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Functional redundancy limits detailed analysis of genes in many organisms . Here , we report a method to efficiently overcome this obstacle by combining gene expression data with analysis of gene-indexed mutants . Using a rice NSF45K oligo-microarray to compare 2-week-old light- and dark-grown rice leaf tissue , we ide...	Rice , a model monocot , is the first crop plant to have its entire genome sequenced . Although genome-wide transcriptome analysis tools and genome-wide , gene-indexed mutant collections have been generated for rice , the functions of only a handful of rice genes have been revealed thus far . Functional genomics approa...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "plant", "biology", "plant", "biology/plant-environment", "interactions", "genetics...	2008	Identification and Functional Analysis of Light-Responsive Unique Genes and Gene Family Members in Rice
Reward-related dopaminergic influences on learning and overt behaviour are well established , but any influence on sensory decision-making is largely unknown . We used functional magnetic resonance imaging ( fMRI ) while participants judged electric somatosensory stimuli on one hand or other , before being rewarded for...	The rewards one receives during decision-making has a profound impact on learning . Much recent interest has focused on the role of the neurotransmitter dopamine in the basal ganglia for influencing learning and behaviour . Here , we ask whether reward can influence low-level sensory processing , for instance in primar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/cognitive", "neuroscience", "neuroscience/sensory", "systems" ]	2009	Influence of Dopaminergically Mediated Reward on Somatosensory Decision-Making
Handheld light microscopy using compact optics and mobile phones may improve the quality of health care in resource-constrained settings by enabling access to prompt and accurate diagnosis . Laboratory technicians were trained to operate two handheld diagnostic devices ( Newton Nm1 microscope and a clip-on version of t...	Handheld light microscopes are new technologies that may be helpful in enabling better access to diagnostic testing for people living in resource-constrained settings in tropical and subtropical countries . Recent studies evaluating the accuracy of such devices have focused on their use by expert microscopists and were...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "helminths", "light", "microscopy", "animals", "cell", "phones", "protozoans", "microscopy", "digestive", "system", "research", "and", ...	2016	Accuracy of Mobile Phone and Handheld Light Microscopy for the Diagnosis of Schistosomiasis and Intestinal Protozoa Infections in Côte d’Ivoire
Genetic screens are powerful methods for the discovery of gene–phenotype associations . However , a systems biology approach to genetics must leverage the massive amount of “omics” data to enhance the power and speed of functional gene discovery in vivo . Thus far , few computational methods for gene function predictio...	Genome sequencing and annotation , combined with large-scale molecular experiments to query gene expression and molecular interactions , collectively known as Systems Biology , have resulted in an enormous wealth in biological databases . Yet , it remains a daunting task to use these data to decipher the rules that gov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/bioinformatics", "neuroscience/neurodevelopment" ]	2009	Integrating Computational Biology and Forward Genetics in Drosophila
For Chagas disease , the most serious infectious disease in the Americas , effective disease control depends on elimination of vectors through spraying with insecticides . Molecular genetic research can help vector control programs by identifying and characterizing vector populations and then developing effective inter...	Chagas disease is a protozoan infection caused by the parasite Trypanosoma cruzi . Chagas is prevalent throughout Central and South America , and it remains a chief concern in Bolivia . A movement that began in 1991 called the Southern Cone Initiative has been successful in reducing the incidence of Chagas disease in t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/infectious", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2008	Microsatellites Reveal a High Population Structure in Triatoma infestans from Chuquisaca, Bolivia
Head lice , Pediculus humanus capitis , occur in four divergent mitochondrial clades ( A , B , C and D ) , each having particular geographical distributions . Recent studies suggest that head lice , as is the case of body lice , can act as a vector for louse-borne diseases . Therefore , understanding the genetic divers...	Head lice , Pediculus capitis humanus , and body lice , Pediculus h . humanus , are obligatory ectoparasites that feed exclusively on human blood . Currently , the body louse is the only recognized vector of at least three deadly bacterial pathogens that have killed millions of peoples , namely: Rickettsia prowazekii ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusions" ]	[ "invertebrates", "borrelia", "infection", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "acinetobacter", "infections", "pathogens", "population", "genetics", "microbiology", "animals", "bacterial", "disease...	2016	Head Lice of Pygmies Reveal the Presence of Relapsing Fever Borreliae in the Republic of Congo
Retrotransposons are mobile genetic elements abundant in plant and animal genomes . While efficiently silenced by the epigenetic machinery , they can be reactivated upon stress or during development . Their level of transcription not reflecting their transposition ability , it is thus difficult to evaluate their contri...	Long time considered as « junk DNA » , the evolutive force of transposable elements ( TEs ) is now well established and TEs contribute strongly to eukaryote genome plasticity . However , it is difficult to fully characterize the mobile part of a genome , or active mobilome , and tracking TE activity remains challenging...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "retrotransposons", "brassica", "plant", "science", "model", "organisms", "rice", "genome", "analysis", "experimental", "organism", "systems", "genetic", "elements", "plant", "genomics", "molecular", "biology", "techniques", "plants", "arabidopsis", "thal...	2017	Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants
Single nucleotide polymorphisms ( SNPs ) have been increasingly utilized to investigate somatic genetic abnormalities in premalignancy and cancer . LOH is a common alteration observed during cancer development , and SNP assays have been used to identify LOH at specific chromosomal regions . The design of such studies r...	More than 99% of each person's genome is identical to everyone else's . Many of the differences involve single base pairs , termed single nucleotide polymorphisms ( SNPs ) . SNPs are used as genetic markers to facilitate identification of disease-causing genes , as well as in cancer studies by aiding in determining whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2007	Direct Inference of SNP Heterozygosity Rates and Resolution of LOH Detection
PROSPERO CRD42012002292 Dengue is a growing health concern in the Philippines . Outbreaks were reported in1926 [1] , [2] , and the first recorded epidemic in Southeast Asia occurred in Manila in 1954 [3] , [4] . Further epidemics occurred in 1966 , 1983 , and 1998 , with increasing reported cases of dengue disease [5]–...	Dengue disease is a tropical and subtropical mosquito-borne viral illness and is a major health concern in the Philippines . To determine the dengue disease burden in the Philippines and identify gaps and future research needs , we conducted a literature analysis and review to describe the epidemiology of dengue diseas...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "epidemiology" ]	2014	Epidemiology of Dengue Disease in the Philippines (2000–2011): A Systematic Literature Review
Post-translational modifications ( PTMs ) add a further layer of complexity to the proteome and regulate a wide range of cellular protein functions . With the increasing number of known PTM sites , it becomes imperative to understand their functional interplays . In this study , we proposed a novel analytical strategy ...	In addition to gene expression and translation control , post-translational modifications ( PTMs ) represent another level to regulate proteins functions . Different PTM sites within a protein usually co-operate to fulfill their functional roles . Recent advances in high-throughput mass spectrometry ( MS ) technologies...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "mathematics", "signaling", "cascades", "protein", "structure", "sequence", "motif", "analysis", "protein", "structure", "databases", "discrete", "mathematics", "combinatorics", "research", "and", "analysis", "methods", "protein", "kinase", "signaling", ...	2017	Co-occurring protein phosphorylation are functionally associated
The analysis of introgression of genomic regions between divergent populations provides an excellent opportunity to determine the genetic basis of reproductive isolation during the early stages of speciation . However , hybridization and subsequent gene flow must be relatively common in order to localize individual loc...	A number of laboratory studies of speciation have uncovered individual genes that confer lower fitness when in a divergent genetic background . It is , however , unclear whether these genes were ever relevant to restricting gene flow in nature , or whether they are indirect consequences of functional divergence between...	[ "Abstract", "Introduction", "Results/Discussion", "Conclusions" ]	[ "genome", "sequencing", "genome", "analysis", "tools", "gene", "ontologies", "genomics", "genome", "scans", "speciation", "introgression", "population", "genetics", "hybridization", "biology", "evolutionary", "biology", "gene", "flow", "evolutionary", "processes", "transc...	2014	The Genomic Architecture of Population Divergence between Subspecies of the European Rabbit
Light and microRNAs ( miRNAs ) are key external and internal signals for plant development , respectively . However , the relationship between the light signaling and miRNA biogenesis pathways remains unknown . Here we found that miRNA processer proteins DCL1 and HYL1 interact with a basic helix-loop-helix ( bHLH ) tra...	External light and internal miRNAs are important for plant development . This study revealed that the miRNA-processing enzyme DCL1 interacts with the red-light-regulated transcription factor PIF4 , which modulates the stability of DCL1 during dark-to-red-light or red-light-to-dark transitions and acts as a transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "plant", "growth", "and", "development", "gene", "regulation", "plant", "embryo", "anatomy", "regulatory", "proteins", "dna-binding", "proteins", "plant", "physiology", "developmental", "biology", "micrornas", "plant", "science", "transcription", "fa...	2018	Coordinated regulation of Arabidopsis microRNA biogenesis and red light signaling through Dicer-like 1 and phytochrome-interacting factor 4
