans , possibly resulting in a variety of behavioural alterations . Comparable alterations to those in humans have been described in T . canis-infected mice , however , reports on T . cati-induce...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cognitive", "neurology", "medicine", "and", "health", "sciences", "respiratory", "infections", "vertebrates", "mice", "neuroscience", "learning", "and", "memory", "animals", "mammals", "pulmonology", "developmental", "biology", "cognitive", "neuroscience", "animal", "beh...	2017	Abnormal neurobehaviour and impaired memory function as a consequence of Toxocara canis- as well as Toxocara cati-induced neurotoxocarosis
Chronic intestinal parasite infection is a major global health problem , but mechanisms that promote chronicity are poorly understood . Here we describe a novel cellular and molecular pathway involved in the development of chronic intestinal parasite infection . We show that , early during development of chronic infect...	Infection with intestinal parasitic worms is a major global health problem , with billions of people infected world-wide . Often these worms ( known as helminths ) develop a long-lasting chronic infection , due to failure of the host to mount the correct type of immune response that would normally expel the parasite . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Loss of the TGFβ-Activating Integrin αvβ8 on Dendritic Cells Protects Mice from Chronic Intestinal Parasitic Infection via Control of Type 2 Immunity
The surface coat of Trypanosoma cruzi is predominantly composed of glycosylphosphatidylinositol-anchored proteins , which have been extensively characterized . However , very little is known about less abundant surface proteins and their role in host-parasite interactions . Here , we described a novel family of T . cru...	Trypanosoma cruzi is the etiologic agent of Chagas’ disease , which infects 6–7 million people worldwide , mostly in Latin America . Currently , there are no vaccines available , and the drugs used for treatment are toxic and are not fully effective . To infect mammalian hosts , T . cruzi relies on the ability to invad...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Molecular Characterization of a Novel Family of Trypanosoma cruzi Surface Membrane Proteins (TcSMP) Involved in Mammalian Host Cell Invasion
West Nile virus ( WNV ) has been circulating in California since its first detection in 2003 , causing repeated outbreaks affecting public , wildlife and veterinary health . Epidemics of WNV are difficult to predict due to the multitude of factors influencing transmission dynamics among avian and mosquito hosts . Typic...	West Nile virus ( WNV ) is the cause of the largest mosquito-borne epidemic in the United States in recent history , with over 46 , 000 reported human cases to date , including >2000 deaths . Since the detection of WNV in California in 2003 , repeated outbreaks have been associated with explosive WNV amplification in l...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "united", "states", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "california", "geographical", "locations", "microbiology", "vertebrates", "animals", "viruses", "north", "america", ...	2019	Comparative fitness of West Nile virus isolated during California epidemics
With every breath , the dynamically changing mechanical pressures must work in unison with the cells and soft tissue structures of the lung to permit air to efficiently traverse the airway tree and undergo gas exchange in the alveoli . The influence of mechanics on cell and tissue function is becoming apparent , raisin...	With every breath , mechanical pressures change in the lung and permit air to efficiently traverse the airway tree and undergo gas exchange . These pressure variations also influence cell and tissue function , raising the question: how does the airway tree co-exist within its mechanical environment to maintain normal c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bioengineering", "tissue", "mechanics", "biomedical", "engineering", "biology", "biophysics", "biomechanics", "engineering" ]	2013	A Mechanical Design Principle for Tissue Structure and Function in the Airway Tree
Dengue has emerged as one of the most important infectious diseases in the last five decades . Evidence indicates the expansion of dengue virus endemic areas and consequently the exponential increase of dengue virus infections across the subtropics . The clinical manifestations of dengue virus infection include sudden ...	Dengue is the fastest spreading mosquito borne diseases in the world and is endemic in most tropical and sub-tropical countries with an estimated 96 million infections resulting in clinical disease annually . Population-based longitudinal prospective studies are essential for understanding dengue virus in the natural s...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "geographical", "locations", "indonesia", ...	2016	The Epidemiology, Virology and Clinical Findings of Dengue Virus Infections in a Cohort of Indonesian Adults in Western Java
Disruption of T cell memory during severe immune suppression results in reactivation of chronic viral infections , such as Epstein Barr virus ( EBV ) and Cytomegalovirus ( CMV ) . How different subsets of memory T cells contribute to the protective immunity against these viruses remains poorly defined . In this study w...	Some viruses have the capacity to establish chronic infections in humans . How different T cell populations effectively control these infections has not been clear . Continuous circulation of memory T cells was thought to be crucial for effective immune surveillance against such infections . Recent studies in mice howe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "spleen", "immunology", "microbiology", "throat", "developmental", "biology", "molecular", "development"...	2016	Compartmentalization of Total and Virus-Specific Tissue-Resident Memory CD8+ T Cells in Human Lymphoid Organs
Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes . Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution . The evolution of such networks within an...	The influence of transcriptional regulatory networks on the evolution of bacterial pangenomes has not yet been elucidated , even though the role of transcriptional regulation is widely recognized . Using the model symbiont Sinorhizobium meliloti we have predicted the regulatory targets of 41 transcription factors in 51...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome
Iron is a key pathogenic determinant of many infectious diseases . Hepcidin , the hormone responsible for governing systemic iron homeostasis , is widely hypothesized to represent a key component of nutritional immunity through regulating the accessibility of iron to invading microorganisms during infection . However ,...	An adequate supply of iron is essential for both human hosts and their infecting pathogens . Hepcidin is the human hormone that controls the quantity and distribution of iron throughout the body . During infections , hepcidin activity may redistribute iron away from serum and into macrophages , potentially affecting pa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Rapidly Escalating Hepcidin and Associated Serum Iron Starvation Are Features of the Acute Response to Typhoid Infection in Humans
Huntington's disease ( HD ) is an autosomal dominantly inherited disorder caused by the expansion of CAG repeats in the Huntingtin ( HTT ) gene . The abnormally extended polyglutamine in the HTT protein encoded by the CAG repeats has toxic effects . Here , we provide evidence to support that the mutant HTT CAG repeats ...	Huntington's disease ( HD ) is a neurodegenerative disorder caused by an abnormal CAG expansion in the Huntingtin gene ( HTT ) , resulting in an expanded polyglutamine track in the HTT protein . Longer CAG expansions correlate with an earlier more severe manifestation of the disease that produces choreic movement , beh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "nucleic", "acids", "gene", "expression", "biology", "genomics", "molecular", "cell", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2012	A Pathogenic Mechanism in Huntington's Disease Involves Small CAG-Repeated RNAs with Neurotoxic Activity
The pathogenesis of Lassa fever ( LF ) , a hemorrhagic fever endemic to West Africa , remains unclear . We previously compared Lassa virus ( LASV ) with its genetically close , but nonpathogenic homolog Mopeia virus ( MOPV ) and demonstrated that the strong activation of antigen-presenting cells ( APC ) , including typ...	Lassa virus ( LASV ) causes a viral hemorrhagic fever that affects about 300 , 000 people and leads to 5 , 000 deaths annually . Lassa fever ( LF ) is a public health problem in West Africa , where it is endemic , because of the number of cases , deaths and disabling effects . There is no vaccine against LASV and the o...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "animal", "models", "of", "infection", "immune", "cells", "emerging", "infectious", "diseases", "immunity", "virology", "innate", "immunity", "emerging", "viral", "diseases", "antigen-presenting", "cells", "immunity", "to", "infections", "immunology", "host-pathogen", "...	2014	Production of CXC and CC Chemokines by Human Antigen-Presenting Cells in Response to Lassa Virus or Closely Related Immunogenic Viruses, and in Cynomolgus Monkeys with Lassa Fever
