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There are many situations where relatives interact while at the same time there is genetic polymorphism in traits influencing survival and reproduction . Examples include cheater-cooperator polymorphism and polymorphic microbial pathogens . Environmental heterogeneity , favoring different traits in nearby habitats , wi...	The theory of kin selection explains the evolution of helping when relatives interact . It can be used when individuals in a social group have different sexes , ages or phenotypic qualities , but the theory has not been worked out for situations where there is genetic polymorphism in helping . That kind of polymorphism...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "biotechnology", "social", "sciences", "social", "theory", "genetic", "polymorphism", "phenotypes", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "population", "biology", "evolutionary", "theory", "evolutionary", "biology", "socio...	2016	Genes as Cues of Relatedness and Social Evolution in Heterogeneous Environments
Vector control has substantially reduced Chagas disease ( ChD ) incidence . However , transmission by household-reinfesting triatomines persists , suggesting that entomological surveillance should play a crucial role in the long-term interruption of transmission . Yet , infestation foci become smaller and harder to det...	Blood-sucking triatomine bugs are the vectors of Chagas disease , a potentially fatal illness that affects millions in Latin America . With no vaccines available , prevention heavily depends on controlling household-infesting triatomines . Insecticide-spraying campaigns have effectively reduced incidence , but persiste...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "chagas", "disease", "neglected", "tropical", "diseases", "infectious", "disease", "control", "public", "health" ]	2011	Community Participation in Chagas Disease Vector Surveillance: Systematic Review
Crosses between closely related species give two contrasting results . One result is that species hybrids may be inferior to their parents , for example , being less fertile [1] . The other is that F1 hybrids may display superior performance ( heterosis ) , for example with increased vigour [2] . Although various hypot...	A major conundrum in biology is why hybrids between species display two opposing features . On the one hand , hybrids are often more vigorous or productive than their parents , a phenomenon called hybrid vigor or hybrid superiority . On the other hand they often show reduced vigour and fertility , known as hybrid infer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/systems", "biology", "computer", "science/applications", "developmental", "biology", "computational", "biology/transcriptional", "regulation", "computational", "biology/molecular", "genetics", "developmental", "biology/developmental", "evolution", "evolution...	2010	Cryptic Variation between Species and the Basis of Hybrid Performance
Dipteran or “true” flies occupy nearly every terrestrial habitat , and have evolved to feed upon a wide variety of sources including fruit , pollen , decomposing animal matter , and even vertebrate blood . Here we analyze the molecular , genetic and cellular basis of odor response in the tsetse fly Glossina morsitans ,...	African trypanosomiasis , also known as “sleeping sickness” in humans and “wasting disease” in livestock , is a lethal and economically burdensome disease that afflicts rural communities throughout sub-Saharan Africa . The parasite that causes the disease is spread by the tsetse fly , which feeds on the blood of humans...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "neuroscience", "animals", "organic", "compounds", "parasitic", "protozoans", "animal", "antennae", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "animal", "anatom...	2019	The molecular and cellular basis of olfactory response to tsetse fly attractants
Cercarial elastase is the major invasive larval protease in Schistosoma mansoni , a parasitic blood fluke , and is essential for host skin invasion . Genome sequence analysis reveals a greatly expanded family of cercarial elastase gene isoforms in Schistosoma mansoni . This expansion appears to be unique to S . mansoni...	Schistosome parasites are a major cause of disease in the developing world . The larval stage of the parasite transitions between an intermediate snail host and a definitive human host in a dramatic fashion , burrowing out of the snail and subsequently penetrating human skin . This process is facilitated by secreted pr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "biology", "microbiology" ]	2012	Investigation of the Proteolytic Functions of an Expanded Cercarial Elastase Gene Family in Schistosoma mansoni
The regulation of the G1- to S-phase transition is critical for cell-cycle progression . This transition is driven by a transient transcriptional wave regulated by transcription factor complexes termed MBF/SBF in yeast and E2F-DP in mammals . Here we apply genomic , genetic , and biochemical approaches to show that the...	Cells proliferate by growth and division , which is supported by different gene groups that are periodically induced at specific times when they are required during the cell cycle . These genes not only need to be induced at the right time but also repressed when they are no longer required; mistakes in gene regulation...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/fun...	2009	The Fission Yeast Homeodomain Protein Yox1p Binds to MBF and Confines MBF-Dependent Cell-Cycle Transcription to G1-S via Negative Feedback
Rheumatoid arthritis is an autoimmune disease with a complex etiology , leading to inflammation of synovial tissue and joint destruction . Through a genome-wide association study ( GWAS ) and two replication studies in the Japanese population ( 7 , 907 cases and 35 , 362 controls ) , we identified two gene loci associa...	Rheumatoid arthritis ( RA ) is a chronic autoimmune disease affecting approximately 1% of the general adult population . More than 30 susceptibility loci for RA have been identified through genome-wide association studies ( GWAS ) , but the disease-causal variants at most loci remain unknown . Here , we performed repli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "rheumatology", "immune", "cells", "immunology", "histone", "modification", "rheumatoid", "arthritis", "chromatin", "autoimmunity", "gene", "expression", "t", "cells", "biology", "b", "cells", "genetic", "association", ...	2012	Functional Variants in NFKBIE and RTKN2 Involved in Activation of the NF-κB Pathway Are Associated with Rheumatoid Arthritis in Japanese