Cysteine peptidases play a central role in the biology of Leishmania . In this work , we sought to further elucidate the mechanism ( s ) by which the cysteine peptidase CPB contributes to L . mexicana virulence and whether CPB participates in the formation of large communal parasitophorous vacuoles induced by these par...	The parasite Leishmania mexicana expresses several cysteine peptidases of the papain family that are involved in processes such as virulence and evasion of host immune responses . The cysteine peptidase CPB is required for survival within macrophages and for lesion formation in susceptible mice . Upon their internaliza...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "parasite", "replication", "pathogens", "immunology", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protoz...	2016	Cysteine Peptidase B Regulates Leishmania mexicana Virulence through the Modulation of GP63 Expression
The nature of the “toxic gain of function” that results from amyotrophic lateral sclerosis ( ALS ) - , Parkinson- , and Alzheimer-related mutations is a matter of debate . As a result no adequate model of any neurodegenerative disease etiology exists . We demonstrate that two synergistic properties , namely , increased...	Amyotrophic lateral sclerosis ( ALS ) , also known in America as Lou Gehrig's disease , is a fatal neurodegenerative disease with no effective treatment . Paralysis occurs as the result of the death of cells that connect the brain to various muscles , namely , the motor neurons of the brain and spinal cord . Ninety per...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders" ]	2008	Protein Aggregation and Protein Instability Govern Familial Amyotrophic Lateral Sclerosis Patient Survival
As antimicrobial resistance increases , it is crucial to develop new treatment strategies to counter the emerging threat . In this paper , we consider combination therapies involving conventional antibiotics and debridement , coupled with a novel anti-adhesion therapy , and their use in the treatment of antimicrobial r...	Since the development of the first antibiotics , bacteria have utilised and developed resistance mechanisms , helping them to avoid being eliminated and to survive within a host . Traditionally , the solution to this problem has been to treat with multiple antibiotics , switching to a new type when the one currently in...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "binding", "antimicrobials", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "dose", "prediction", "methods", "pathogens", "drugs", "microbiology", "pseudom...	2019	Mathematical model predicts anti-adhesion–antibiotic–debridement combination therapies can clear an antibiotic resistant infection
During viral infection , a massive demand for viral glycoproteins can overwhelm the capacity of the protein folding and quality control machinery , leading to an accumulation of unfolded proteins in the endoplasmic reticulum ( ER ) . To restore ER homeostasis , cells initiate the unfolded protein response ( UPR ) by ac...	Viruses abuse the cell's protein synthesis and folding machinery to produce large amounts of viral proteins . This enforced synthesis overloads the cell's capacity and leads to an accumulation of unfolded proteins in the endoplasmic reticulum ( ER ) resulting in ER stress , which can compromise cell viability . To rest...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "molecular", "cell", "biology", "viral", "immune", "evasion", "virology", "biology", "microbiology", "pathogenesis" ]	2013	Cytomegalovirus Downregulates IRE1 to Repress the Unfolded Protein Response
Double strand breaks ( DSBs ) and interstrand crosslinks ( ICLs ) are toxic DNA lesions that can be repaired through multiple pathways , some of which involve shared proteins . One of these proteins , DNA Polymerase θ ( Pol θ ) , coordinates a mutagenic DSB repair pathway named microhomology-mediated end joining ( MMEJ...	Error-prone DNA Polymerase θ ( Pol θ ) plays a conserved role in a mutagenic DNA double-strand break repair mechanism called microhomology-mediated end joining ( MMEJ ) . In many organisms , it also participates in a process crucial to the removal/repair of DNA interstrand crosslinks . The exact mechanism by which Pol ...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Materials", "and", "methods" ]	[ "invertebrates", "nucleic", "acid", "synthesis", "enzymes", "annealing", "(genetics)", "dna-binding", "proteins", "enzymology", "animals", "microhomology-mediated", "end", "joining", "phosphatases", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "po...	2017	Drosophila DNA polymerase theta utilizes both helicase-like and polymerase domains during microhomology-mediated end joining and interstrand crosslink repair
Visual stimuli evoke activity in visual cortical neuronal populations . Neuronal activity can be selectively modulated by particular visual stimulus parameters , such as the direction of a moving bar of light , resulting in well-defined trial averaged tuning properties . However , given any single stimulus parameter , ...	V1 populations have historically been characterized by single cell response properties and pairwise co-variability . Many cells , however , do not show obvious dependencies to a given stimulus or behavioral task , and have consequently gone unanalyzed . We densely record from large V1 populations to measure how trial-t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "social", "sciences", "vertebrates", "neuroscience", "animals", "mammals", "primates", "mathematics", "network", "analysis", "computational", "neuroscience", "vision", "neuroimaging", "neuronal", "tuning", "old", "world", "monkeys", "research", "and", "analysis", "methods...	2018	Functional triplet motifs underlie accurate predictions of single-trial responses in populations of tuned and untuned V1 neurons
Kaposi’s sarcoma ( KS ) is a highly prevalent cancer in AIDS patients , especially in sub-Saharan Africa . Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is the etiological agent of KS and other cancers like Primary Effusion Lymphoma ( PEL ) . In KS and PEL , all tumors harbor latent KSHV episomes and express latency...	KS is the most prevalent cancer associated with AIDS in sub-Saharan Africa , and is also common in males not affected by AIDS . KSHV manipulates human cells by targeting protein-coding genes and cell signaling . Here we show that KSHV alters the expression of hundreds of human lncRNAs , a broad class of regulatory mole...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "endothelial", "cells", "microbiology", "long", "non-coding", "rnas", "epithelial", "cells", "viruses", "oncology", "micrornas", "dna", "viruses", ...	2017	microRNA dependent and independent deregulation of long non-coding RNAs by an oncogenic herpesvirus
Genome-wide association studies have identified more than 200 genetic variants to be associated with an increased risk of developing multiple sclerosis ( MS ) . Still , little is known about the causal molecular mechanisms that underlie the genetic contribution to disease susceptibility . In this study , we investigate...	More than 200 genetic loci have been associated with an increased risk of developing multiple sclerosis ( MS ) . Here , we investigated the role of a single-nucleotide polymorphism ( SNP ) , which is located within the microRNA-548ac stem-loop sequence in the first intron of the CD58 gene . We analyzed expression data ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "multiple", "sclerosis", "natural", "antisense", "transcripts", "gene", "regulation", "neurodegenerative", "diseases", "immunology", "plasmid", "construction", "micrornas", "clinical", "medicine", "demyelinating", "disorders", "dna",...	2019	A genetic variant associated with multiple sclerosis inversely affects the expression of CD58 and microRNA-548ac from the same gene
Pneumococcal conjugate vaccination has proved highly effective in eliminating vaccine-type pneumococcal carriage and disease . However , the potential adverse effects of serotype replacement remain a major concern when implementing routine childhood pneumococcal conjugate vaccination programmes . Applying a concise pre...	The bacterial pathogen Streptococcus pneumoniae ( pneumococcus ) is a major contributor to child mortality worldwide . Hence , effective pneumococcal vaccination programmes are globally among the most cost-effective public health interventions . Three different conjugate vaccine compositions , targeting 7 , 10 or 13 pn...	[ "Abstract", "Introduction", "Methods", "Search", "for", "optimal", "vaccine", "serotype", "compositions", "Uncertainty", "in", "carriage", "proportions", "Proportionality", "assumption", "(A1)", "Results", "Discussion" ]	[ "algorithms", "medicine", "bacterial", "diseases", "infectious", "diseases", "computer", "science", "pediatric", "epidemiology", "mathematics", "pneumococcus", "epidemiology", "statistics", "global", "health", "applied", "mathematics", "infectious", "disease", "control" ]	2014	Optimal Serotype Compositions for Pneumococcal Conjugate Vaccination under Serotype Replacement
Given that dengue disease is growing and may progress to dengue hemorrhagic fever ( DHF ) , data on economic cost and disease burden are important . However , data for Mexico are limited . Burden of dengue fever ( DF ) and DHF in Mexico was assessed using official databases for epidemiological information , disabilitie...	Dengue fever is caused by a flavivirus transmitted predominantly by the mosquito Aedes aegypti . Infection causes a broad spectrum of clinical signs and symptoms , from mild disease , such as dengue fever to a life threatening form known as dengue hemorrhagic fever . The disease is widespread in tropical regions . Meas...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "disabilities", "economic", "analysis", "tropical", "diseases", "geographical", "locations", "social", "sciences", "health", "care", "north", "america", "neglected", "tropical", "diseases", "infectious", "disease", "control", "pu...	2018	Economic impact of dengue in Mexico considering reported cases for 2012 to 2016
In the fungal pathogen Cryptococcus neoformans , the switch from yeast to hypha is an important morphological process preceding the meiotic events during sexual development . Morphotype is also known to be associated with cryptococcal virulence potential . Previous studies identified the regulator Znf2 as a key decisio...	The involvement of non-protein regulators in developmental processes in higher eukaryotes is an area that has come to light more recently . Earlier known as the dark matter of the genome , the non-protein coding genes are now recognized for their important regulatory roles in the life of eukaryotes . Using forward gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The lncRNA RZE1 Controls Cryptococcal Morphological Transition
The Drosophila sex determination hierarchy controls all aspects of somatic sexual differentiation , including sex-specific differences in adult morphology and behavior . To gain insight into the molecular-genetic specification of reproductive behaviors and physiology , we identified genes expressed in the adult head an...	The fruit fly Drosophila is an excellent model system to use to understand the molecular-genetic basis of male courtship behavior , as the potential for this behavior is specified by a well-understood genetic regulatory hierarchy , called the sex determination hierarchy . The sex hierarchy consists of a pre-mRNA splici...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "drosophila", "genetics", "and", "genomics" ]	2007	Genomic and Functional Studies of Drosophila Sex Hierarchy Regulated Gene Expression in Adult Head and Nervous System Tissues