Chromosomal rearrangements are a major driver of eukaryotic genome evolution , affecting speciation , pathogenicity and cancer progression . Changes in chromosome structure are often initiated by mis-repair of double-strand breaks in the DNA . Mis-repair is particularly likely when telomeres are lost or when dispersed ...	Chromosomal rearrangements are a hallmark of genetic differences between species . But changes in chromosome structure can also occur spontaneously within species , within populations , or even within individuals . The causes and consequences of chromosomal rearrangements affecting natural populations are poorly unders...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "mycology", "plant", "science", "genome", "evolution", "chromosome", "biology", "fungal", "evolution", "plant", "pathogens", "microbial", "pathogens", "plant", "pathology", "population", "genetics", "comparative", "genomics", "biology", "genomics",...	2013	Breakage-fusion-bridge Cycles and Large Insertions Contribute to the Rapid Evolution of Accessory Chromosomes in a Fungal Pathogen
Inflammation , which is directly regulated by interleukin-6 ( IL-6 ) signaling , is implicated in the etiology of several chronic diseases . Although a common , non-synonymous variant in the IL-6 receptor gene ( IL6R Asp358Ala; rs2228145 A>C ) is associated with the risk of several common diseases , with the 358Ala all...	Interleukin-6 ( IL-6 ) is a complex cytokine , which plays a critical role in the regulation of inflammatory responses . Genetic variation in the IL-6 receptor gene is associated with the risk of several human diseases with an inflammatory component , including coronary heart disease , rheumatoid arthritis , and asthma...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "genetic", "association", "studies", "personalized", "medicine", "genetics", "immunology", "biology", "human", "genetics", "genetics", "of", "disease", "genomic", "medicine", "pharmacogenomics", "autoimmunity" ]	2013	Functional IL6R 358Ala Allele Impairs Classical IL-6 Receptor Signaling and Influences Risk of Diverse Inflammatory Diseases
Five X-linked severe combined immunodeficiency patients ( SCID-X1 ) successfully treated with autologous bone marrow stem cells infected ex vivo with an IL2RG-containing retrovirus subsequently developed T-cell leukemia and four contained insertional mutations at LMO2 . Genetic evidence also suggests a role for IL2RG i...	Twenty patients with X-linked severe combined immunodeficiency ( SCID-X1 ) have been successfully treated by gene therapy . Unfortunately , five of these patients have developed T-cell leukemia two or more years after receiving the therapeutic gene IL2RG on a retroviral vector . The leukemias developed because the vect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "hematology/acute", "lymphoblastic", "leukemia", "genetics", "and", "genomics/disease", "models", "virology/viruses", "and", "cancer", "oncology/hematological", "malignancies", "genetics", "and", "genomics/cancer", "genetics" ]	2009	Murine Leukemias with Retroviral Insertions at Lmo2 Are Predictive of the Leukemias Induced in SCID-X1 Patients Following Retroviral Gene Therapy
Hepatitis C virus ( HCV ) has infected around 160 million individuals . Current therapies have limited efficacy and are fraught with side effects . To identify cellular HCV dependency factors , possible therapeutic targets , we manipulated signaling cascades with pathway-specific inhibitors . Using this approach we ide...	The human genome encodes more than 30 phospholipase A2s . These enzymes cleave fatty acids at the C2 atom of phosphoglycerides and thus modulate membrane properties . Among all PLA2s only PLA2G4A , which is recruited to perinuclear membranes by Ca2+ and activated by extracellular stimuli via the mitogen activated prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dengue", "hepatitis", "gastroenterology", "and", "hepatology", "lipid", "signaling", "infectious", "disease", "control", "mapk", "signaling", "cascades", "erk", "signaling", "cascade", "hepatitis", "c", "infectious", "diseases", "signaling", "in", "cellular...	2012	MAP-Kinase Regulated Cytosolic Phospholipase A2 Activity Is Essential for Production of Infectious Hepatitis C Virus Particles
Danforth's short tail ( Sd ) is a semidominant mutation on mouse chromosome 2 , characterized by spinal defects , urogenital defects , and anorectal malformations . However , the gene responsible for the Sd phenotype was unknown . In this study , we identified the molecular basis of the Sd mutation . By positional clon...	Caudal regression syndrome ( CRS ) is a congenital heterogeneous constellation of caudal anomalies that includes varying degrees of agenesis of the spinal column , anorectal malformations , and genitourinary anomalies . Its pathogenesis is unclear . However , it could be the result of excessive physiologic regression o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genetics", "and", "genomics" ]	2013	Ectopic Expression of Ptf1a Induces Spinal Defects, Urogenital Defects, and Anorectal Malformations in Danforth's Short Tail Mice
Genome-wide expression Quantitative Trait Loci ( eQTL ) studies in humans have provided numerous insights into the genetics of both gene expression and complex diseases . While the majority of eQTL identified in genome-wide analyses impact a single gene , eQTL that impact many genes are particularly valuable for networ...	The discovery of expression Quantitative Trait Loci ( eQTL ) from the analysis of genome-wide genotype and gene expression data has played an important role in the study of cellular processes and complex disease . Here , we introduce CONFETI: Confounding Factor Estimation Through Independent component analysis , an ana...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "variant", "genotypes", "random", "variables", "covariance", "factor", "analysis", "twins", "genetic", "mapping", "simulation", "and", "modeling", "multivariate", "analysis", "developmental", "biology", "mathematics", "statistics", "(mathematics)", "research", "and", "ana...	2017	An independent component analysis confounding factor correction framework for identifying broad impact expression quantitative trait loci
Holoprosencephaly ( HPE ) is a remarkably common congenital anomaly characterized by failure to define the midline of the forebrain and midface . HPE is associated with heterozygous mutations in Sonic hedgehog ( SHH ) pathway components , but clinical presentation is extremely variable and many mutation carriers are un...	Holoprosencephaly ( HPE ) , a congenital anomaly characterized by failure to form the midline of the forebrain and midface , occurs as frequently as 1 in 250 conceptions . Mutations in genes that direct formation of the forebrain and facial midline are associated with HPE , but the clinical outcome is extremely variabl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "genetics", "and", "genomics", "toxicology" ]	2012	Cdon Mutation and Fetal Ethanol Exposure Synergize to Produce Midline Signaling Defects and Holoprosencephaly Spectrum Disorders in Mice
T cell immunoglobulin and mucin protein 3 ( TIM-3 ) is a type I cell surface protein that was originally identified as a marker for murine T helper type 1 cells . TIM-3 was found to negatively regulate murine T cell responses and galectin-9 was described as a binding partner that mediates T cell inhibitory effects of T...	Inhibitory costimulatory receptors are a hallmark of exhausted T cells , which accumulate during chronic infection with viruses like HIV-1 . Recently , TIM-3 was described as functional receptor on exhausted human T cells . Galectin-9 was reported as an inhibitory ligand for TIM-3 on murine T cells , but it was not kno...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "hiv", "immunology", "biology", "viral", "diseases", "immunomodulation", "immune", "response" ]	2013	TIM-3 Does Not Act as a Receptor for Galectin-9
Trypanosoma vivax is one of the most common parasites responsible for animal trypanosomosis , and although this disease is widespread in Africa and Latin America , very few studies have been conducted on the parasite's biology . This is in part due to the fact that no reproducible experimental methods had been develope...	Trypanosoma vivax is a major parasite of domestic animals in Africa and Americas . Most studies on this parasite have focused on gathering epidemiological data in the field . Studies on its biology , metabolism and interaction with the host immune system have been hindered by a lack of suitable tools for its maintenanc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "trypanosoma", "genetics", "molecular", "genetics", "biology", "microbiology", "protozoology", "genetics", "and", "genomics" ]	2011	Genetic Engineering of Trypanosoma (Dutonella) vivax and In Vitro Differentiation under Axenic Conditions