Tetherin/BST2 was identified in 2008 as the cellular factor responsible for restricting HIV-1 replication at a very late stage in the lifecycle . Tetherin acts to retain virion particles on the plasma membrane after budding has been completed . Infected cells that express large amounts of tetherin display large strings...	Tetherin or BST2 is a cellular protein that was recently found to limit the ability of HIV to escape from cells . HIV counteracts this cellular restriction to its lifecycle by expressing the small viral accessory protein Vpu . Upon viral infection , cells expressing high levels of tetherin accumulate large clusters or ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "antiviral", "responses", "virology/immunodeficiency", "viruses", "virology" ]	2010	Immunoelectron Microscopic Evidence for Tetherin/BST2 as the Physical Bridge between HIV-1 Virions and the Plasma Membrane
Heme metabolism is central to malaria parasite biology . The parasite acquires heme from host hemoglobin in the intraerythrocytic stages and stores it as hemozoin to prevent free heme toxicity . The parasite can also synthesize heme de novo , and all the enzymes in the pathway are characterized . To study the role of t...	We demonstrated about two decades ago that the malaria parasite could make heme on its own , although it imports heme from red blood cell hemoglobin during the blood stages of infection . We investigated the role of parasite-synthesized heme in all stages of parasite growth by knocking out two genes in the heme-biosynt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "malaria", "parasitic", "diseases" ]	2013	Malaria Parasite-Synthesized Heme Is Essential in the Mosquito and Liver Stages and Complements Host Heme in the Blood Stages of Infection
Kinases are heavily pursued pharmaceutical targets because of their mechanistic role in many diseases . Small molecule kinase inhibitors ( SMKIs ) are a compound class that includes marketed drugs and compounds in various stages of drug development . While effective , many SMKIs have been associated with toxicity inclu...	Small molecule kinase inhibitors ( SMKIs ) are a class of chemicals that have successfully been used for the treatment of a number of oncological diseases that are now being pursued by the pharmaceutical industry for inflammatory diseases , such as rheumatoid arthritis . SMKIs are generally designed to specifically inh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics/statistics", "molecular", "biology", "genetics", "and", "genomics/chromosome", "biology" ]	2009	Identification of a Kinase Profile that Predicts Chromosome Damage Induced by Small Molecule Kinase Inhibitors
To reach the global goal of elimination of lymphatic filariasis as a public health problem by 2020 , national programs will have to implement a series of transmission assessment surveys ( TAS ) to determine prevalence of the disease by evaluation unit . It is expected that 4 , 671 surveys will be required by 2020 . Pla...	As national programs are nearing elimination of lymphatic filariasis as a public health problem , questions have been raised about the cost of collecting the data necessary for documenting validation of elimination . A series of standardized population-based surveys is necessary to determine prevalence of infection in ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "filariasis", "global", "health", "neglected", "tropical", "diseases", "population", "biology", "lymphatic", "filariasis", "africa"...	2017	Costs of Transmission Assessment Surveys to Provide Evidence for the Elimination of Lymphatic Filariasis
Macrocyclic lactones ( MLs ) are widely used parasiticides against nematodes and arthropods , but resistance is frequently observed in parasitic nematodes of horses and livestock . Reports claiming resistance or decreased susceptibility in human nematodes are increasing . Since no target site directed ML resistance mec...	Macrocyclic lactones ( MLs ) are widely used drugs against parasitic nematodes , but drug resistance is rapidly increasing in prevalence and spatial distribution in parasites of ruminants and horses , and is suspected in human nematodes after mass drug applications . Changes in expression levels or the amino acid seque...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Macrocyclic Lactones Differ in Interaction with Recombinant P-Glycoprotein 9 of the Parasitic Nematode Cylicocylus elongatus and Ketoconazole in a Yeast Growth Assay
Scabies is recognised as a major public health problem in many countries , and is responsible for significant morbidity due to secondary bacterial infection of the skin causing impetigo , abscesses and cellulitis , that can in turn lead to serious systemic complications such as septicaemia , kidney disease and , potent...	Recently added to the World Health Organization list of neglected tropical diseases , scabies is an under-recognised cause of morbidity in many developing countries , due to secondary bacterial infection of the skin that can in turn lead to serious systemic complications such as kidney disease and , potentially , rheum...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Scabies and Impetigo Prevalence and Risk Factors in Fiji: A National Survey
Programmed cell death ( PCD ) is the physiological death of a cell mediated by an intracellular suicide program . Although key components of the PCD execution pathway have been identified , how PCD is regulated during development is poorly understood . Here , we report that the epidermal growth factor ( EGF ) -like lig...	Programmed cell death ( PCD ) is an evolutionarily conserved cellular process that is important for metazoan development and homeostasis . The epidermal growth factor ( EGF ) promotes cell proliferation , differentiation and survival during animal development . Surprisingly , we found that the EGF-like ligand LIN-3 als...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "cell", "biology", "biology", "and", "life", "sciences", "cell", "processes", "molecular", "cell", "biology" ]	2014	LIN-3/EGF Promotes the Programmed Cell Death of Specific Cells in Caenorhabditis elegans by Transcriptional Activation of the Pro-apoptotic Gene egl-1