Salmonella enterica serovar Typhi is transmitted by fecally contaminated food and water and causes approximately 22 million typhoid fever infections worldwide each year . Most cases occur in developing countries , where approximately 4% of patients develop intestinal perforation ( IP ) . In Kasese District , Uganda , a...	Typhoid fever is an acute febrile illness caused by the bacteria Salmonella Typhi and transmitted through food and water contaminated with the feces of typhoid fever patients or carriers . We investigated typhoid fever outbreaks in two neighboring Ugandan districts , Kasese and Bundibugyo , where typhoid fever outbreak...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "global", "health", "epidemiology", "biology", "microbiology", "public", "health" ]	2014	Shifts in Geographic Distribution and Antimicrobial Resistance during a Prolonged Typhoid Fever Outbreak — Bundibugyo and Kasese Districts, Uganda, 2009–2011
Epistatic interactions between residues determine a protein’s adaptability and shape its evolutionary trajectory . When a protein experiences a changed environment , it is under strong selection to find a peak in the new fitness landscape . It has been shown that strong selection increases epistatic interactions as wel...	Evolution is often viewed as a process that occurs “mutation by mutation” , suggesting that the effect of each mutation is independent of that of others . However , in reality the effect of a mutation often depends on the context of other mutations , a dependence known as “epistasis” . Even though epistasis can constra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "enzymes", "pathogens", "enzymology", "microbiology", "retroviruses", "epistasis", "immunodeficiency", "viruses", "viruses", "rna", ...	2016	Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein
Extracellular phosphorylation of proteins was suggested in the late 1800s when it was demonstrated that casein contains phosphate . More recently , extracellular kinases that phosphorylate extracellular serine , threonine , and tyrosine residues of numerous proteins have been identified . However , the functional signi...	The activity of proteins can be finely and reversibly tuned by post-translational modifications . The attachment of phosphate groups to tyrosine residues is one of such modifications . While the existence of extracellular phosphoproteins has been known , the functional significance of extracellular phosphorylation is p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "protein", "interactions", "chemical", "compounds", "nervous", "system", "enzymes", "immunology", "enzymology", "neuroscience", "organic", "compounds", "clinical", "medicine", "tyrosine", "immunoprecipitation", "am...	2017	Extracellular phosphorylation of a receptor tyrosine kinase controls synaptic localization of NMDA receptors and regulates pathological pain
Marburg virus ( MARV ) , a zoonotic pathogen causing severe hemorrhagic fever in man , has emerged in Angola resulting in the largest outbreak of Marburg hemorrhagic fever ( MHF ) with the highest case fatality rate to date . A mobile laboratory unit ( MLU ) was deployed as part of the World Health Organization outbrea...	A mobile laboratory unit ( MLU ) was deployed to Uige , Angola as part of the World Health Organization response to an outbreak of viral hemorrhagic fever caused by Marburg virus ( MARV ) . Utilizing mainly quantitative real-time PCR assays , this laboratory provided specific MARV diagnostics in the field . The MLU ope...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2011	The Use of a Mobile Laboratory Unit in Support of Patient Management and Epidemiological Surveillance during the 2005 Marburg Outbreak in Angola
Epigenetic variations of phenotypes , especially those associated with DNA methylation , are often inherited over multiple generations in plants . The active and inactive chromatin states are heritable and can be maintained or even be amplified by positive feedback in a transgenerational manner . However , mechanisms c...	DNA methylation is important for controlling activity of transposable elements and genes . An intriguing feature of DNA methylation in plants is that its pattern can be inherited over multiple generations at high fidelity in a Mendelian manner . However , mechanisms controlling the trans-generational DNA methylation dy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Wide Negative Feedback Drives Transgenerational DNA Methylation Dynamics in Arabidopsis
Blood is a dense suspension of soft non-Brownian cells of unique importance . Physiological blood flow involves complex interactions of blood cells with each other and with the environment due to the combined effects of varying cell concentration , cell morphology , cell rheology , and confinement . We analyze these in...	Viewed from a distance , flowing blood looks like a uniform fluid , but up close the cells in the blood change their position and speed somewhat heterogeneously . These individual cell movements may play a role in the physiology and pathophysiology of nutrient and gas transport , clotting , and diseases where normal pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "science", "hematology/hemoglobinopathies", "pathology/pathophysiology", "physics/condensed", "matter", "physiology/cardiovascular", "physiology", "and", "circulation", "physics/fluids,", "plasmas,", "and", "electric", "discharges", "physiology/integrative", "physiology",...	2009	Statistical Dynamics of Flowing Red Blood Cells by Morphological Image Processing
Gram-positive bacteria , including Staphylococcus aureus are endemic in the U . S . , which cause life-threatening necrotizing pneumonia . Neutrophils are known to be critical for clearance of S . aureus infection from the lungs and extrapulmonary organs . Therefore , we investigated whether the NLRP6 inflammasome regu...	Gram-positive bacteria , including Staphylococcus aureus remain a major cause of acute pneumonia worldwide . Due to emergence of multidrug-resistant strains , alternative strategies for treatment of S . aureus pneumonia are needed . To this end , it may be possible to harness host defenses to eradicate the infection in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell", "processes", "microbiology", "staphylococcus", "aureus", "pulmonology", "salmonellosis", "pneu...	2018	NLRP6 negatively regulates pulmonary host defense in Gram-positive bacterial infection through modulating neutrophil recruitment and function
Dishevelled ( Dvl ) proteins are important signaling components of both the canonical β-catenin/Wnt pathway , which controls cell proliferation and patterning , and the planar cell polarity ( PCP ) pathway , which coordinates cell polarity within a sheet of cells and also directs convergent extension cell ( CE ) moveme...	Multi-gene families , comprising a set of very similar genes with shared nucleotide sequences , are common in mammals . Individual family members may be expressed in different places and perform separate functions . Alternatively , the genes may have redundant functions , but distinct dosage requirements . Mammals shar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling", "cell", "biology/developmental", "molecular", "mechanisms", "developmental", "biology/molecular", "development", "molecular", "biology", "genetics", "and", "genomics", "ca...	2008	Murine Dishevelled 3 Functions in Redundant Pathways with Dishevelled 1 and 2 in Normal Cardiac Outflow Tract, Cochlea, and Neural Tube Development
Pore-forming toxins are potent virulence factors secreted by a large array of bacteria . Here , we deciphered the action of ExlA from Pseudomonas aeruginosa and ShlA from Serratia marcescens on host cell-cell junctions . ExlA and ShlA are two members of a unique family of pore-forming toxins secreted by a two-component...	Pore-forming toxins are the most widespread toxins delivered by pathogenic bacteria and are required for full virulence . Pore-forming toxins perforate membranes of host cells for intracellular delivery of bacterial factors , for bacterial escape from phagosomes or in order to kill cells . Loss of membrane integrity , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "endothelial", "cells", "microbiology", "cadherins", "toxic", "agents", "toxicology", "pseudomonas", "aeruginosa", ...	2017	Pseudomonas aeruginosa ExlA and Serratia marcescens ShlA trigger cadherin cleavage by promoting calcium influx and ADAM10 activation
Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein-coding regions , which are subject to ongoing inactivation and deletion . However , these same forces operate on intergenic spacers ( IGSs ) and affect their contents , maintenance , and rates of evoluti...	Endosymbiotic associations , such as that between Buchnera aphidicola and its aphid hosts , persist for millions of years and result in substantial changes to symbiont genomes . Most notably , symbionts exhibit reductions in genome size , the accumulation of slightly deleterious mutations , and rapid rates of evolution...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "genome", "evolution", "microbial", "evolution", "genetics", "and", "genomics", "biology", "evolutionary", "biology", "genomic", "evolution", "comparative", "genomics", "evolutionary", "genetics", "microbiology" ]	2011	Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera
People make numerous decisions every day including perceptual decisions such as walking through a crowd , decisions over primary rewards such as what to eat , and social decisions that require balancing own and others’ benefits . The unifying principles behind choices in various domains are , however , still not well u...	One critical question that concerns all disciplines involved in the study of human decision-making is whether different types of decisions are made in different ways , or whether there exists a common decision mechanism that underlies human choices . If the latter , what are the properties of that mechanism ? Here we c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Common Mechanism Underlying Food Choice and Social Decisions
Successful treatment of aspergillosis caused by Aspergillus fumigatus is threatened by an increasing incidence of drug resistance . This situation is further complicated by the finding that strains resistant to azoles , the major antifungal drugs for aspergillosis , have been widely disseminated across the globe . To e...	Better survival of chronically ill patients has produced an increased number of cases involving fungal infectious disease . This is partly due to a larger number of immunocompromised patients . Meanwhile , the catalogue of antifungal drugs remains quite limited and the appearance of resistant isolates is becoming more ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "aspergillus", "fumigatus", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "aspergillus", "fungal", "genetics", "gene", "regulation", "pathogens", "regulatory", "proteins", "microbiology", "dna-binding", "pr...	2017	A Novel Zn2-Cys6 Transcription Factor AtrR Plays a Key Role in an Azole Resistance Mechanism of Aspergillus fumigatus by Co-regulating cyp51A and cdr1B Expressions
Basement membranes ( BMs ) are thin sheet-like specialized extracellular matrices found at the basal surface of epithelia and endothelial tissues . They have been conserved across evolution and are required for proper tissue growth , organization , differentiation and maintenance . The major constituents of BMs are two...	Basement membranes ( BMs ) are thin layers of specialized extracellular matrices present in every tissue of the human body . Its main constituents are two networks of laminin and Type IV Collagen linked by Nidogen ( Ndg ) and proteoglycans . They form an organized scaffold that regulates organ morphogenesis and functio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "invertebrates", "caenorhabditis", "animals", "collagens", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "embryos", "drosophila", "res...	2018	Dissection of Nidogen function in Drosophila reveals tissue-specific mechanisms of basement membrane assembly