Identifying and eliminating snail habitats is the key measure for schistosomiasis control , critical for the nationwide strategy of eliminating schistosomiasis in China . Here , our aim was to construct a new analytical framework to predict high-risk snail habitats based on a large sample field survey for Oncomelania h...	Oncomelania hupensis is the sole intermediate host of Schistosoma japonicum and it is critical for the long-term sustainable control and elimination of schistosomiasis . We suggest a new analytical framework to predict high-risk snail habitats based on ecological models . Their predictive performance were compared via ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "malacology", "china", "population", "dynamics", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "oncomelania", "gastropods", ...	2019	Identification of high-risk habitats of Oncomelania hupensis, the intermediate host of schistosoma japonium in the Poyang Lake region, China: A spatial and ecological analysis
The cellular endosomal sorting complex required for transport ( ESCRT ) machinery participates in membrane scission and cytoplasmic budding of many RNA viruses . Here , we found that expression of dominant negative ESCRT proteins caused a blockade of Epstein-Barr virus ( EBV ) release and retention of viral BFRF1 at th...	Herpesviruses are large DNA viruses associated with human and animal diseases . After viral DNA replication , the herpesviral nucleocapsids egress through the nuclear membrane for subsequent cytoplasmic virion maturation . However , the mechanism by which the virus regulates the nuclear membrane and cellular machinery ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "transmission", "and", "infection", "microbiology", "host-pathogen", "interaction", "viral", "structure", "viruslike", "particles", "membranes", "and", "sorting", "biology", "host", "cells", "cell", "biology", "virology", "molecular", "cell", "biolo...	2012	The ESCRT Machinery Is Recruited by the Viral BFRF1 Protein to the Nucleus-Associated Membrane for the Maturation of Epstein-Barr Virus
The fundamental aim of structural analyses in biophysics is to reveal a mutual relation between a molecule’s dynamic structure and its physiological function . Small-angle X-ray scattering ( SAXS ) is an experimental technique for structural characterization of macromolecules in solution and enables time-resolved analy...	Proteins are the molecular nanomachines in biological cells and thus vital to any known form of life . From the evolutionary perspective , viable protein structure emerges on the basis of a ‘form-follows-function’ principle . A protein’s designated function is inextricably linked to dynamic conformational changes , whi...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "molecular", "dynamics", "nmr", "spectroscopy", "simulation", "and", "modeling", "protein", "structure", "thermodynamics", "research", "and", "analysis", "methods", "proteins", "chemistry", "biophysics", "molecular", "biology", "free", "energy", "physics", "biochemistry",...	2019	Rapid interpretation of small-angle X-ray scattering data
The explosive spread of Zika virus ( ZIKV ) and associated complications in flavivirus-endemic regions underscore the need for sensitive and specific serodiagnostic tests to distinguish ZIKV , dengue virus ( DENV ) and other flavivirus infections . Compared with traditional envelope protein-based assays , several nonst...	Although there was a decrease of Zika virus ( ZIKV ) infection since late 2017 , the specter of congenital Zika syndrome and its re-emergence in flavivirus-endemic regions emphasize the need for sensitive and specific serological tests to distinguish ZIKV , dengue virus ( DENV ) and other flaviviruses . Compared with t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viruses", "rna", "viruses", "antibodies", "immunologic", "techniq...	2019	A high-throughput and multiplex microsphere immunoassay based on non-structural protein 1 can discriminate three flavivirus infections
The contactin-associated protein-like 2 ( CNTNAP2 ) gene is a member of the neurexin superfamily . CNTNAP2 was first implicated in the cortical dysplasia-focal epilepsy ( CDFE ) syndrome , a recessive disease characterized by intellectual disability , epilepsy , language impairments and autistic features . Associated S...	Genetic mutations that disrupt both copies of the CNTNAP2 gene lead to severe disease , characterized by profound intellectual disability , epilepsy , language difficulties and autistic traits , leading to the hypothesis that this gene may also be involved in autism given some overlapping clinical features with this di...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuropsychiatric", "disorders", "medicine", "and", "health", "sciences", "adhd", "anxiety", "disorders", "pervasive", "developmental", "disorders", "obsessive-compulsive", "disorder", "bipolar", "disorder", "social", "sciences", "autism", "developmental", "psychology", "ne...	2018	Comprehensive cross-disorder analyses of CNTNAP2 suggest it is unlikely to be a primary risk gene for psychiatric disorders
Many complex systems have been found to exhibit critical transitions , or so-called tipping points , which are sudden changes to a qualitatively different system state . These changes can profoundly impact the functioning of a system ranging from controlled state switching to a catastrophic break-down; signals that pre...	Neurons efficiently convey information by being able to switch rapidly between two different states: quiescence and spiking . Such sudden shifts to a qualitatively different state are observed in many complex systems; the often dramatic consequences of these tipping points for diverse fields such as economics , ecology...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Critical Slowing Down Governs the Transition to Neuron Spiking
RNAi is a ubiquitous pathway that serves central functions throughout eukaryotes , including maintenance of genome stability and repression of transposon expression and movement . However , a number of organisms have lost their RNAi pathways , including the model yeast Saccharomyces cerevisiae , the maize pathogen Usti...	Genome instability and mutations provoked by transposon movement are counteracted by novel defense mechanisms in organisms as diverse as fungi , plants , and mammals . In the human fungal pathogen Cryptococcus neoformans , an RNAi silencing pathway operates to defend the genome against mobile elements and transgene rep...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biotechnology", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "rna", "interference", "cryptococcus", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "gene", "regulation", "pathogens", "regulatory", "proteins", "microbiology", ...	2016	Gene Network Polymorphism Illuminates Loss and Retention of Novel RNAi Silencing Components in the Cryptococcus Pathogenic Species Complex
The basal nucleus of the amygdala ( BA ) is involved in the formation of context-dependent conditioned fear and extinction memories . To understand the underlying neural mechanisms we developed a large-scale neuron network model of the BA , composed of excitatory and inhibitory leaky-integrate-and-fire neurons . Excita...	The amygdaloid complex is one of the key brain structures involved in fear-related processes . A typical way to study neural correlates of fear expression ( e . g . freezing response ) in the amygdala is to perform a fear conditioning paradigm , which yields a conditioned fear response . This response can be reversed b...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/animal", "cognition", "neuroscience/theoretical", "neuroscience" ]	2011	Context-Dependent Encoding of Fear and Extinction Memories in a Large-Scale Network Model of the Basal Amygdala
Trachoma programs rely on guidelines made in large part using expert opinion of what will happen with and without intervention . Large community-randomized trials offer an opportunity to actually compare forecasting methods in a masked fashion . The Program for the Rapid Elimination of Trachoma trials estimated longitu...	Clinicaltrials . gov NCT00792922	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Short-term Forecasting of the Prevalence of Trachoma: Expert Opinion, Statistical Regression, versus Transmission Models