ChIP-seq ( Chromatin Immunoprecipitation followed by sequencing ) is a high-throughput technique to identify genomic regions that are bound in vivo by a particular protein , e . g . , a transcription factor ( TF ) . Biological factors , such as chromatin state , indirect and cooperative binding , as well as experimenta...	DNA-binding proteins perform many key roles in biology , such as transcriptional regulation of gene expression and chromatin modification . ChIP-seq ( Chromatin immunoprecipitation followed by high-throughput sequencing ) is a widely used experimental technique to identify DNA-binding sites of specific proteins of inte...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "simulation", "and", "modeling", "probability", "distribution", "mathematics", "genome", "analysis", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "epigenetics", "chromatin", "research", "and", "analysis", "methods", "sequence", "analysis", "genom...	2019	ChIPulate: A comprehensive ChIP-seq simulation pipeline
NF-κB transcription factors are crucial for many cellular processes . NF-κB is activated by viral infections to induce expression of antiviral cytokines . Here , we identified a novel member of the human NF-κB family , denoted RelAp43 , the nucleotide sequence of which contains several exons as well as an intron of the...	The homeostasis of living cells is tightly regulated by signaling pathways , most of them being pleiotropic , which makes their understanding crucial in biology . One of them , the NF-κB pathway , includes a family of transcription factors involved in cell survival , proliferation , differentiation , and cell immunity ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "immune", "evasion", "immunity", "virology", "innate", "immunity", "emerging", "viral", "diseases", "biology", "microbiology", "host-pathogen", "interaction", "pathogenesis" ]	2012	RelAp43, a Member of the NF-κB Family Involved in Innate Immune Response against Lyssavirus Infection
Ribosomal RNA gene ( rDNA ) copy number variation modulates heterochromatin formation and influences the expression of a large fraction of the Drosophila ge-nome . This discovery , along with the link between rDNA , aging , and disease , high-lights the importance of understanding how natural rDNA copy number variation...	We show that altering the nutritional medium of Drosophila cultures , emulating dietary largess in the wild , increases expression of the high copy-number ribosomal RNA genes and results in rDNA instability and loss . The reduction in gene copy number occurs both in somatic and germ cells , such that altered copy numbe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Transgenerational Inheritance of Diet-Induced Genome Rearrangements in Drosophila
Quorum sensing ( QS ) , a mechanism of microbial communication dependent on cell density , governs developmental decisions in many bacteria and in some pathogenic and non-pathogenic fungi including yeasts . In these simple eukaryotes this response is mediated by the release into the growth medium of quorum-sensing mole...	Quorum sensing is a relevant mechanism of communication dependent on population density that controls cell development and pathogenesis in microorganisms including fungi . We describe a quorum sensing mediated by the release of aromatic alcohols in the growth medium that blocks hyphal development in the fission yeast S...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "cellular", "stress", "responses", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "cell", "processes", "microbiology", "carbohydrates", "organic", "compounds", "glucose", "cel...	2019	Quorum sensing and stress-activated MAPK signaling repress yeast to hypha transition in the fission yeast Schizosaccharomyces japonicus
Most of our understanding of plant genome structure and evolution has come from the careful annotation of small ( e . g . , 100 kb ) sequenced genomic regions or from automated annotation of complete genome sequences . Here , we sequenced and carefully annotated a contiguous 22 Mb region of maize chromosome 4 using an ...	Maize is a major cereal crop and key experimental system for eukaryotic biology . Previous investigations of the maize genome at the sequence level have primarily focused on analyses of genome survey sequences and BAC contigs . Here we used a comprehensive set of resources to construct an ordered and oriented 22-Mb seq...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "genetics", "and", "genomics/bioinformatics" ]	2009	Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome
West Nile virus ( WNV ) has been maintained in North America in enzootic cycles between mosquitoes and birds since it was first described in North America in 1999 . House sparrows ( HOSPs; Passer domesticus ) are a highly competent host for WNV that have contributed to the rapid spread of WNV across the U . S . ; howev...	West Nile virus ( WNV ) emerged in North America in 1999 and rapidly spread across the U . S . due to the presence of highly susceptible mosquito vectors and avian hosts . One of the major avian reservoirs for WNV in the U . S . is the house sparrow ( HOSP ) , which has low mortality during WNV infection . Here , we in...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology", "biology", "and", "life", "sciences", "microbiology" ]	2014	Evidence for Co-evolution of West Nile Virus and House Sparrows in North America
N-methyl-D-aspartate receptors ( NMDARs ) , ligand-gated ionotropic glutamate receptors , play key roles in normal brain development and various neurological disorders . Here we use standing variation data from the human population to assess which protein domains within NMDAR GluN1 , GluN2A and GluN2B subunits show the...	The increased use of next-generation sequencing for neurological patients has led to a growing catalog of patient-ascertained variants in N-methyl-D-aspartate receptor ( NMDAR ) subunits , which play important roles in normal brain development and have been implicated in epilepsy , language disorders , motor disorders ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfection", "single", "channel", "recording", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "aliphatic", "amino", "acids", "membrane", "potential", "electrophysiology", "neuroscience", "organic", "compounds", "membrane", "electrophy...	2017	Molecular Mechanism of Disease-Associated Mutations in the Pre-M1 Helix of NMDA Receptors and Potential Rescue Pharmacology