During Alzheimer's Disease , sustained exposure to amyloid-β42 oligomers perturbs metabolism of ether-linked glycerophospholipids defined by a saturated 16 carbon chain at the sn-1 position . The intraneuronal accumulation of 1-O-hexadecyl-2-acetyl-sn-glycerophosphocholine ( C16:0 PAF ) , but not its immediate precurso...	Accelerated cognitive decline in Alzheimer's patients is associated with accumulation of choline-containing lipids . One of these lipids , C16:0 platelet activating factor ( PAF ) , is specifically elevated in brains of Alzheimer's patients . As elevated exposure to C16:0 PAF ultimately leads to neuronal death , it is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "geriatrics/dementia", "biochemistry/chemical", "biology", "of", "the", "cell", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/gene", "function", "biochemistry/cell", "signaling", "and", "t...	2011	Srf1 Is a Novel Regulator of Phospholipase D Activity and Is Essential to Buffer the Toxic Effects of C16:0 Platelet Activating Factor
Bacterial pathogens often manipulate host immune pathways to establish acute and chronic infection . Many Gram-negative bacteria do this by secreting effector proteins through a type III secretion system that alter the host response to the pathogen . In this study , we determined that the phage-encoded GogB effector pr...	Bacterial pathogens have evolved sophisticated ways to subvert the innate defenses of their host . One way in which pathogens do so is by blocking or dampening the inflammatory response that is triggered once a microorganism is detected by the innate immune system . In this way , the microorganism can limit the activat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "inflammation", "immunity", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "microbial", "growth", "and", "development", "bacterial", "pathogens" ]	2012	GogB Is an Anti-Inflammatory Effector that Limits Tissue Damage during Salmonella Infection through Interaction with Human FBXO22 and Skp1
Plus-stranded RNA viruses replicate in infected cells by assembling viral replicase complexes consisting of viral- and host-coded proteins . Previous genome-wide screens with Tomato bushy stunt tombusvirus ( TBSV ) in a yeast model host revealed the involvement of seven ESCRT ( endosomal sorting complexes required for ...	Plus-stranded RNA viruses , which are important pathogens of humans , animals and plants , replicate in infected cells by assembling viral replicase complexes consisting of viral- and host-coded proteins . In this paper , we show that a group of host factors called ESCRT proteins ( endosomal sorting complexes required ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2009	A Unique Role for the Host ESCRT Proteins in Replication of Tomato bushy stunt virus
Genetic analyses of human lice have shown that the current taxonomic classification of head lice ( Pediculus humanus capitis ) and body lice ( Pediculus humanus humanus ) does not reflect their phylogenetic organization . Three phylotypes of head lice A , B and C exist but body lice have been observed only in phylotype...	While being phenotypically and physiologically different , human head and body lice are indistinguishable based on mitochondrial and nuclear genes . As protein-coding genes are too conserved to provide significant genetic diversity , we performed strain-typing of a large collection of human head and body lice using var...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "microbiology/medical", "microbiology", "infectious", "diseases/bacterial", "infections" ]	2010	Genotyping of Human Lice Suggests Multiple Emergences of Body Lice from Local Head Louse Populations
Several vertebrate microRNAs ( miRNAs ) have been implicated in cellular processes such as muscle differentiation , synapse function , and insulin secretion . In addition , analysis of Dicer null mutants has shown that miRNAs play a role in tissue morphogenesis . Nonetheless , only a few loss-of-function phenotypes for...	The striking tissue-specific expression patterns of microRNAs ( miRNAs ) suggest that they play a role in tissue development . These small RNA molecules ( ∼22 bases in length ) are processed from long primary transcripts ( pri-miRNA ) and regulate gene expression at the posttranscriptional level . There are hundreds of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "danio", "(zebrafish)", "vertebrates", "molecular", "biology" ]	2007	Targeted Inhibition of miRNA Maturation with Morpholinos Reveals a Role for miR-375 in Pancreatic Islet Development
Sister chromatid cohesion , which is mediated by the cohesin complex , is essential for the proper segregation of chromosomes in mitosis and meiosis . The establishment of stable sister chromatid cohesion occurs during DNA replication and involves acetylation of the complex by the acetyltransferase CTF7 . In higher euk...	Wapl has been shown to play an integral role in the removal of cohesin from chromosomes during mitotic prophase . While Wapl's role appears to be conserved between yeast , fly and animal cells , structural and possible mechanistic differences have also been identified . As part of a study to better understand the prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "plant", "growth", "and", "development", "cell", "cycle", "and", "cell", "division", "plant", "cell", "biology", "cell", "processes", "brassica", "cytogenetic", "analysis", "developmental", "biology", "plant", "science", "model", "organisms", "plants", "a...	2014	Arabidopsis thaliana WAPL Is Essential for the Prophase Removal of Cohesin during Meiosis
We develop a quantitative single cell-based mathematical model for multi-cellular tumor spheroids ( MCTS ) of SK-MES-1 cells , a non-small cell lung cancer ( NSCLC ) cell line , growing under various nutrient conditions: we confront the simulations performed with this model with data on the growth kinetics and spatial ...	We here present how to parameterize a mathematical agent-based model of growing MCTS almost completely from experimental data . MCTS show a similar establishment of pathophysiological gradients and concentric arrangement of heterogeneous cell populations as found in avascular tumor nodules . We build a process chain of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "carbohydrate", "metabolism", "cell", "death", "chemical", "compounds", "oxygen", "cell", "cycle", "and", "cell", "division", "cell", "processes", "carbohydrates", "glucose", "metabolism", "organic", "compounds", "glucose", "oxygen", "metabolism", "cellular", "structure...	2016	Inferring Growth Control Mechanisms in Growing Multi-cellular Spheroids of NSCLC Cells from Spatial-Temporal Image Data
Although Plasmodium vivax infection is a frequent cause of malaria worldwide , severe presentations have been more regularly described only in recent years . In this setting , despite clinical descriptions of multi-organ involvement , data associating it with kidney dysfunction are relatively scarce . Here , renal dysf...	Severe clinical presentations of Plasmodium vivax malaria are not completely understood . Multi-organ involvement is described in severe vivax cases , however data associating it with kidney dysfunction are relatively scarce , in part because the clinical signs only appear late during kidney injury . We analyzed biomar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "heme", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "pathology", "and", "laboratory", "medicine", "plasmodium", "immunology", "tropical", "diseases", "bile", "biomarkers", "parasitic", "diseases", "parasit...	2018	Distinct inflammatory profile underlies pathological increases in creatinine levels associated with Plasmodium vivax malaria clinical severity
Most cancer cells harbor multiple drivers whose epistasis and interactions with expression context clouds drug and drug combination sensitivity prediction . We constructed a mechanistic computational model that is context-tailored by omics data to capture regulation of stochastic proliferation and death by pan-cancer d...	Cancer is a complex and diverse disease . Two people with the same cancer type often respond differently to the same treatment . These differences are primarily driven by the fact that two type-matched tumors can possess distinct sets of mutations and gene expression profiles , provoking differential sensitivity to dru...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "messenger", "rna", "hormones", "erk", "signaling", "cascade", "insulin", "endocrinology", "biochemistry", "rna", ...	2018	A mechanistic pan-cancer pathway model informed by multi-omics data interprets stochastic cell fate responses to drugs and mitogens
Since cholera appeared in Africa during the 1970s , cases have been reported on the continent every year . In Sub-Saharan Africa , cholera outbreaks primarily cluster at certain hotspots including the African Great Lakes Region and West Africa . In this study , we applied MLVA ( Multi-Locus Variable Number Tandem Repea...	Cholera is caused by the toxigenic bacterium Vibrio cholerae . Since cholera was imported into the West African country of Guinea in 1970 , cases have been reported on the continent every year . In Sub-Saharan Africa , cholera occurs in a heterogeneous manner; outbreaks primarily cluster at certain hotspots including t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Relationship between Distinct African Cholera Epidemics Revealed via MLVA Haplotyping of 337 Vibrio cholerae Isolates
Recent advances in sequencing technologies have enabled the production of massive amounts of data on somatic mutations from cancer genomes . These data have led to the detection of characteristic patterns of somatic mutations or “mutation signatures” at an unprecedented resolution , with the potential for new insights ...	Somatic ( non-inherited ) mutations are acquired throughout our lives in cells throughout our body . These mutations can be caused , for example , by DNA replication errors or exposure to environmental mutagens such as tobacco smoke . Some of these mutations can lead to cancer . Different cancers , and even different i...	[ "Abstract", "Introduction", "Result", "Discussion", "Methods" ]	[]	2015	A Simple Model-Based Approach to Inferring and Visualizing Cancer Mutation Signatures
The galactosaminogalactan ( GAG ) is a cell wall component of Aspergillus fumigatus that has potent anti-inflammatory effects in mice . However , the mechanisms responsible for the anti-inflammatory property of GAG remain to be elucidated . In the present study we used in vitro PBMC stimulation assays to demonstrate , ...	Aspergillus fumigatus is an opportunistic pathogenic fungus that primarily causes infections in the immunocompromised host . It is known that Aspergillus employs various strategies to evade immune recognition by the host's immune system . Recently , galactosaminogalactan ( GAG ) , a new component of the Aspergillus cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "mycology", "medical", "microbiology", "immunology", "biology", "microbiology", "pathogenesis" ]	2014	A Polysaccharide Virulence Factor from Aspergillus fumigatus Elicits Anti-inflammatory Effects through Induction of Interleukin-1 Receptor Antagonist
Phenotype switching is commonly observed in nature . This prevalence has allowed the elucidation of a number of underlying molecular mechanisms . However , little is known about how phenotypic switches arise and function in their early evolutionary stages . The first opportunity to provide empirical insight was deliver...	Phenotype switching—the ability to switch rapidly between phenotypic states—is an evolutionary survival strategy commonly used by organisms in the face of unpredictable environmental conditions . However , little is known about how phenotype switches emerge and function in their early evolutionary stages . A previous s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens
The gammaherpesviruses , including Epstein-Barr virus ( EBV ) and Kaposi's sarcoma-associated herpesvirus ( KSHV ) , establish latency in memory B lymphocytes and promote lymphoproliferative disease in immunocompromised individuals . The precise immune mechanisms that prevent gammaherpesvirus reactivation and tumorigen...	Herpesviruses establish life-long infection in a non-replicating state termed latency . During immune compromise , herpesviruses can reactivate and cause severe disease , including cancer . We investigated mechanisms by which interferons alpha/beta ( IFNαβ ) , a family of antiviral immune genes , inhibit reactivation o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "models", "animal", "models", "of", "infection", "model", "organisms", "viral", "immune", "evasion", "immunity", "virology", "innate", "immunity", "viral", "persistence", "and", "latency", "immune", "defense", "biology", "microbiology", "mouse", "pathogenesi...	2011	A Gammaherpesvirus Cooperates with Interferon-alpha/beta-Induced IRF2 to Halt Viral Replication, Control Reactivation, and Minimize Host Lethality
Influenza virus infection remains a public health problem worldwide . The mechanisms underlying viral control during an uncomplicated influenza virus infection are not fully understood . Here , we developed a mathematical model including both innate and adaptive immune responses to study the within-host dynamics of equ...	Influenza , commonly referred to as the flu , is a contagious respiratory illness caused by influenza virus infections . Although most infected subjects with intact immune systems are able to clear the virus without developing serious flu complications , the mechanisms underlying viral control are not fully understood ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "nonlinear", "dynamics", "mathematics", "theoretical", "biology", "viral", "transmission", "and", "infection", "population", "modeling", "virology", "immunology", "biology", "computational", "biology", "microbiology", "viral", "load", "immune", "response" ]	2012	Modeling Within-Host Dynamics of Influenza Virus Infection Including Immune Responses
Polycomb group ( PcG ) proteins are transcriptional repressors of genes involved in development and differentiation , and also maintain repression of key genes involved in the cell cycle , indirectly regulating cell proliferation . The human SCML2 gene , a mammalian homologue of the Drosophila PcG protein SCM , encodes...	The processes of development and differentiation require an exquisite coordination of the gene expression program with the proliferation of the cells . The Polycomb group of proteins are important development regulators and most research to date has focused on their involvement in maintaining epigenetic silencing of ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Polycomb Protein SCML2 Regulates the Cell Cycle by Binding and Modulating CDK/CYCLIN/p21 Complexes
During nervous system development , neuronal cell bodies and their axodendritic projections are precisely positioned through transiently expressed patterning cues . We show here that two neuronally expressed , secreted immunoglobulin ( Ig ) domain-containing proteins , ZIG-5 and ZIG-8 , have no detectable role during e...	The structure of nervous systems is determined during embryonic development . After this developmental patterning phase , active maintenance mechanisms are required to uphold the structural integrity of the nervous system . This concept was revealed through the genetic elimination of factors in the nematode Caenorhabdi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "caenorhabditis", "elegans", "cellular", "neuroscience", "animal", "genetics", "model", "organisms", "genetics", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	The Secreted Immunoglobulin Domain Proteins ZIG-5 and ZIG-8 Cooperate with L1CAM/SAX-7 to Maintain Nervous System Integrity
Current methods for studying the genetic basis of adaptation evaluate genetic associations with ecologically relevant traits or single environmental variables , under the implicit assumption that natural selection imposes correlations between phenotypes , environments and genotypes . In practice , observed trait and en...	Finding genes involved in adaptation to the environment has long been of interest to evolutionary biologists and ecologists . Most commonly , researchers look for loci whose differences in allelic state correlate with differences in a particular trait or environmental variable such as temperature . The implicit assumpt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits
Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems . Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains . We developed a novel...	The importance of gene duplication to biological evolution has been recognized since the 1930s . For more than a decade , substantial evidence has been collected from genomic sequence data in order to elucidate the importance and the mechanisms of gene duplication; however , most biological characteristics arise from c...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "plasmodium", "computational", "biology", "evolutionary", "biology", "eubacteria" ]	2007	Using Likelihood-Free Inference to Compare Evolutionary Dynamics of the Protein Networks of H. pylori and P. falciparum
Invasive infections associated with non-typhoidal Salmonella ( NTS ) serovars Enteritidis ( SE ) , Typhimurium ( STm ) and monophasic variant 1 , 4 , [5] , 12:i:- are a major health problem in infants and young children in sub-Saharan Africa , and currently , there are no approved human NTS vaccines . NTS O-polysacchar...	In sub-Saharan Africa , invasive non-typhoidal Salmonella ( NTS ) infections with serovars Enteritidis ( SE ) and Typhimurium ( STm ) are widespread in children , where up to 30% of cases are fatal . There are several licensed typhoid vaccines but no NTS vaccines . We previously reported that conjugates of SE lipopolys...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vaccines", "bacterial", "diseases", "enterobacteriaceae", "infectious", ...	2017	Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa
Neural circuits in the medial entorhinal cortex ( MEC ) encode an animal’s position and orientation in space . Within the MEC spatial representations , including grid and directional firing fields , have a laminar and dorsoventral organization that corresponds to a similar topography of neuronal connectivity and cellul...	Higher brain functions such as spatial cognition are carried out in specialized brain areas . Within a specialized brain area nerve cells with different functions are organized in layers and gradients . It is possible that this topographical organization reflects underlying differences in molecular organization of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Laminar and Dorsoventral Molecular Organization of the Medial Entorhinal Cortex Revealed by Large-scale Anatomical Analysis of Gene Expression
Recorded potentials in the extracellular space ( ECS ) of the brain is a standard measure of population activity in neural tissue . Computational models that simulate the relationship between the ECS potential and its underlying neurophysiological processes are commonly used in the interpretation of such measurements ....	When electrical potentials are measured in the extracellular space ( ECS ) of the brain , they are interpreted as a signature of neural signalling . The relationship between the ECS potentials and the underlying neuronal processes is often studied with the aid of computer models . The ECS potential is typically assumed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "membrane", "potential", "ions", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "computational", "neuroscience", "neuronal", "dendrites", "physical", "chemistry", "research", "and", "anal...	2016	Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue
Extreme differences in allele frequency between West Africans and Eurasians were observed for a leucine-to-valine substitution ( Leu372Val ) in the human intestinal zinc uptake transporter , ZIP4 , yet no further evidence was found for a selective sweep around the ZIP4 gene ( SLC39A4 ) . By interrogating allele frequen...	Zinc is an essential trace element with many biological functions in the body , whose concentrations are tightly regulated by different membrane transporters . Here we report an unusual case of positive natural selection for an amino acid replacement in the human intestinal zinc uptake transporter ZIP4 . This substitut...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutation", "haplotypes", "genomics", "adaptation", "genetic", "mutation", "genetic", "polymorphism", "natural", "selection", "genetics", "population", "genetics", "evolutionary", "selection", "biology", "comparative", "genomics", "evolutionary", "biology", "evolutionary", ...	2014	Extreme Population Differences in the Human Zinc Transporter ZIP4 (SLC39A4) Are Explained by Positive Selection in Sub-Saharan Africa
Metazoans protect themselves from environmental toxins and virulent pathogens through detoxification and immune responses . We previously identified a small molecule xenobiotic toxin that extends survival of Caenorhabditis elegans infected with human bacterial pathogens by activating the conserved p38 MAP kinase PMK-1 ...	Metazoans respond to environmental threats in part through conserved pathways that coordinate protective transcriptional responses . During infection with an invasive pathogen , for example , innate immune pathways regulate the secretion of antimicrobial immune effectors . Likewise , exposure to toxic molecules leads t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "caenorhabditis", "immunology", "microbiology", "animals", "animal", "models", "bacterial", "diseases", "caenorhabditis", "elegans", "mode...	2014	The Evolutionarily Conserved Mediator Subunit MDT-15/MED15 Links Protective Innate Immune Responses and Xenobiotic Detoxification
Populations of human cytomegalovirus ( HCMV ) , a large DNA virus , are highly polymorphic in patient samples , which may allow for rapid evolution within human hosts . To understand HCMV evolution , longitudinally sampled genomic populations from the urine and plasma of 5 infants with symptomatic congenital HCMV infec...	The large , dsDNA virus Human cytomegalovirus ( HCMV ) is the most genetically complex viral pathogen of humans . HCMV populations are highly variable , which may allow the virus to evolve in human hosts on short timescales . We tested this hypothesis by longitudinally sampling HCMV populations from the urine and/or pl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Rapid Intrahost Evolution of Human Cytomegalovirus Is Shaped by Demography and Positive Selection
Basal gene expression levels have been shown to be predictive of cellular response to cytotoxic treatments . However , such analyses do not fully reveal complex genotype- phenotype relationships , which are partly encoded in highly interconnected molecular networks . Biological pathways provide a complementary way of u...	Gene expression levels have been used to study the cellular response to drug treatments . However , analysis of gene expression without considering gene interactions cannot fully reveal complex genotype-phenotype relationships . Biological pathways reveal the interactions among genes , thus providing a complementary wa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "genetic", "networks", "protein", "interactions", "protein", "interaction", "networks", "basic", "cancer", "research", "oncology", "integrins", "pharmaceutics", "network", "analysis", "cellular", "structures",...	2019	Identification of pathways associated with chemosensitivity through network embedding