The lack of effective and well-tolerated therapies against antibiotic-resistant bacteria is a global public health problem leading to prolonged treatment and increased mortality . To improve the efficacy of existing antibiotic compounds , we introduce a new method for strategically inducing antibiotic hypersensitivity ...	Antibiotic resistance is a global health threat . While genome sequencing and genetic manipulation tools have elucidated many resistance mechanisms , these tools have not yet been developed into successful therapeutics . One tool with such potential are peptide-conjugated phosphorodiamidate morpholino oligomers ( PPMOs...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "antimicrobials", "deletion", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "messenger", "rna", "microbiology", "pigments", "antibiotic", "resistance", "mutation", "antibiotics", "materials", "scie...	2016	Sequence-Specific Targeting of Bacterial Resistance Genes Increases Antibiotic Efficacy
Noncoding RNAs are integral to a wide range of biological processes , including translation , gene regulation , host-pathogen interactions and environmental sensing . While genomics is now a mature field , our capacity to identify noncoding RNA elements in bacterial and archaeal genomes is hampered by the difficulty of...	We have analysed more than 400 public transcriptomes , generated using RNA-seq , from almost 40 strains of Bacteria and Archaea . We discovered that the capacity to identify noncoding RNA outputs from this data is strongly dependent on phylogenetic sampling . Our results show that , for the full potential of transcript...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "next-generation", "sequencing", "genome", "expression", "analysis", "bacterial", "genomics", "genomics", "genome", "evolution", "genome", "analysis", "transcriptome", "analysis", "genome", "annotation", "biology", "and", "life", "sciences", "comparative", "genomics", "mo...	2014	Robust Identification of Noncoding RNA from Transcriptomes Requires Phylogenetically-Informed Sampling
The major weaknesses of subunit vaccines are their low immunogenicity and poor efficacy . Adjuvants can help to overcome some of these inherent defects with subunit vaccines . Here , we evaluated the efficacy of the newly developed water-in-oil-in-water multiphase emulsion system , termed PELC , in potentiating the pro...	Dengue is a mosquito-borne disease . Infection of dengue virus can cause clinical manifestations ranging from self-limiting dengue fever to potentially life-threatening dengue hemorrhagic fever or dengue shock syndrome . In recent years , dengue has spread to most tropical and subtropical areas , making it a global hea...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "medicine", "viral", "vaccines", "immunology", "microbiology", "dengue", "adaptive", "immunity", "immune", "defense", "infectious", "disease", "control", "immunizations", "infectious", "diseases", "biology", "immune", "response", "immunity", "virolo...	2012	Dengue-1 Envelope Protein Domain III along with PELC and CpG Oligodeoxynucleotides Synergistically Enhances Immune Responses
A fundamental stage in viral infection is the internalization of viral genomes in host cells . Although extensively studied , the mechanisms and factors responsible for the genome internalization process remain poorly understood . Here we report our observations , derived from diverse imaging methods on genome internal...	Although extensively studied , the mechanisms responsible for internalization of viral genomes into their host cells remain unclear . A particularly interesting case of genome release and internalization is provided by the large Paramecium bursaria chlorella virus-1 ( PBCV-1 ) , which infects unicellular eukaryotic pho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "viral", "transmission", "and", "infection", "plant", "cell", "biology", "microbiology", "chloroplasts", "plant", "science", "membrane", "fusion", "viral", "genome", "cellular", "structures", "and", "organelles", "microbial", "genomics", "viral", "genomics", "viral", ...	2017	Structural studies demonstrating a bacteriophage-like replication cycle of the eukaryote-infecting Paramecium bursaria chlorella virus-1
Schistosome cercariae only elicit high levels of protective immunity against a challenge infection if they are optimally attenuated by exposure to ionising radiation that truncates their migration in the lungs . However , the underlying molecular mechanisms responsible for the altered phenotype of the irradiated parasi...	Schistosoma mansoni is a blood-dwelling parasitic worm that causes schistosomiasis in humans throughout Africa and parts of South America . A vaccine would enhance attempts to control and eradicate the disease that currently relies on treatment with a single drug . Although a manufactured vaccine has yet to generate hi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/neglected", "tropical", "diseases", "cell", "biology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/preventive", "medicine", "microbiology/parasitology" ]	2008	Altered Patterns of Gene Expression Underlying the Enhanced Immunogenicity of Radiation-Attenuated Schistosomes
The ventromedial nucleus of the hypothalamus ( VMN ) has an important role in diverse behaviours . The common involvement in these of sex steroids , nutritionally-related signals , and emotional inputs from other brain areas , suggests that , at any given time , its output is in one of a discrete number of possible sta...	When the needs of an animal require the execution of particular behaviours , the brain must decide which of these needs to prioritise–whether to flee from or fight an aggressor for example , or whether to hunt for food or pursue sex . The ventromedial nucleus of the hypothalamus is involved in such decisions , in the r...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "membrane", "potential", "microbiology", "signaling", "networks", "electrophysiology", "neuroscience", "network", "analysis", "computational", "neuroscience", "excitatory", "postsynaptic", ...	2019	Emergent decision-making behaviour and rhythm generation in a computational model of the ventromedial nucleus of the hypothalamus
The human T-lymphotropic virus type 1 ( HTLV-1 ) which is associated with the diseases of adult T-cell leukemia/lymphoma , HTLV-1 associated myelopathy / tropical spastic paraparesis ( HAM/TSP ) and HTLV-associated uveitis , can cause transfusion-transmitted infections . Although HTLV screening of blood donors was alre...	The human T-lymphotropic virus type 1 ( HTLV-1 ) which is associated with the diseases of adult T-cell leukemia/lymphoma , tropical spastic paraparesis etc . , can cause transfusion-transmitted infections , it also can be transmitted by sex or breastfeeding . Globally , approximately 20 million people are estimated to ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	The Prevalence of Human T-Lymphotropic Virus Infection among Blood Donors in Southeast China, 2004-2013
Deep-coverage metabolomic profiling has revealed a well-defined development of metabolic decay in human red blood cells ( RBCs ) under cold storage conditions . A set of extracellular biomarkers has been recently identified that reliably defines the qualitative state of the metabolic network throughout this metabolic d...	While deep-coverage omics data sets are allowing for more complete characterization of biological systems , there has been a concerted effort to identify a subset of measurements that are representative of qualitative network-level behavior . For some systems—like the human red blood cell ( RBC ) —such biomarkers have ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "carbohydrate", "metabolism", "metabolic", "networks", "mathematical", "models", "biomarkers", "glucose", "metabolism", "metabolomics", "mathematics", "metabolites", "forecasting", "statistics", "(mathematics)", "network", "analysis", "research", "and", "analysis", "methods",...	2017	Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells
The Asian tiger mosquito ( Aedes albopictus ) is an important vector for pathogens that affect human health , including the viruses that cause dengue and Chikungunya fevers . It is also one of the world's fastest-spreading invasive species . For these reasons , it is crucial to identify strategies for controlling the r...	The highly invasive Asian tiger mosquito ( Aedes albopictus ) transmits several pathogens that cause disease in humans and other animals . Therefore , Ae . albopictus poses a large and growing threat to public health across the world . One step toward managing the reproduction and threat of this species is to determine...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "spectrometric", "identification", "of", "proteins", "organismal", "evolution", "invertebrates", "medicine", "and", "health", "sciences", "genome", "evolution", "animals", "developmental", "biology", "animal", "behavior", "genome", "analysis", "molecular", "genetics", "zo...	2014	Identification and Characterization of Seminal Fluid Proteins in the Asian Tiger Mosquito, Aedes albopictus