Herpes simplex virus type-1 ( HSV-1 ) establishes latency in peripheral neurons , creating a permanent source of recurrent infections . The latent genome is assembled into chromatin and lytic cycle genes are silenced . Processes that orchestrate reentry into productive replication ( reactivation ) remain poorly underst...	Herpes simplex virus is a widespread human pathogen that establishes permanent infections in nerves innervating the lips , eyes and other surfaces . The viral DNA genome is transported to the neuronal nucleus located in the nerve ganglia , where it establishes a semi-dormant state known as latency . Periodically , late...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "oral", "medicine", "neurological", "disorders", "neurology", "biology", "microbiology", "molecular", "cell", "biology", "neuroscience" ]	2012	Transient Reversal of Episome Silencing Precedes VP16-Dependent Transcription during Reactivation of Latent HSV-1 in Neurons
The spread of pathogens into new environments poses a considerable threat to human , animal , and plant health , and by extension , human and animal wellbeing , ecosystem function , and agricultural productivity , worldwide . Early detection through effective surveillance is a key strategy to reduce the risk of their e...	Emerging pathogens are an increasing threat to human , animal , and plant health . In areas where these pathogens have not yet become established , surveillance is needed to detect incursions early enough to implement control measures . However , most epidemiological systems are heterogeneous in nature , and it is uncl...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "vector-borne", "diseases", "simulation", "and", "modeling", "plant", "science", "plant", "pathology", "infectious", "disease", "control", "plants", "research", "and", ...	2017	A method of determining where to target surveillance efforts in heterogeneous epidemiological systems
Brucellosis is a widespread zoonotic disease that is also a potential agent of bioterrorism . Current serological assays to diagnose human brucellosis in clinical settings are based on detection of agglutinating anti-LPS antibodies . To better understand the universe of antibody responses that develop after B . meliten...	Brucellosis is a bacterial disease transmitted from infected animals to humans . This disease often presents as a prolonged but non-specific illness primarily characterized as fever without specific organ localization . Because infections can result after ingestion ( typically from unpasteurized animal milk or milk pro...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "immunology/immune", "response", "molecular", "biology/bioinformatics", "biotechnology/protein", "chemistry", "and", "proteomics", "infectious", "diseases/bacterial", "infections" ]	2010	Large Scale Immune Profiling of Infected Humans and Goats Reveals Differential Recognition of Brucella melitensis Antigens
The family Reduviidae ( Hemiptera: Heteroptera ) , or assassin bugs , is among the most diverse families of the true bugs , with more than 6 , 000 species . The subfamily Triatominae ( kissing bugs ) is noteworthy not simply because it is the only subfamily of the Reduviidae whose members feed on vertebrate blood but p...	We present the first comprehensive phylogenetic study aiming to understand the geological events that led to Triatominae diversification . We gathered the most diverse sampling of Reduviidae and Triatominae to construct a robust and accurate phylogeny and to be able to use more than the two Triatominae fossils as calib...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "biogeography", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "population", "genetics", "animals", "fossil", "calibration", "animal", "models", "organisms", "phylogenetics", "data", "management", "mode...	2016	Geological Changes of the Americas and their Influence on the Diversification of the Neotropical Kissing Bugs (Hemiptera: Reduviidae: Triatominae)
Competence stimulating peptide ( CSP ) is a 17-amino acid peptide pheromone secreted by Streptococcus pneumoniae . Upon binding of CSP to its membrane-associated receptor kinase ComD , a cascade of signaling events is initiated , leading to activation of the competence regulon by the response regulator ComE . Genes enc...	Streptococcus pneumoniae is a major cause of pneumonia , ear infection and meningitis . Antibiotic resistance among S . pneumoniae isolates is increasingly a major clinical problem . The acquisition of antibiotic resistance genes in S . pneumoniae is controlled by a peptide pheromone called competence-stimulating pepti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	Inhibition of Competence Development, Horizontal Gene Transfer and Virulence in Streptococcus pneumoniae by a Modified Competence Stimulating Peptide
To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics , we present a rapid self-consistent approximation of the side chain free energy at every integration step . In analogy with the adiabatic Born-Oppenheimer approximation for...	To address the large gap between time scales that can be easily reached by molecular simulations and those required to understand protein dynamics , we propose a new methodology that computes a self-consistent approximation of the side chain free energy at every integration step . As a result , the method largely elimi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "chemical", "bonding", "molecular", "dynamics", "protein", "interactions", "simulation", "and", "modeling", "protein", "structure", "thermodynamics", "hydrogen", "bonding", "physical", "chemistry", "research", "and", "analysis", "methods", "entropy", "proteins", "chemistr...	2018	Accurate calculation of side chain packing and free energy with applications to protein molecular dynamics
Prochlorococcus is a marine cyanobacterium that numerically dominates the mid-latitude oceans and is the smallest known oxygenic phototroph . Numerous isolates from diverse areas of the world's oceans have been studied and shown to be physiologically and genetically distinct . All isolates described thus far can be ass...	Prochlorococcus—the most abundant photosynthetic microbe living in the vast , nutrient-poor areas of the ocean—is a major contributor to the global carbon cycle . Prochlorococcus is composed of closely related , physiologically distinct lineages whose differences enable the group as a whole to proliferate over a broad ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "eubacteria", "microbiology", "computational", "biology" ]	2007	Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus
A potentially serious disadvantage of association mapping is the fact that marker-trait associations may arise from confounding population structure as well as from linkage to causative polymorphisms . Using genome-wide marker data , we have previously demonstrated that the problem can be severe in a global sample of 9...	There is currently tremendous interest in using association mapping to find the genes responsible for natural variation , particularly for human disease . In association mapping , researchers seek to identify regions of the genome where individuals who are phenotypically similar ( e . g . , they all have the same disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "arabidopsis", "(thale", "cress)" ]	2007	An Arabidopsis Example of Association Mapping in Structured Samples
Crossing over between homologs is initiated in meiotic prophase by the formation of DNA double-strand breaks that occur throughout the genome . In the major interference-responsive crossover pathway in baker’s yeast , these breaks are resected to form 3' single-strand tails that participate in a homology search , ultim...	In sexually reproducing organisms , crossing over between homologous chromosomes in meiosis creates physical linkages required to segregate chromosomes into haploid gametes . In baker’s yeast , which utilizes meiotic recombination pathways conserved in mice and humans , the majority of meiotic crossovers are initiated ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "enzymes", "dna-binding", "proteins", "enzymology", "nucleotides", "phosphatases", "fungi", "materials", "science", "forms", "of", "dna", "circular", "dna", "dna", "gel", "electrophoresis", "macromolecules", "materials", "by", "structure", "research", "and", "analysis",...	2017	The mismatch repair and meiotic recombination endonuclease Mlh1-Mlh3 is activated by polymer formation and can cleave DNA substrates in trans
The innate immune factors controlling Candida albicans are mostly unknown . Vulvovaginal candidiasis is common in women and affects approximately 70–75% of all women at least once . Despite the propensity of Candida to colonize the vagina , transmission of Candida albicans following sexual intercourse is very rare . Th...	The innate immune factors controlling Candida albicans are mostly unknown . Sexual transmission of Candida during vaginal intercourse is very rare . This prompted us to investigate whether the post coital vaginal milieu contained innate immune factors active against Candida . We found potent candidacidal activity of ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "model", "organisms", "clinical", "immunology", "immunity", "immunology", "biology", "microbiology", "yeast", "and", "fungal", "models" ]	2012	β-Microseminoprotein Endows Post Coital Seminal Plasma with Potent Candidacidal Activity by a Calcium- and pH-Dependent Mechanism
Characterizing the DNA-binding specificities of transcription factors is a key problem in computational biology that has been addressed by multiple algorithms . These usually take as input sequences that are putatively bound by the same factor and output one or more DNA motifs . A common practice is to apply several su...	Regulation of gene expression plays a central role in the activity of living cells and in their response to internal ( e . g . , cell division ) or external ( e . g . , stress ) stimuli . Key players in determining gene-specific regulation are transcription factors that bind sequence-specific sites on the DNA , modulat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "genetics", "and", "genomics/gene", "expression", "computational", "biology/transcriptional", "regulation", "biochemistry/transcription", "and", "translation", "computational", "biology/systems", "biology" ]	2008	A Novel Bayesian DNA Motif Comparison Method for Clustering and Retrieval
Circadian clocks provide an internal measure of external time allowing organisms to anticipate and exploit predictable daily changes in the environment . Rhythms driven by circadian clocks have a temperature compensated periodicity of approximately 24 hours that persists in constant conditions and can be reset by envir...	Circadian clocks are internal timekeepers that integrate signals from the environment and orchestrate cellular events to occur at the most favourable time of day . Circadian clocks in animals , plants , fungi and bacteria have similar characteristic properties and molecular architecture . They have a periodicity of app...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "yeast", "and", "fungal", "models", "biology", "computational", "biology", "microbiology" ]	2012	Comprehensive Modelling of the Neurospora Circadian Clock and Its Temperature Compensation
Mosquitoes rely on RNA interference ( RNAi ) as their primary defense against viral infections . To this end , the combination of RNAi and invertebrate cell culture systems has become an invaluable tool in studying virus-vector interactions . Nevertheless , a recent study failed to detect an active RNAi response to Wes...	Cell culture systems are invaluable tools for studying virus-host interactions . These systems are typically easy to maintain and manipulate; however , they can fail to accurately mimic the host environment encountered by viruses . Therefore , defining the limitations of each system is critical to properly interpreting...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology/virus", "evolution", "and", "symbiosis", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/innate", "immunity", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "...	2010	C6/36 Aedes albopictus Cells Have a Dysfunctional Antiviral RNA Interference Response
The concept of coding efficiency holds that sensory neurons are adapted , through both evolutionary and developmental processes , to the statistical characteristics of their natural stimulus . Encouraged by the successful invocation of this principle to predict how neurons encode natural auditory and visual stimuli , w...	Efficient coding is an overarching principle , well tested in visual and auditory neurobiology , which states that sensory neurons are adapted to the statistical characteristics of their natural stimulus - in brief , neurons best process those stimuli that occur most frequently . To assess its validity in olfaction , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2008	Efficient Olfactory Coding in the Pheromone Receptor Neuron of a Moth