Borrelia burgdorferi , the agent of Lyme disease , has cholesterol and cholesterol-glycolipids that are essential for bacterial fitness , are antigenic , and could be important in mediating interactions with cells of the eukaryotic host . We show that the spirochetes can acquire cholesterol from plasma membranes of epi...	Lyme disease , the most prevalent arthropod-borne disease in North America , is caused by the spirochete Borrelia burgdorferi . Cholesterol is a significant component of the B . burgdorferi membrane lipids , and is processed to make cholesterol-glycolipids . Our interest in the presence of cholesterol in B . burgdorfer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gram", "negative", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens" ]	2013	Lipid Exchange between Borrelia burgdorferi and Host Cells
Type 1 fimbriae are a crucial factor for the virulence of uropathogenic Escherichia coli during the first steps of infection by mediating adhesion to epithelial cells . They are also required for the consequent colonization of the tissues and for invasion of the uroepithelium . Here , we studied the role of the special...	Attachment of bacteria to the surface of host tissues is a crucial initial step in the establishment of bacterial infections . This process is mediated by adhesins , such as the type 1 fimbriae of Escherichia coli , which play a key role during urinary tract infections by mediating adhesion to the uroepithelium . The e...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "physiology", "and", "metabolism", "microbiology/microbial", "growth", "and", "development", "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	Type 1 Fimbriae, a Colonization Factor of Uropathogenic Escherichia coli, Are Controlled by the Metabolic Sensor CRP-cAMP
The mammalian odorant receptor ( OR ) repertoire is an attractive model to study evolution , because ORs have been subjected to rapid evolution between species , presumably caused by changes of the olfactory system to adapt to the environment . However , functional assessment of ORs in related species remains largely u...	The mammalian odorant receptor repertoire has been subjected to significant gene duplication and gene loss between species , presumably to adapt to the environment of an organism . However , even in distantly related species , a clear orthologous relationship exists for many genes . While ligands have been identified f...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "genetics", "and", "genomics", "gene", "function" ]	2012	Functional Evolution of Mammalian Odorant Receptors
Hypoxia induces the expression of genes that alter metabolism through the hypoxia-inducible factor ( HIF ) . A theoretical model based on differential equations of the hypoxia response network has been previously proposed in which a sharp response to changes in oxygen concentration was observed but not quantitatively e...	A complex biomolecular network utilizes different pathways to perform different functions . However , the interactions within the network are typically so complicated that the pathway structure is usually hidden . By some mathematical techniques , the pathways can be identified and possibly decoupled , whereby the insi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "computational", "biology", "biophysics", "animals" ]	2007	Pathway Switching Explains the Sharp Response Characteristic of Hypoxia Response Network
Myxococcus xanthus cells self-organize into periodic bands of traveling waves , termed ripples , during multicellular fruiting body development and predation on other bacteria . To investigate the mechanistic basis of rippling behavior and its physiological role during predation by this Gram-negative soil bacterium , w...	Myxococcus xanthus cells collectively move on solid surfaces and reorganize their colonies in response to environmental cues . Under some conditions , cells exhibit an intriguing form of collective motility by self-organizing into bands of travelling alternating-density waves termed ripples . These waves are distinct f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "complex", "systems", "cell", "motility", "mathematics", "applied", "mathematics", "biology", "computational", "biology", "microbiology", "biophysics", "microbial", "growth", "and", "development" ]	2012	The Mechanistic Basis of Myxococcus xanthus Rippling Behavior and Its Physiological Role during Predation
Chagas' disease is caused by the protozoan parasite Trypanosoma cruzi and affects approximately 10 million people in endemic areas of Mexico and Central and South America . Currently available chemotherapies are limited to two compounds: Nifurtimox and Benznidazole . Both drugs reduce the symptoms of the disease and mo...	Trypanosoma cruzi is a parasite transmitted to mammal hosts by insect vectors known as kissing bugs . This species can result pathogenic for humans , causing Chagas' disease in the Americas . Its treatment relies on two drugs discovered more than 40 years ago . Besides their toxicity , a main drawback of these drugs is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "protozoology", "biology", "microbiology", "parasitology" ]	2014	Memantine, an Antagonist of the NMDA Glutamate Receptor, Affects Cell Proliferation, Differentiation and the Intracellular Cycle and Induces Apoptosis in Trypanosoma cruzi
It is now widely recognized that robustness is an inherent property of biological systems [1] , [2] , [3] . The contribution of close sequence homologs to genetic robustness against null mutations has been previously demonstrated in simple organisms [4] , [5] . In this paper we investigate in detail the contribution of...	Genetic robustness is the ability of an organism to buffer deleterious genetic mutations . It has been previously demonstrated that the functional compensation by duplicates plays an important role in protection against gene deletions in model organisms . Close duplicates often share similar functions , and loss of one...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics" ]	2008	Role of Duplicate Genes in Robustness against Deleterious Human Mutations
The 24-nucleotides ( nt ) phased secondary small interfering RNA ( phasiRNA ) is a unique class of plant small RNAs abundantly expressed in monocot anthers at early meiosis . Previously , 44 intergenic regions were identified as the loci for longer precursor RNAs of 24-nt phasiRNAs ( 24-PHASs ) in the rice genome . How...	Meiotic crossover formation shuffles homologous genes between parental genomes , and enables transmission of new gene sets to the offspring . Frequency and positions of crossovers are determined by numerous genetic and epigenetic factors , and low nucleosome-density regions are associated with crossover hot spots in ye...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "meiosis", "plant", "anatomy", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "plant", "science", "rice", "genetically", "modified", "plants", "experimental", "organism", "systems", "sequence", "motif", "analysi...	2018	EAT1 transcription factor, a non-cell-autonomous regulator of pollen production, activates meiotic small RNA biogenesis in rice anther tapetum
While the contribution of CD8+ cytotoxic T lymphocytes to early containment of HIV-1 spread is well established , a role for NK cells in controlling HIV-1 replication during primary infection has been uncertain . The highly polymorphic family of KIR molecules expressed on NK cells can inhibit or activate these effector...	NK cells are effector cells of the innate immune system that contribute to protection against virus infections through their ability to lyse virus-infected cells without prior antigen sensitization . Their role in controlling HIV-1 replication during primary infection has been uncertain . NK cell activation is regulate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "nk", "cells", "immunity", "innate", "immunity", "hiv", "immunology", "biology", "viral", "diseases" ]	2011	Association of Activating KIR Copy Number Variation of NK Cells with Containment of SIV Replication in Rhesus Monkeys
Our actions take place in space and time , but despite the role of time in decision theory and the growing acknowledgement that the encoding of time is crucial to behaviour , few studies have considered the interactions between neural codes for objects in space and for elapsed time during perceptual decisions . The spe...	Studies in neuroscience have characterized how the brain represents objects in space and how these objects are selected for detailed perceptual processing . The selection process entails a decision about which object is favoured by the available evidence over time . This period of time is typically in the range of hund...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "neuroscience", "sensory", "systems", "biology", "computational", "biology" ]	2013	Trading Speed and Accuracy by Coding Time: A Coupled-circuit Cortical Model
Genome wide association studies ( GWAS ) have revealed 11 independent risk loci for polycystic ovary syndrome ( PCOS ) , a common disorder in young women characterized by androgen excess and oligomenorrhea . To put these risk loci and the single nucleotide polymorphisms ( SNPs ) therein into functional context , we mea...	Polycystic ovary syndrome ( PCOS ) is the most common hormonal disturbance in reproductive age women and features high levels of male sex hormones , such as testosterone , and infrequent ovulation . Twin studies have demonstrated that inheritance plays a significant role in PCOS , and recent genome wide association stu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Systems Genetics Reveals the Functional Context of PCOS Loci and Identifies Genetic and Molecular Mechanisms of Disease Heterogeneity
Anthrax is hyper-endemic in West Africa . Despite the effectiveness of livestock vaccines in controlling anthrax , underreporting , logistics , and limited resources makes implementing vaccination campaigns difficult . To better understand the geographic limits of anthrax , elucidate environmental factors related to it...	Anthrax is a soil-borne zoonotic disease found worldwide . In the West African nation of Ghana , anthrax outbreaks occur annually with a high burden to livestock keepers and their animals . To control anthrax in both humans and animals , annual livestock vaccination is recommended in endemic regions . However , in reso...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "immunology", "geographical", "locations", "vaccines", "preventive", "medicine", "bacterial", "diseases", "infectious", "disease", "control", "vaccination", "and", "immunization", "africa", "veterinary", "science", "ve...	2017	Modeling the environmental suitability of anthrax in Ghana and estimating populations at risk: Implications for vaccination and control