Neuronal degeneration is a hallmark of many DNA repair syndromes . Yet , how DNA damage causes neuronal degeneration and whether defects in different repair systems affect the brain differently is largely unknown . Here , we performed a systematic detailed analysis of neurodegenerative changes in mouse models deficient...	Metabolism produces reactive oxygen species that damage our DNA and other cellular components , and as such it contributes to the aging process , including neuronal degeneration . Accordingly , genetic disorders associated with impaired DNA damage repair are frequently associated with premature onset of aging pathology...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurological", "disorders", "neurology", "biology", "neuroscience" ]	2011	Age-Related Neuronal Degeneration: Complementary Roles of Nucleotide Excision Repair and Transcription-Coupled Repair in Preventing Neuropathology
Chagas Disease , caused by the protozoan Trypanosoma cruzi , is a major health and economic problem in Latin America for which no vaccine or appropriate drugs for large-scale public health interventions are yet available . Accurate diagnosis is essential for the early identification and follow up of vector-borne cases ...	Chagas disease , caused by the parasite Trypanosoma cruzi , is a life-long and debilitating illness of major significance throughout Latin America , and an emergent threat to global public health . Diagnostic tests are key tools to support disease surveillance , and to ultimately help stop transmission of the parasite ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biotechnology", "synthetic", "biotechnology", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "engineering", "and", "technology", "synthetic", "biology", "immunology", "tropical", "diseases", "parasitic", "diseases", "paras...	2017	Next-generation ELISA diagnostic assay for Chagas Disease based on the combination of short peptidic epitopes
Elucidation of new biomarkers and potential drug targets from high-throughput profiling data is a challenging task due to a limited number of available biological samples and questionable reproducibility of differential changes in cross-dataset comparisons . In this paper we propose a novel computational approach for d...	Comparison of gene expression in diseased and normal tissue is a powerful tool of studying processes involved in pathogenesis and searching for potential drug targets and biomarkers of the disease's progression and treatment outcome . We have developed a novel approach for systematic knowledge-driven analysis of gene e...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "medicine", "pathology", "drugs", "and", "devices", "sports", "and", "exercise", "medicine", "pediatrics", "pharmacology", "pediatrics", "and", "child", "health", "biology", "systems", "biology", "diagnostic", "medicine", "drug", "research", "and", "development", "neu...	2012	Novel Approach to Meta-Analysis of Microarray Datasets Reveals Muscle Remodeling-related Drug Targets and Biomarkers in Duchenne Muscular Dystrophy
Chronic inflammation promotes oncogenic transformation and tumor progression . Many inflammatory agents also generate a toxic microenvironment , implying that adaptive mechanisms must be deployed for cells to survive and undergo transformation in such unfavorable contexts . A paradigmatic case is represented by cancers...	Chronic inflammation associated to the sustained exposure to toxic chemicals can lead to cancer , but how transforming cells acquire the ability to oppose chemo-toxicity and eventually thrive is unclear . In this study , we set out to profile the molecular changes occurring in a mouse model of liver disease caused by d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "liver", "body", "fluids", "pathology", "and", "laboratory", "medicine", "cancer", "treatment", "immunology", "bile", "cancers", "and", "neoplasms", "carcinomas", "gastrointestinal", "tumors", "liver", "diseases", "toxicology", ...	2018	Sustained activation of detoxification pathways promotes liver carcinogenesis in response to chronic bile acid-mediated damage
The folding of proteins with a complex knot is still an unresolved question . Based on representative members of Ubiquitin C-terminal Hydrolases ( UCHs ) that contain the 52 knot in the native state , we explain how UCHs are able to unfold and refold in vitro reversibly within the structure-based model . In particular ...	Self-tying of knotted proteins remains a challenge both for theoreticians and experimentalist . In this work , we study the proteins with complex , the 52 knot , in a bulk and confined within a chaperonin box . We show that in our model we recreate the experimental results , identify two topologically distinct folding ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results" ]	[ "chemical", "compounds", "dna-binding", "proteins", "organic", "compounds", "materials", "science", "protein", "structure", "amino", "acids", "macromolecules", "materials", "by", "structure", "research", "and", "analysis", "methods", "polymers", "polymer", "chemistry", ...	2018	The exclusive effects of chaperonin on the behavior of proteins with 52 knot
The establishment and maintenance of Epstein-Barr Virus ( EBV ) latent infection requires distinct viral gene expression programs . These gene expression programs , termed latency types , are determined largely by promoter selection , and controlled through the interplay between cell-type specific transcription factors...	Epstein-Barr Virus ( EBV ) establishes a latent infection that is associated with several lymphoid and epithelial cell malignancies . The latent virus persists as a circular minichromosome in the nucleus of infected cells . Epigenetic modifications of the viral DNA and chromatin are known to control viral gene expressi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/transcription", "and", "translation", "genetics", "and", "genomics/gene", "function", "virology/viruses", "and", "cancer" ]	2010	CTCF Prevents the Epigenetic Drift of EBV Latency Promoter Qp
Bacterial strains isolated from attine ants showed activity against the insect specialized fungal pathogen Escovopsis and also against the human protozoan parasite Leishmania donovani . The bioassay guided fractionation of extracts from cultures of Streptomyces sp . ICBG292 , isolated from the exoskeleton of Cyphomyrme...	Visceral leishmaniasis , caused by Leishmania infantum and L . donovani , is characterized by high rate mortality worldwide . Current treatments for this disease suffer from toxicity , variable efficacy , requirements for parenteral administration and length of treatment regimens . New chemical entities and development...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "blood", "cells", "antimicrobials", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "immunology", "microbiology", "antifungals", "parasitic", "protozoans", "animals", "protozo...	2019	Antifungal compounds from Streptomyces associated with attine ants also inhibit Leishmania donovani
Sensitive diagnostic tools are required for an accurate assessment of prevalence and intensity of helminth infections in areas undergoing regular deworming , and for monitoring anthelmintic drug efficacy . We compared the diagnostic accuracy of the Kato-Katz and FLOTAC techniques in the frame of a drug efficacy trial ....	In areas where parasitic worm infections have been successfully reduced as a result of deworming campaigns , the level of infections and drug efficacy must be carefully monitored . For this purpose , diagnostic methods with a high sensitivity are needed . We compared the accuracy of the widely used Kato-Katz method wit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology" ]	2011	Diagnostic Accuracy of Kato-Katz and FLOTAC for Assessing Anthelmintic Drug Efficacy
In all sexually reproducing organisms , cells of the germ line must transition from mitosis to meiosis . In mice , retinoic acid ( RA ) , the extrinsic signal for meiotic initiation , activates transcription of Stra8 , which is required for meiotic DNA replication and the subsequent processes of meiotic prophase . Here...	The transition from mitosis to meiosis is a defining feature of germ cells , the precursors of eggs and sperm . In mice , retinoic acid ( RA ) , a vitamin A derivative , induces expression of the gene Stra8 , which in turn is required for the first critical steps of meiosis . The timing of Stra8 expression in mammalian...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "animal", "genetics", "model", "organisms", "gene", "regulatory", "networks", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "research", "and", "analysis", "methods", "gene", "function" ]	2014	Retinoic Acid Activates Two Pathways Required for Meiosis in Mice