It is generally believed that the last eukaryotic common ancestor ( LECA ) was a unicellular organism with motile cilia . In the vertebrates , the winged-helix transcription factor FoxJ1 functions as the master regulator of motile cilia biogenesis . Despite the antiquity of cilia , their highly conserved structure , an...	Cilia are microtubule-based , hair-like organelles that project from the surfaces of eukaryotic cells . Protists use motile cilia for locomotion as well as for sensory perception . In metazoans , motile cilia also function in fluid transport over epithelia , such as in the mammalian lungs . Most vertebrate and some inv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "evolutionary", "biology", "biology", "evolutionary", "genetics", "evolutionary", "developmental", "biology" ]	2012	Evolutionarily Ancient Association of the FoxJ1 Transcription Factor with the Motile Ciliogenic Program
The genetic architecture of adaptive traits is of key importance to predict evolutionary responses . Most adaptive traits are polygenic—i . e . , result from selection on a large number of genetic loci—but most molecularly characterized traits have a simple genetic basis . This discrepancy is best explained by the diff...	It is widely assumed that adaptation is mainly polygenic , with the underlying frequency changes being so small that they are difficult to detect and characterize . Taking advantage of laboratory-based natural selection of replicated populations of the fruit fly Drosophila simulans exposed to a high temperature regime ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrate", "genomics", "alleles", "genetic", "mapping", "simulation", "and", "modeling", "molecular", "genetics", "evolutionary", "adaptation", "research", "and", "analysis", "methods", "lipids", "fats", "molecular", "biology", "animal", "genomics", "genetic", "loc...	2019	Genetic redundancy fuels polygenic adaptation in Drosophila
During biogenesis of the 40S and 60S ribosomal subunits , the pre-40S particles are exported to the cytoplasm prior to final cleavage of the 20S pre-rRNA to mature 18S rRNA . Amongst the factors involved in this maturation step , Fap7 is unusual , as it both interacts with ribosomal protein Rps14 and harbors adenylate ...	Ribosomes are the cellular machines responsible for all protein synthesis . In eukaryotes , the assembly of ribosomes from their protein and RNA components is extremely complicated and involves more than 200 nonribosomal factors—three times the number of proteins in the mature complex . Among these factors , the Fap7 p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "enzyme", "structure", "rna", "protein", "interactions", "molecular", "complexes", "nucleic", "acids", "proteins", "molecular", "biology", "enzyme", "regulation", "enzymes", "chaperone", "proteins", "transferases", ...	2014	RNA Mimicry by the Fap7 Adenylate Kinase in Ribosome Biogenesis
Healing times following treatment with antibiotics , and factors that influence healing , have not been reported in Australian patients with Mycobacterium ulcerans . Healing times were determined for all M . ulcerans cases treated by a single physician with antibiotics at Barwon Health , Victoria , from 1/1/13-31/12/16...	In our study we have described for the first time in a large cohort of Australian patients the natural history of wound healing of Mycobacterium ulcerans lesions following treatment with antibiotics . We have shown that the lesions usually initially clinically improve with a reduction in induration size , and then dete...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "drugs", "microbiology", "surgical", "and", "invasive", "medical", "procedures", "physiological", "processes", "signs", "and", "symptoms", "antibiotics", "pharmacology...	2018	Wound healing: Natural history and risk factors for delay in Australian patients treated with antibiotics for Mycobacterium ulcerans disease
Divisive normalization in primary visual cortex has been linked to adaptation to natural image statistics in accordance to Barlow's redundancy reduction hypothesis . Using recent advances in natural image modeling , we show that the previously studied static model of divisive normalization is rather inefficient in redu...	The redundancy reduction hypothesis postulates that neural representations adapt to sensory input statistics such that their responses become as statistically independent as possible . Based on this hypothesis , many properties of early visual neurons—like orientation selectivity or divisive normalization—have been lin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "biology", "computational", "biology", "sensory", "systems" ]	2013	Temporal Adaptation Enhances Efficient Contrast Gain Control on Natural Images
Any organism is embedded in an environment that changes over time . The timescale for and statistics of environmental change , the precision with which the organism can detect its environment , and the costs and benefits of particular protein expression levels all will affect the suitability of different strategies–suc...	All organisms live in environments that dynamically change in ways that are only partially predictable . The seasons , diurnal cycles , oceanic fluid dynamics , and the progression of food through the human gut , all impose some predictability on common microbial ecosystems . Microbes are also at the whim of random pro...	[ "Abstract", "Introduction", "Results/Discussion", "Conclusions", "Models", "Precise", "measurement", "and", "the", "suitability", "of", "thresholding", "versus", "graded", "response", "Imperfect", "measurement", "and", "the", "value", "of", "Bayesian", "response", "stra...	[ "systems", "biology", "theoretical", "biology", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Environmental Statistics and Optimal Regulation
Feedforward inhibition and synaptic scaling are important adaptive processes that control the total input a neuron can receive from its afferents . While often studied in isolation , the two have been reported to co-occur in various brain regions . The functional implications of their interactions remain unclear , howe...	The inputs a neuron receives from its presynaptic partners strongly fluctuate as a result of either varying sensory information or ongoing intrinsic activity . To represent this wide range of signals effectively , neurons use various mechanisms that regulate the total input they receive . On the one hand , feedforward ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "neuroscience" ]	2012	Feedforward Inhibition and Synaptic Scaling – Two Sides of the Same Coin?