Chagas disease ( CD ) is a major public health concern in Latin America and a potentially serious emerging threat in non-endemic countries . Although the association between CD and cardiac abnormalities is widely reported , study design diversity , sample size and quality challenge the information , calling for its upd...	Chagas disease ( CD ) is a major public health concern in Latin America and a potentially serious emerging threat in non-endemic countries . Although the association between CD and cardiac abnormalities is widely reported , study design diversity , sample size and quality challenge the information , calling for its upd...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "database", "searching", "parasitic", "diseases", "parasitic", "protozoans", "electrocardiography", "mathematics", "protozoans", "statistics", "(mathematics)", "bioassays", "and", "physiological", "analysis", ...	2018	Electrocardiographic abnormalities in Chagas disease in the general population: A systematic review and meta-analysis
Antisense transcription is a prevalent feature at mammalian promoters . Previous studies have primarily focused on antisense transcription initiating upstream of genes . Here , we characterize promoter-proximal antisense transcription downstream of gene transcription starts sites in human breast cancer cells , investig...	Gene transcription is regulated by the coordinated interaction of genetic , epigenetic and trans-acting factors . The chromatin environment at gene promoters , including positioned nucleosomes that may display functional histone modifications , is a key regulator of gene expression , contributing to transcriptional act...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "dna", "transcription", "transcription", "factors", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "epigenetics", "chromatin", "research", "and", ...	2016	Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters
Neutrophil abscess formation is critical in innate immunity against many pathogens . Here , the mechanism of neutrophil abscess formation was investigated using a mouse model of Staphylococcus aureus cutaneous infection . Gene expression analysis and in vivo multispectral noninvasive imaging during the S . aureus infec...	Invasive infections caused by the human pathogen Staphylococcus aureus result in more deaths annually than infections caused by any other single infectious agent in the United States . Although neutrophil recruitment and abscess formation is crucial for effective host defense against this pathogen , how neutrophils sen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dermatology", "immunity", "to", "infections", "immunology", "microbiology", "staphylococcus", "aureus", "animal", "models", "bacterial", "diseases", "model", "organisms", "skin", "infections", "staphylococci", "immunologic", "techniques", "bacterial", "pathogen...	2012	Neutrophil-derived IL-1β Is Sufficient for Abscess Formation in Immunity against Staphylococcus aureus in Mice
The concept of dynamical compensation has been recently introduced to describe the ability of a biological system to keep its output dynamics unchanged in the face of varying parameters . However , the original definition of dynamical compensation amounts to lack of structural identifiability . This is relevant if mode...	A robust behaviour is a desirable feature in many biological systems . The study of mechanisms capable of maintaining the transient response unchanged despite environmental disturbances has recently motivated the introduction of a new concept: Dynamical Compensation ( DC ) . However , the original definition of DC with...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "diabetic", "endocrinology", "carbohydrates", "organic", "compounds", "glucose", "hormones", "physiological", "processes", "systems", "science", "mathematics", "homeostasis", "evolutionary", "adaptation", "in...	2017	Dynamical compensation and structural identifiability of biological models: Analysis, implications, and reconciliation
Listeria monocytogenes is a bacterial pathogen whose genome encodes many cell wall proteins that bind covalently to peptidoglycan . Some members of this protein family have a key role in virulence , and recent studies show that some of these , such as Lmo0514 , are upregulated in bacteria that colonize eukaryotic cells...	Listeria monocytogenes has evolved to adapt to numerous environments , including the intracellular niche of eukaryotic cells . Small RNAs ( sRNA ) play important regulatory roles in changing environments , and are thus predicted to modulate L . monocytogenes adaption to the intracellular lifestyle . This study shows ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "molecular", "biology", "biology", "and", "life", "sciences", "microbiology" ]	2014	The Listeria Small RNA Rli27 Regulates a Cell Wall Protein inside Eukaryotic Cells by Targeting a Long 5′-UTR Variant
Pattern separation is a central concept in current theories of episodic memory: this computation is thought to support our ability to avoid confusion between similar memories by transforming similar cortical input patterns of neural activity into dissimilar output patterns before their long-term storage in the hippocam...	Pattern separation ( the process of disambiguating incoming patterns of neuronal activity ) is a central concept in all current theories of episodic memory , as it is hypothesized to support our ability to avoid confusion between similar memories . For the last thirty years , pattern separation has been attributed to t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2019	Temporal pattern separation in hippocampal neurons through multiplexed neural codes
Cells must make reliable decisions under fluctuating extracellular conditions , but also be flexible enough to adapt to such changes . How cells reconcile these seemingly contradictory requirements through the dynamics of cellular decision-making is poorly understood . To study this issue we quantitatively measured gen...	Cells must continuously make decisions in response to changes in their environment . These decisions must be irreversible , to prevent cells from reverting back to unfit cellular states , but also be flexible , to allow cells to go back to their previous state upon environmental changes . Using single-cell time-lapse f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2011	Reversible and Noisy Progression towards a Commitment Point Enables Adaptable and Reliable Cellular Decision-Making
In plants , nutrient provision of shoots depends on the uptake and transport of nutrients across the root tissue to the vascular system . Nutrient delivery to the vasculature is mediated via the apoplastic transport pathway ( ATP ) , which uses the free space in the cell walls and is controlled by apoplastic barriers a...	Radial transport of nutrients from the soil to the vascular system of plant roots occurs via the symplastic transport pathway ( STP ) and apoplastic transport pathway ( ATP ) . Nutrients move along the STP when crossing the plasma membrane of outer cells and moving to xylem through the cytoplasmic continuum formed by p...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "plant", "anatomy", "chemical", "compounds", "apoplastic", "space", "vascular", "bundles", "plant", "physiology", "nitrates", "xylem", "plant", "science", "biological", "transport", "cellular", "structures", "and", "organelles", "proteins", "endodermis", "chemistry", "l...	2018	Root zone–specific localization of AMTs determines ammonium transport pathways and nitrogen allocation to shoots
The World Health Organization’s 2020 Goals for Chagas disease include access to antiparasitic treatment and care of all infected/ill patients . Policy makers need to know the economic value of identifying and treating patients earlier . However , the economic value of earlier treatment to cure and prevent the Chagas’ s...	The World Health Organization’s 2020 Goals for Chagas disease include access to antiparasitic treatment and care of all infected/ill patients . Policy makers need to know the economic value of identifying and treating patients earlier and what can be invested . We evaluated the impact and economic outcomes ( costs , co...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "tropical", "diseases", "vector-borne", "diseases", "social", "sciences", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "health", "care", "north", "america", "protozoans", "neg...	2018	The economic value of identifying and treating Chagas disease patients earlier and the impact on Trypanosoma cruzi transmission
Novel technologies that include recombinant pathogens and rapid detection methods are contributing to the development of drugs for neglected diseases . Recently , the results from the first high throughput screening ( HTS ) to test compounds for activity against Trypanosoma cruzi trypomastigote infection of host cells ...	Chagas is a devastating disease affecting about 100 million people in Latin America . The drugs available for treatment against the causative agent , the parasite Trypanosoma cruzi , have associated toxicity and are not completely effective against the chronic form of the disease , which is the most common presentation...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "chagas", "disease", "neglected", "tropical", "diseases" ]	2011	Activity In Vivo of Anti-Trypanosoma cruzi Compounds Selected from a High Throughput Screening
Sensory loss induces cross-modal plasticity , often resulting in altered performance in remaining sensory modalities . Whereas much is known about the macroscopic mechanisms underlying cross-modal plasticity , only scant information exists about its cellular and molecular underpinnings . We found that Caenorhabditis el...	The brain has the remarkable capacity to respond to sensory loss by boosting remaining functioning senses . For example , certain features of hearing are improved in blind people . What are the cellular and molecular mechanisms underlying this effect ? How is a certain sense strengthened ? If it is possible to hear bet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Neuropeptide-Driven Cross-Modal Plasticity following Sensory Loss in Caenorhabditis elegans
Cryptosporidium parvum is a highly prevalent zoonotic and anthroponotic protozoan parasite that causes a diarrheal syndrome in children and neonatal livestock , culminating in growth retardation and mortalities . Despite the high prevalence of C . parvum , there are no fully effective and safe drugs for treating infect...	Cryptosporidium parvum is a protozoan parasite that can cause a life-threatening gastrointestinal disease in children and in immunocompromised adults . The only approved drug for treatment of Cryptosporidium infections in humans is nitazoxanide , but it is not effective in immunocompromised individuals or in children w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "oocysts", "chemical", "compounds", "respiratory", "infections", "ketones", "enzymology", "cryptosporidium", "parasitic", "diseases", "parasitic", "protozoans", "pyruvate", "pulmonology", "parasitology", "apicom...	2019	Novel lactate dehydrogenase inhibitors with in vivo efficacy against Cryptosporidium parvum
Filarial parasites ( e . g . , Brugia malayi , Onchocerca volvulus , and Wuchereria bancrofti ) are causative agents of lymphatic filariasis and onchocerciasis , which are among the most disabling of neglected tropical diseases . There is an urgent need to develop macro-filaricidal drugs , as current anti-filarial chem...	Human filarial nematodes are causative agents of elephantiasis and African river blindness , which are among the most debilitating tropical diseases . Currently used drugs mainly affect microfilariae ( mf ) and have less effect on adult filarial nematodes , which can live in the human host for more than a decade . Fila...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "evolutionary", "biology/human", "evolution", "microbiology/microbial", "evolution", "and", "genomics", "infectious", "diseases/helminth", "infections", "microbiology/parasitology", "microbiology/microbial", "physiology", "and", "metabolism" ]	2009	The Heme Biosynthetic Pathway of the Obligate Wolbachia Endosymbiont of Brugia malayi as a Potential Anti-filarial Drug Target