As most of the heritability of complex traits is attributed to common and low frequency genetic variants , imputing them by combining genotyping chips and large sequenced reference panels is the most cost-effective approach to discover the genetic basis of these traits . Association summary statistics from genome-wide ...	Genome-wide association studies ( GWASs ) quantify the effect of genetic variants and traits , such as height . Such estimates are called association summary statistics and are typically publicly shared through publication . Typically , GWASs are carried out by genotyping ∼ 500′000 SNVs for each individual which are th...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "variant", "genotypes", "sociology", "social", "sciences", "alleles", "genetic", "mapping", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "molecular", "biology", "techniques", "genotyping", "research", "and", ...	2018	Evaluation and application of summary statistic imputation to discover new height-associated loci
The structural flexibility or ‘breathing’ of the envelope ( E ) protein of flaviviruses allows virions to sample an ensemble of conformations at equilibrium . The molecular basis and functional consequences of virus conformational dynamics are poorly understood . Here , we identified a single mutation at residue 198 ( ...	Flaviviruses include emerging pathogens such as WNV , DENV , and ZIKV that threaten global health . Despite causing significant morbidity , effective vaccines or therapeutic agents to protect humans against many flaviviruses are lacking . Because of the importance of antibodies in flavivirus immunity and vaccine protec...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "radiochemistry", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "viral", "structure", "nuclear", "decay", "viruses", "physiological", "processes", "rna", "viruses",...	2017	A single mutation in the envelope protein modulates flavivirus antigenicity, stability, and pathogenesis
c-Myc ( hereafter called Myc ) belongs to a family of transcription factors that regulates cell growth , cell proliferation , and differentiation . Myc initiates the transcription of a large cast of genes involved in cell growth by stimulating metabolism and protein synthesis . Some of these , like those involved in gl...	Cancer occurs when cells change their behavior and start to divide in an uncontrolled manner . To achieve this altered behavior , cells need to change their metabolism to be able to grow even when nutrient and oxygen supplies are limiting . Therefore , targeting metabolic pathways could be used to treat patients suffer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cancers", "and", "neoplasms", "basic", "cancer", "research", "gastrointestinal", "tumors", "hematologic", "cancers", "and", "related", "disorders", "animal", "models", "oncology", "model", "organisms", "molecular", "genetics", "lymphomas", "signaling", "in"...	2012	Mouse Genetics Suggests Cell-Context Dependency for Myc-Regulated Metabolic Enzymes during Tumorigenesis
The presence of 5-methylcytidine ( m5C ) in tRNA and rRNA molecules of a wide variety of organisms was first observed more than 40 years ago . However , detection of this modification was limited to specific , abundant , RNA species , due to the usage of low-throughput methods . To obtain a high resolution , systematic...	Ribonucleic acids are universally used to express genetic information in the form of gene transcripts . Although we envision RNA as a mere copy of the DNA four-base code , modification of specific RNA bases can expand the information code . Such modifications are abundant in transfer RNA ( tRNA ) and ribosomal RNA ( rR...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "bacterial", "biochemistry", "escherichia", "coli", "genome", "complexity", "prokaryotic", "models", "model", "organisms", "gene", "regulation", "bacillus", "subtilis", "molecular", "genetics", "biology", "genomics", "microbiology", "computational", "biology...	2013	Transcriptome-Wide Mapping of 5-methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C within Archaeal mRNAs
Aphids are amongst the most devastating sap-feeding insects of plants . Like most plant parasites , aphids require intimate associations with their host plants to gain access to nutrients . Aphid feeding induces responses such as clogging of phloem sieve elements and callose formation , which are suppressed by unknown ...	Aphids are insects that can induce feeding damage , achieve high population densities , and most importantly , transmit economically important plant diseases worldwide . To develop durable approaches to control aphids , it is critical to understand how aphids interact with plants at the molecular level . Aphid feeding ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/functional", "genomics" ]	2010	A Functional Genomics Approach Identifies Candidate Effectors from the Aphid Species Myzus persicae (Green Peach Aphid)
The neurotrophic tyrosine kinase receptor type 2 ( Ntrk2 , also known as TrkB ) and its ligands brain derived neurotrophic factor ( Bdnf ) , neurotrophin-4 ( NT-4/5 ) , and neurotrophin-3 ( NT-3 ) are known primarily for their multiple effects on neuronal differentiation and survival . Here , we provide evidence that N...	Visceral leishmaniasis ( VL ) , a globally important parasitic disease responsible for over 40 , 000 deaths p . a . , results in pronounced changes in splenic organisation associated with impaired immune function and persistent parasite infection . We have previously shown that receptor tyrosine kinase ( RTKi ) inhibit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Neurotrophic Receptor Ntrk2 Directs Lymphoid Tissue Neovascularization during Leishmania donovani Infection
Organ and tissue formation requires a finely tuned temporal and spatial regulation of differentiation programmes . This is necessary to balance sufficient plasticity to undergo morphogenesis with the acquisition of the mature traits needed for physiological activity . Here we addressed this issue by analysing the depos...	In this work we studied the maturation of the extracellular matrix during Drosophila embryogenesis . Drosophila deposit a chitin-rich extracellular matrix with key physiological functions , such as the control of organ size and shape , and cuticle formation . Chitin synthesis depends on chitin synthases , and in Drosop...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Deciphering the Genetic Programme Triggering Timely and Spatially-Regulated Chitin Deposition
Genetic redundancy , whereby two genes carry out seemingly overlapping functions , may in large part be attributable to the intricacy and robustness of genetic networks that control many developmental processes . We have previously described a complex set of genetic interactions underlying foregut development in the ne...	One of the more puzzling aspects of genetics is that the inactivation of many genes fails to produce strong deleterious effects on the organisms that carry those genes . In some cases , however , the combined inactivation of two or more such genes can lead to the expression of robust abnormal phenotypes . These types o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/gene", "function", "developmental", "biology/organogenesis", "developmental", "biology/developmental", "molecular", "mechanisms" ]	2009	A Mechanistic Basis for the Coordinated Regulation of Pharyngeal Morphogenesis in Caenorhabditis elegans by LIN-35/Rb and UBC-18–ARI-1
Proteins with low-complexity domains continue to emerge as key players in both normal and pathological cellular processes . Although low-complexity domains are often grouped into a single class , individual low-complexity domains can differ substantially with respect to amino acid composition . These differences may st...	Low-complexity domains in protein sequences are regions that are composed of only a few amino acids in the protein “alphabet” . These domains often have unique chemical properties and play important biological roles in both normal and disease-related processes . While a number of approaches have been developed to defin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "protein", "abundance", "membrane", "proteins", "fungi", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "proteins", "proteomics", "molecular", "biology", "cell", ...	2018	Proteome-scale relationships between local amino acid composition and protein fates and functions
The characterization of the blood virome is important for the safety of blood-derived transfusion products , and for the identification of emerging pathogens . We explored non-human sequence data from whole-genome sequencing of blood from 8 , 240 individuals , none of whom were ascertained for any infectious disease . ...	Novel sequencing technologies offer insight into the virome in human samples . Here , we identify the viral DNA sequences in blood of over 8 , 000 individuals undergoing whole genome sequencing . This approach serves to identify 94 viruses; however , many are shown to reflect widespread DNA contamination of commercial ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "microbiology", "human", "genomics", "viruses", "rna", "viruses", "dna", "viruses", "genome", "analysis", "microbial", "genomics", "res...	2017	The blood DNA virome in 8,000 humans
The opportunistic fungal pathogen Cryptococcus neoformans is a major cause of mortality in immunocompromised individuals , resulting in more than 600 , 000 deaths per year . Many human fungal pathogens secrete peptidases that influence virulence , but in most cases the substrate specificity and regulation of these enzy...	Many pathogenic organisms secrete peptidases . The activity of these enzymes often contributes to virulence , making their study crucial for understanding host-pathogen biology and developing therapeutics . In this report , we employed an unbiased , activity-based profiling assay to examine the secreted peptidases of a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "immune", "cells", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "animal", "models", "of", "disease", "immunology", "enzymology", "microbiolo...	2016	Integrated Activity and Genetic Profiling of Secreted Peptidases in Cryptococcus neoformans Reveals an Aspartyl Peptidase Required for Low pH Survival and Virulence
Hebbian plasticity describes a basic mechanism for synaptic plasticity whereby synaptic weights evolve depending on the relative timing of paired activity of the pre- and postsynaptic neurons . Spike-timing-dependent plasticity ( STDP ) constitutes a central experimental and theoretical synaptic Hebbian learning rule ....	The brain’s capacity to treat information , learn and store memory relies on synaptic connectivity patterns , which are altered through synaptic plasticity mechanisms . Experimentally , such plasticities were evidenced through protocols involving numerous repetitive stimulations of a given synapse , and were shown to b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "synaptic", "plasticity", "calcium", "signaling", "neuronal", "plasti...	2018	Interplay of multiple pathways and activity-dependent rules in STDP
Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the causative agent of Kaposi's sarcoma ( KS ) and primary effusion lymphoma ( PEL ) , which are aggressive malignancies associated with immunocompromised patients . For many non-viral malignancies , therapeutically targeting the ubiquitin proteasome system ( UPS ) ha...	Kaposi’s sarcoma-associated herpesvirus ( KSHV ) causes Kaposi’s sarcoma ( KS ) and primary effusion lymphoma ( PEL ) , often fatal malignancies afflicting HIV-infected patients . Previous research has shown that blockade of the ubiquitin proteasome system ( UPS , a normal quality control pathway that degrades cellular...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	NEDDylation Is Essential for Kaposi’s Sarcoma-Associated Herpesvirus Latency and Lytic Reactivation and Represents a Novel Anti-KSHV Target
Low oxygen conditions ( hypoxia ) can impair essential physiological processes and cause cellular damage and death . We have shown that specific hypoxic conditions disrupt protein homeostasis in C . elegans , leading to protein aggregation and proteotoxicity . Here , we show that nutritional cues regulate this effect o...	When blood flow to various parts of the body becomes restricted , those tissues suffer from a lack of oxygen , a condition called hypoxia . Hypoxia can cause cellular damage and death , as in stroke and cardiovascular disease . We have found that in the model organism C . elegans ( a roundworm ) specific concentrations...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "caenorhabditis", "gene", "regulation", "protein", "aggregation", "regulatory", "proteins", "dna-binding", "proteins", "light", "microscopy", "animals", "pulmonology", "hormones", "animal...	2019	Fasting prevents hypoxia-induced defects of proteostasis in C. elegans
Significant departures from expected Mendelian inheritance ratios ( transmission ratio distortion , TRD ) are frequently observed in both experimental crosses and natural populations . TRD on mouse Chromosome ( Chr ) 2 has been reported in multiple experimental crosses , including the Collaborative Cross ( CC ) . Among...	One of the strongest expectations in genetics is that chromosomes segregate randomly during meiosis . However , genetic loci that exhibit transmission ratio distortion ( TRD ) are sometimes observed in offspring of F1 hybrids . Meiotic drive is a type of non-Mendelian inheritance in which a “selfish” genetic element ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Multi-Megabase Copy Number Gain Causes Maternal Transmission Ratio Distortion on Mouse Chromosome 2
The human membrane cofactor protein ( MCP , CD46 ) is a central component of the innate immune system . CD46 protects autologous cells from complement attack by binding to complement proteins C3b and C4b and serving as a cofactor for their cleavage . Recent data show that CD46 also plays a role in mediating acquired im...	The human membrane cofactor protein ( MCP , CD46 ) is expressed on all nucleated cells and serves as a marker that prevents host cells from destruction by the immune system . It functions as a cofactor that helps to inactivate the C3b and C4b molecules , which are central components of the complement system . In additi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immune", "response", "immunology/innate", "immunity", "cell", "biology/cell", "adhesion", "microbiology/cellular", "microbiology", "and", "pathogenesis", "virology/host", "invasion", "and", "cell", "entry" ]	2010	Structure of the Extracellular Portion of CD46 Provides Insights into Its Interactions with Complement Proteins and Pathogens
The ability to induce a defense response after pathogen attack is a critical feature of the immune system of any organism . Nucleotide-binding leucine-rich repeat receptors ( NLRs ) are key players in this process and perceive the occurrence of nonself-activities or foreign molecules . In plants , coevolution with a va...	The ability to induce defenses in response to pathogen attack is a critical feature of immunity in any organism . Nucleotide-binding leucine-rich repeat receptors ( NLRs ) are key players in this process and have evolved to perceive the occurrence of nonself-activities or foreign molecules . In plants , coevolution wit...	[ "Abstract", "Introduction", "Results", "Discussion", "and", "conclusions", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cell", "processes", "brassica", "immune", "receptor", "signaling", "model", "organisms", "signs", "and", "symptoms", "membrane", "receptor", "signaling", "experime...	2018	Genome-wide functional analyses of plant coiled–coil NLR-type pathogen receptors reveal essential roles of their N-terminal domain in oligomerization, networking, and immunity
We have previously described the generation of a novel Ebola virus ( EBOV ) vaccine platform based on ( a ) replication-competent rabies virus ( RABV ) , ( b ) replication-deficient RABV , or ( c ) chemically inactivated RABV expressing EBOV glycoprotein ( GP ) . Mouse studies demonstrated safety , immunogenicity , and...	Ebola virus ( EBOV ) has been associated with outbreaks in human and nonhuman primate populations since 1976 . With a fatality rate approaching 90% , EBOV is one of the most lethal infectious diseases in humans . The increased frequency of EBOV outbreaks along with its potential to be used as a bioterrorism agent has d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "vaccines", "rna", "viruses", "emerging", "infectious", "diseases", "immunity", "viral", "classification", "virology", "host-pathogen", "interaction", "biology", "microbiology" ]	2013	Antibody Quality and Protection from Lethal Ebola Virus Challenge in Nonhuman Primates Immunized with Rabies Virus Based Bivalent Vaccine
Dengue viruses 1–4 ( DENV1-4 ) rely heavily on the host cell machinery to complete their life cycle , while at the same time evade the host response that could restrict their replication efficiency . These requirements may account for much of the broad gene-level changes to the host transcriptome upon DENV infection . ...	Dengue is the most common insect-borne viral disease globally . The continued absence of an effective therapy stems from an incomplete understanding of disease pathogenesis , of which the host response to infection is thought to play a central role . While previous studies have described the changes in total gene expre...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "genome", "expression", "analysis", "infectious", "diseases", "dengue", "fever", "neglected", "tropical", "diseases", "biology", "genomics", "genetics", "and", "genomics" ]	2013	Host Cell Transcriptome Profile during Wild-Type and Attenuated Dengue Virus Infection