Protein export is central for the survival and virulence of intracellular P . falciparum blood stage parasites . To reach the host cell , exported proteins cross the parasite plasma membrane ( PPM ) and the parasite-enclosing parasitophorous vacuole membrane ( PVM ) , a process that requires unfolding , suggestive of p...	P . falciparum parasites , the deadliest agent of human malaria , develop within erythrocytes where they are surrounded by a parasitophorous vacuolar membrane ( PVM ) . To ensure intracellular survival , the parasite exports a large repertoire of proteins into the host cell . Exported proteins require unfolding for tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "viral", "transmission", "and", "infection", "enzymes", "enzymology", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "membrane", "proteins", "apicomplexa", "p...	2016	Stable Translocation Intermediates Jam Global Protein Export in Plasmodium falciparum Parasites and Link the PTEX Component EXP2 with Translocation Activity
Zika virus ( ZIKV ) is a mosquito-borne flavivirus first isolated in Uganda in 1947 . Although entomological and virologic surveillance have reported ZIKV enzootic activity in diverse countries of Africa and Asia , few human cases were reported until 2007 , when a Zika fever epidemic took place in Micronesia . In the c...	Zika fever is a mosquito-borne illness caused by a flavivirus . Human infections with Zika virus ( ZIKV ) could cause fever , malaise and cutaneous rash . Despite several ZIKV reports since 1947 when it was first isolated at Zika forest in Uganda , molecular evolution of ZIKV as an emerging agent remains poorly underst...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "medicine" ]	2014	Molecular Evolution of Zika Virus during Its Emergence in the 20th Century
To map the neural substrate of mental function , cognitive neuroimaging relies on controlled psychological manipulations that engage brain systems associated with specific cognitive processes . In order to build comprehensive atlases of cognitive function in the brain , it must assemble maps for many different cognitiv...	Cognitive neuroscience uses neuroimaging to identify brain systems engaged in specific cognitive tasks . However , linking unequivocally brain systems with cognitive functions is difficult: each task probes only a small number of facets of cognition , while brain systems are often engaged in many tasks . We develop a n...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cognitive", "neurology", "medicine", "and", "health", "sciences", "ontologies", "social", "sciences", "neuroscience", "learning", "and", "memory", "face", "recognition", "perception", "data", "management", "cognitive", "neuroscience", "cognitive", "psychology", "cognitio...	2018	Atlases of cognition with large-scale human brain mapping
Although persistent viral diseases are a global health concern , the mechanisms of differential susceptibility to such infections among individuals are unknown . Here , we report that differential interactions between dendritic cells ( DCs ) and virus are critical in determining resistance versus susceptibility in the ...	Many chronic viral diseases are associated with prolonged viral persistence levels , which vary from one individual to another . However , the mechanisms of differential susceptibility to persistent viral infections are unknown . Theiler murine encephalomyelitis virus ( TMEV ) induces a chronic demyelinating disease si...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "virology", "in", "vitro", "immunology", "mus", "(mouse)" ]	2007	Role of Dendritic Cells in Differential Susceptibility to Viral Demyelinating Disease
Autosomal recessive nonsyndromic hearing loss is a genetically heterogeneous disorder . Here , we report a severe-to-profound sensorineural hearing loss locus , DFNB100 on chromosome 5q13 . 2-q23 . 2 . Exome enrichment followed by massive parallel sequencing revealed a c . 2510G>A transition variant in PPIP5K2 that seg...	Exome sequencing coupled with homozygosity mapping was used to identify a missense variant [c . 2510G>A; p . ( Arg837His ) ] in PPIP5K2 at the DFNB100 locus that is associated with nonsyndromic , prelingual sensorineural deafness in two large consanguineous Pakistani families . PPIP5Ks are pivotal enzymes for regulatin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "enzymes", "ears", "enzymology", "neuroscience", "phosphatases", "animal", "models", "outer", "hair", "cells", "otology", "inner", "ear", "model", "organisms", "experimental", "organism", "systems", "hearing", "disorders", "res...	2018	Mutations in Diphosphoinositol-Pentakisphosphate Kinase PPIP5K2 are associated with hearing loss in human and mouse
Travelers who acquire dengue infection are often routes for virus transmission to other regions . Nevertheless , the interplay between infected travelers , climate , vectors , and indigenous dengue incidence remains unclear . The role of foreign-origin cases on local dengue epidemics thus has been largely neglected by ...	Dengue/dengue hemorrhagic fever is the world's most widely spread mosquito-borne arboviral disease and threatens more than two-thirds of the world's population . Cases are mainly distributed in tropical and subtropical areas in accordance with vector habitats for Aedes aegypti and Ae . albopictus . However , the role o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "infectious", "diseases/epidemiology"...	2010	The Role of Imported Cases and Favorable Meteorological Conditions in the Onset of Dengue Epidemics
Phenotypic plasticity is the ability of a genotype to produce contrasting phenotypes in different environments . Although many examples have been described , the responsible mechanisms are poorly understood . In particular , it is not clear how phenotypic plasticity is related to buffering , the maintenance of a consta...	The phenotype of an individual is not fully controlled by its genes . Environmental conditions ( food , light , temperature , pathogens , etc . ) can also contribute to phenotypic variation . This phenomenon is called phenotypic plasticity . We investigate here the genetic basis of the phenotypic plasticity of pigmenta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "drosophila", "genetics", "and", "genomics" ]	2007	Phenotypic Plasticity in Drosophila Pigmentation Caused by Temperature Sensitivity of a Chromatin Regulator Network
Hypoxia inducible factors ( HIFs ) are transcription factors belonging to the basic helix−loop−helix PER-ARNT-SIM ( bHLH-PAS ) protein family with a role in sensing oxygen levels in the cell . Under hypoxia , the HIF-α degradation pathway is blocked and dimerization with the aryl hydrocarbon receptor nuclear translocat...	A low oxygen condition , called hypoxia , often occurs in tumor masses and generally correlates with worse prognosis . Cells in a tumor react to low oxygen levels with a metabolism modification induced by the activation of hypoxia inducible factors ( HIFs ) through dimerization with a partner protein and binding to a D...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dimers", "(chemical", "physics)", "crystal", "structure", "condensed", "matter", "physics", "dna-binding", "proteins", "mutation", "mutation", "databases", "crystallography", "basic", "helix-loop-helix", "domains", "physical", "chemistry", "chemical", "properties", "resear...	2018	Ligand-induced perturbation of the HIF-2α:ARNT dimer dynamics
Many microbes exhibit quorum sensing ( QS ) to cooperate , share and perform a social task in unison . Recent studies have shown the emergence of reversible phenotypic heterogeneity in the QS-responding pathogenic microbial population under laboratory conditions as a possible bet-hedging survival strategy . However , v...	Pathogenic bacteria synchronize and coordinate the production of virulence associated function-components in a density dependent fashion via quorum sensing . In general , QS-response and regulation has been studied under laboratory conditions in vitro , where the QS-responding bacterial population exhibits heterogeneou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "plant", "anatomy", "plant", "cell", "biology", "brassica", "light", "microscopy", "plant", "science", "confocal", "laser", "microscopy", "microscopy", "confocal", "microscopy", "plant", "pathology", "plants", "research", "and", "analysis", ...	2019	New insight into bacterial social communication in natural host: Evidence for interplay of heterogeneous and unison quorum response
HIV-1 set-point viral load—the approximately stable value of viraemia in the first years of chronic infection—is a strong predictor of clinical outcome and is highly variable across infected individuals . To better understand HIV-1 pathogenesis and the evolution of the viral population , we must quantify the heritabili...	The severity of the outcome of infection by a pathogen depends on many distinct factors . These include the environment and the genetic sequences of both the host and the pathogen , among others . The fraction of variability in disease outcome explained by pathogen genetic factors is termed “heritability” , because the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "phylogenetics",...	2017	Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe
Heterochromatin preferentially assembles at repetitive DNA elements , playing roles in transcriptional silencing , recombination suppression , and chromosome segregation . The RNAi machinery is required for heterochromatin assembly in a diverse range of organisms . In fission yeast , RNA splicing factors are also requi...	Heterochromatin formation at specific genomic regions is critical for processes as diverse as gene expression and chromosome segregation . The formation of silent heterochromatin at repetitive DNA elements requires processing of transcripts by the RNA interference machinery . Curiously , factors involved in proper RNA ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "rna", "interference", "chromosome", "structure", "and", "function", "gene", "function", "histone", "modification", "fungi", "model", "organisms", "epigenetics", "chromatin", "schizosaccharomyces", "genetic", "engineering", "research", "and", "analysis", ...	2014	The Proper Splicing of RNAi Factors Is Critical for Pericentric Heterochromatin Assembly in Fission Yeast
Operant learning requires that reinforcement signals interact with action representations at a suitable neural interface . Much evidence suggests that this occurs when phasic dopamine , acting as a reinforcement prediction error , gates plasticity at cortico-striatal synapses , and thereby changes the future likelihood...	A key component of survival is the ability to learn which actions , in what contexts , yield useful and rewarding outcomes . Actions are encoded in the brain in the cortex but , as many actions are possible at any one time , there needs to be a mechanism to select which one is to be performed . This problem of action s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "neuroscience", "cellular", "neuroscience", "synaptic", "plasticity", "behavioral", "neuroscience", "computational", "neuroscience", "single", "neuron", "function", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "neuronal", ...	2015	A New Framework for Cortico-Striatal Plasticity: Behavioural Theory Meets In Vitro Data at the Reinforcement-Action Interface

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