HIV is adept at avoiding naturally generated T cell responses; therefore , there is a need to develop HIV-specific T cells with greater potency for use in HIV cure strategies . Starting with a CD4-based chimeric antigen receptor ( CAR ) that was previously used without toxicity in clinical trials , we optimized the vec...	Conventional T cells rarely provide durable control over HIV replication . Chimeric antigen receptors ( CARs ) alter how T cells recognize infected T cells , bypassing many of HIV’s immune escape mechanisms . Therefore , we hypothesized that T cells engineered to express these receptors would be more potent ( supraphys...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", ...	2017	Supraphysiologic control over HIV-1 replication mediated by CD8 T cells expressing a re-engineered CD4-based chimeric antigen receptor
Viruses are obligate intracellular parasites and therefore their replication completely depends on host cell factors . In case of the hepatitis C virus ( HCV ) , a positive-strand RNA virus that in the majority of infections establishes persistence , cyclophilins are considered to play an important role in RNA replicat...	Owing to limited genetic information , viruses have to exploit host cells to achieve efficient production of virus progeny . Host cell factors and pathways therefore play an important role for virus replication and thus represent a possible target for antiviral therapy . In case of the hepatitis C virus ( HCV ) , an RN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "infectious", "diseases", "virology/viral", "replication", "and", "gene", "regulation", "gastroenterology", "and", "hepatology/hepatology", "biochemistry/protein", "folding", "cell", "biology", "infectious", "diseases/gastro...	2009	Essential Role of Cyclophilin A for Hepatitis C Virus Replication and Virus Production and Possible Link to Polyprotein Cleavage Kinetics
As organisms adaptively evolve to a new environment , selection results in the improvement of certain traits , bringing about an increase in fitness . Trade-offs may result from this process if function in other traits is reduced in alternative environments either by the adaptive mutations themselves or by the accumula...	Microorganisms such as yeast have been used for decades to study adaptive evolution by natural selection . Thirty years ago in now seminal experiments , a strain of yeast was evolved multiple times under carbon limitation . The adaptive changes that gave rise to increases in fitness have previously been studied both ph...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "carbohydrate", "metabolism", "organismal", "evolution", "genome", "evolution", "population", "genetics", "microbiology", "mutation", "model", "organisms", "microbial", "evolution", "metabolic", "pathways", "biology", "evolutionary", "theory", "evolutionary", "genetics", "b...	2011	Hunger Artists: Yeast Adapted to Carbon Limitation Show Trade-Offs under Carbon Sufficiency
Pili have been identified on the cell surface of Streptococcus pneumoniae , a major cause of morbidity and mortality worldwide . In contrast to Gram-negative bacteria , little is known about the structure of native pili in Gram-positive species and their role in pathogenicity . Triple immunoelectron microscopy of the e...	Streptococcus pneumoniae ( pneumococcus ) is one of the most important human pathogens and a major cause of morbidity and mortality worldwide , causing respiratory tract infections , community acquired pneumonia , and invasive diseases . Although the pneumococcus is a well-studied bacterial pathogen , first described i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biochemistry/macromolecular", "assemblies", "and", "machines", "microbiology", "infectious", "diseases/respiratory", "infections", "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2008	Pneumococcal Pili Are Composed of Protofilaments Exposing Adhesive Clusters of Rrg A
Reports of therapeutic failure to meglumine antimoniate ( MA ) and miltefosine in cutaneous leishmaniasis ( CL ) varies between species , populations and geographic regions . This study aimed to determine the clinical , drug-related factors , and Leishmania species associated with treatment failure in children and adul...	Cutaneous leishmaniasis ( CL ) is a parasitic disease that causes chronic , often ulcerated , skin lesions . Treatment require administration of systemic and poorly tolerated drugs , of which , the most commonly used is meglumine antimoniate ( MA ) injections during 20 days . Although children and adults might have dif...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "pediatrics", "protozoans", "signs", "and", "symptoms", "pharmaceutics", "leishm...	2017	Risk factors for therapeutic failure to meglumine antimoniate and miltefosine in adults and children with cutaneous leishmaniasis in Colombia: A cohort study
A major challenge in systems biology is to understand how complex and highly connected metabolic networks are organized . The structure of these networks is investigated here by identifying sets of metabolites that have a similar biosynthetic potential . We measure the biosynthetic potential of a particular compound by...	Life is based on the ability of cells to convert raw materials into complex chemicals like proteins or DNA . This ability is obtained through the interplay of a large number of enzymes , which are specialized proteins , each facilitating one specific chemical transformation . Since the products of one reaction can agai...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/metabolic", "networks" ]	2008	Biosynthetic Potentials of Metabolites and Their Hierarchical Organization
The type VI secretion system ( T6SS ) has emerged as an important mediator of interbacterial interactions . A T6SS from Pseudomonas aeruginosa targets at least three effector proteins , type VI secretion exported 1–3 ( Tse1–3 ) , to recipient Gram-negative cells . The Tse2 protein is a cytoplasmic effector that acts as...	Bacterial species have been at war with each other for over a billion years . During this period they have evolved many pathways for besting the competition; one of the most recent of these to be described is the type VI secretion system ( T6SS ) . The T6SS of Pseudomonas aeruginosa is a complex machine that the bacter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "gram", "negative", "protein", "interactions", "proteins", "microbial", "evolution", "chaperone", "proteins", "protein", "structure", "microbial", "pathogens", "biology", "microbiology", "bacterial", "pathogens", "microbial", "ecology" ]	2012	Structural Basis for Type VI Secretion Effector Recognition by a Cognate Immunity Protein
The Americas were the last continent colonized by humans carrying malaria parasites . Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium , compared with its African counterparts , and is clearly subdivided into local , highly divergent populations . However ,...	Plasmodium vivax is the most common human malaria parasite in the Americas , but how and when this species arrived in the New World remains unclear . Here we describe high-quality whole-genome sequence data for nine P . vivax isolates from Brazil , a country that accounts for 37% of the malaria burden in this continent...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "population", "genetics", "geographical", "locations", "microbiology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "peru", "apicomplexa", "protozoans...	2017	Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax
The asymmetrically dividing yeast S . cerevisiae assembles a bipolar spindle well after establishing the future site of cell division ( i . e . , the bud neck ) and the division axis ( i . e . , the mother-bud axis ) . A surveillance mechanism called spindle position checkpoint ( SPOC ) delays mitotic exit and cytokine...	In asymmetrically dividing cells , proper positioning of the mitotic spindle relative to polarity determinants is crucial to ensure the unequal fate of daughter cells . In stem cells , derangement of the mechanisms controlling asymmetric cell division , including spindle positioning , affects the developmental fate of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Asymmetry of the Budding Yeast Tem1 GTPase at Spindle Poles Is Required for Spindle Positioning But Not for Mitotic Exit
The study of the chronological life span of Saccharomyces cerevisiae , which measures the survival of populations of non-dividing yeast , has resulted in the identification of homologous genes and pathways that promote aging in organisms ranging from yeast to mammals . Using a competitive genome-wide approach , we perf...	Model organisms have been instrumental in uncovering genes that function to control life span and to identify the molecular pathways whose role in aging is conserved between the evolutionarily distant unicellular yeast and mice . Because yeast are particularly amenable to genetics and genomics studies , they have been ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics" ]	2010	Genome-Wide Screen in Saccharomyces cerevisiae Identifies Vacuolar Protein Sorting, Autophagy, Biosynthetic, and tRNA Methylation Genes Involved in Life Span Regulation

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