Brucellosis is a highly contagious zoonosis and still a major human health problem in endemic areas of the world . Although several diagnostic tools are available , most of them are difficult to implement especially in developing countries where complex health facilities are limited . Taking advantage of the identical ...	Brucellosis is one of the most widespread zoonoses in the world and still represents a mayor animal and human health problem in many endemic areas . Central for early diagnosis and appropriate treatment of the disease in humans is to have an easy to implement , fast and accurate diagnostic test for the disease . Curren...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "infectious", "diseases", "veterinary", "diseases", "diagnostic", "medicine", "biology", "microbiology", "veterinary", "science" ]	2013	Development and Validation of a Novel Diagnostic Test for Human Brucellosis Using a Glyco-engineered Antigen Coupled to Magnetic Beads
The One Health initiative is a global effort fostering interdisciplinary collaborations to address challenges in human , animal , and environmental health . While One Health has received considerable press , its benefits remain unclear because its effects have not been quantitatively described . We systematically surve...	A cohesive reaction to emerging threats requires the efficient dissemination of knowledge and methodologies across multiple disciplinary boundaries . A “One Health” approach has been advocated to facilitate cross-disciplinary communication and research in responding to challenges in human , animal , and environmental h...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "animal", "types", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "animals", "theoretical", "ecology", "zoology", "veterinary", "science", "veterinary", "medicine", "meta-research", "article", "veterinary", "diseases", "disease", ...	2016	“One Health” or Three? Publication Silos Among the One Health Disciplines
During 2015–16 Brazil experienced the largest epidemic of Zika virus ever reported . This arthropod-borne virus ( arbovirus ) has been linked to Guillain-Barré syndrome ( GBS ) in adults but other neurological associations are uncertain . Chikungunya virus has caused outbreaks in Brazil since 2014 but associated neurol...	During 2015–16 , Brazil experienced the largest outbreak of the mosquito-borne Zika virus ever reported and saw a subsequent increase in cases of Guillain-Barré syndrome ( GBS ) , a disorder of the peripheral nervous system ( nerves outside the brain and spinal cord ) that can result in paralysis and sometimes death . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "zika", "fever", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "nervous", "system", "pathogens", "tropical", "diseases", "microbiology", "alphaviruse...	2018	The spectrum of neurological disease associated with Zika and chikungunya viruses in adults in Rio de Janeiro, Brazil: A case series
It has recently been discovered that single neuron stimulation can impact network dynamics in immature and adult neuronal circuits . Here we report a novel mechanism which can explain in neuronal circuits , at an early stage of development , the peculiar role played by a few specific neurons in promoting/arresting the ...	To which extent a single neuron can influence brain circuits/networks dynamics ? Why only a few neurons display such a strong power ? These open questions are inspired by recent experimental observations in developing and adult neuronal circuits , as well as by classical debates within the framework of the single neuro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "complex", "systems", "physics", "computer", "and", "information", "sciences", "systems", "science", "mathematics", "statistical", "mechanics", "computational", "neuroscience", "applied", "mathematics", "biology", "and", "life", "sciences", "physical", "sciences", "comput...	2014	Clique of Functional Hubs Orchestrates Population Bursts in Developmentally Regulated Neural Networks
Many cognitive and motor functions are enabled by the temporal representation and processing of stimuli , but it remains an open issue how neocortical microcircuits can reliably encode and replay such sequences of information . To better understand this , a modular attractor memory network is proposed in which meta-sta...	From one moment to the next , in an ever-changing world , and awash in a deluge of sensory data , the brain fluidly guides our actions throughout an astonishing variety of tasks . Processing this ongoing bombardment of information is a fundamental problem faced by its underlying neural circuits . Given that the structu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "synaptic", "plasticity", "cognitive", ...	2016	Spike-Based Bayesian-Hebbian Learning of Temporal Sequences
Human neurocysticercosis ( NC ) is caused by the establishment of Taenia solium larvae in the central nervous system . NC is a severe disease still affecting the population in developing countries of Latin America , Asia , and Africa . While great improvements have been made on NC diagnosis , treatment , and prevention...	Neurocysticercosis ( NC ) is caused by the implantation of the larval stage of Taenia solium in the human central nervous system . Although NC diagnosis , treatment , and prevention have clearly improved in the last 40 years , the disease still causes significant morbidity and mortality in endemic regions of Latin Amer...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	Taenia solium: Development of an Experimental Model of Porcine Neurocysticercosis
The cohesin complexes play a key role in chromosome segregation during both mitosis and meiosis . They establish sister chromatid cohesion between duplicating DNA molecules during S-phase , but they also have an important role during postreplicative double-strand break repair in mitosis , as well as during recombinatio...	Meiosis is a specialized cell division by which sexually reproducing organisms prompt the formation of specialized cells presenting a half of the species chromosomal number . These cells , the so-called gametes , are able to fertilize or be fertilized , depending on the sex in which they are produced and thus restore t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "grasshoppers", "cell", "biology", "genetics", "and", "genomics", "insects" ]	2007	Sequential Loading of Cohesin Subunits during the First Meiotic Prophase of Grasshoppers
Protein aggregation is a hallmark of over 30 human pathologies . In these diseases , the aggregation of one or a few specific proteins is often toxic , leading to cellular degeneration and/or organ disruption in addition to the loss-of-function resulting from protein misfolding . Although the pathophysiological consequ...	Protein aggregation has been recognized to contribute to the development of more than 30 human diseases such as Alzheimer and Parkinson disease . Here we have performed an in silico survey of human sequence variations to evaluate whether protein aggregation might impact human disease beyond the above-mentioned aggregat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Increased Aggregation Is More Frequently Associated to Human Disease-Associated Mutations Than to Neutral Polymorphisms
Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity . In C . elegans they are called P granules; without them , the germline undergoes partial masculinization and aberrant differentiation . One key P-granule component is the Argonaute CSR-1 , a small-RNA binding protein th...	Germ cells are unique because of their immortal potential , giving rise to gametes that fertilize and become the next generation . This immortal potential is regulated in both the nucleus and cytoplasm . Within the cytoplasm are special ‘germ granules’ , consisting of a heterogeneous mix of proteins and RNA , that prov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "rna", "interference", "caenorhabditis", "gene", "regulation", "alleles", "animals", "germ", "cells", "animal", "models", "mutation", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems", "epigenetics", "research", "and...	2017	ELLI-1, a novel germline protein, modulates RNAi activity and P-granule accumulation in Caenorhabditis elegans
The control or elimination of neglected tropical diseases has recently become the focus of increased interest and funding from international agencies through the donation of drugs . Resources are becoming available for the treatment of soil-transmitted helminth ( STH ) infection through school-based deworming strategie...	The control or elimination of soil-transmitted helminth diseases through chemotherapy has recently become the focus of increased interest and funding from international agencies , charities , and pharmaceutical companies via drug donations for treatment in the poorer regions of the world . The design of treatment regim...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "computer", "and", "information", "sciences", "plant", "science", "medicine", "and", "health", "sciences", "computer", "modeling", "systems", "science", "helminth", "infections", "soil-transmitted", "helminthiases", "mathematics", "infectious", "...	2014	Modeling the Interruption of the Transmission of Soil-Transmitted Helminths by Repeated Mass Chemotherapy of School-Age Children
Integrating single nucleotide polymorphism ( SNP ) p-values from genome-wide association studies ( GWAS ) across genes and pathways is a strategy to improve statistical power and gain biological insight . Here , we present Pascal ( Pathway scoring algorithm ) , a powerful tool for computing gene and pathway scores from...	Genome-wide association studies ( GWAS ) typically generate lists of trait- or disease-associated SNPs . Yet , such output sheds little light on the underlying molecular mechanisms and tools are needed to extract biological insight from the results at the SNP level . Pathway analysis tools integrate signals from multip...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "crohn's", "disease", "immunology", "clinical", "medicine", "mathematics", "statistics", "(mathematics)", "gastroenterology", "and", "hepatology", "genome", "analysis", "test", "statistics", ...	2016	Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics
The genome projects have unearthed an enormous diversity of genes of unknown function that are still awaiting biological and biochemical characterization . These genes , as most others , can be grouped into families based on sequence similarity . The PFAM database currently contains over 2 , 200 such families , referre...	More than 40% of known proteins lack any annotation within public databases and are usually referred to as hypothetical proteins despite most of them being real and many being evolutionarily conserved and thus expected to play important biological roles . Determination of the three-dimensional structures of representat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/molecular", "evolution", "computational", "biology/macromolecular", "structure", "analysis", "computational", "biology/protein", "homology", "detection", "biochemistry/bioinformatics", "computational", "biology/genomics", "biochemistry/structural", "genomics" ]	2009	Exploration of Uncharted Regions of the Protein Universe
HIV virulence , i . e . the time of progression to AIDS , varies greatly among patients . As for other rapidly evolving pathogens of humans , it is difficult to know if this variance is controlled by the genotype of the host or that of the virus because the transmission chain is usually unknown . We apply the phylogene...	Some untreated patients infected by HIV die within a couple of years , while others survive more than 25 years . To date , it is still unclear whether this variance in the virulence of the infection is due to the host or to the virus genotype . One of the main difficulties in answering this question is that , as for mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virulence", "factors", "and", "mechanisms", "computational", "biology/evolutionary", "modeling", "infectious", "diseases/hiv", "infection", "and", "aids", "public", "health", "and", "epidemiology/epidemiology", "evolutionary", "biology", "genetics", "and", "genomics...	2010	Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load
During a lytic gammaherpesvirus infection , host gene expression is severely restricted by the global degradation and altered 3′ end processing of mRNA . This host shutoff phenotype is orchestrated by the viral SOX protein , yet its functional significance to the viral lifecycle has not been elucidated , in part due to...	Herpesviruses are ubiquitous pathogens infecting a wide range of hosts . They exhibit a biphasic lifecycle comprised of a lytic replicative stage and a relatively dormant latent stage . Members of the gammaherpesvirus subfamily include the human pathogens Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "viral", "persistence", "and", "latency", "viral", "transmission", "and", "infection", "virology", "gene", "expression", "viral", "enzymes", "biology", "microbiology", "molecular", "biology", "rna", "stability" ]	2011	Global mRNA Degradation during Lytic Gammaherpesvirus Infection Contributes to Establishment of Viral Latency
Equine rhinitis A virus ( ERAV ) is closely related to foot-and-mouth disease virus ( FMDV ) , belonging to the genus Aphthovirus of the Picornaviridae . How picornaviruses introduce their RNA genome into the cytoplasm of the host cell to initiate replication is unclear since they have no lipid envelope to facilitate f...	Picornaviruses are small animal viruses comprising an RNA genome protected by a roughly spherical protein shell with icosahedral symmetry . How the RNA is introduced into the cytoplasm of the host cell to initiate replication is unclear since they have no lipid envelope to facilitate fusion with cellular membranes . In...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "infectious", "diseases/viral", "infections", "biochemistry/macromolecular", "assemblies", "and", "machines", "virology" ]	2009	Equine Rhinitis A Virus and Its Low pH Empty Particle: Clues Towards an Aphthovirus Entry Mechanism?
Infection with different Leishmania spp . protozoa can lead to a variety of clinical syndromes associated in many cases with inflammatory responses in the skin . Although macrophages harbor the majority of parasites throughout chronic infection , neutrophils are the first inflammatory cells to migrate to the site of in...	Leishmania spp . are protozoan parasites that cause a spectrum of human diseases , and L . braziliensis causes chronic inflammatory skin lesions in residents of endemic regions of Latin America . Leishmania are obligate intracellular parasites in mammalian hosts , found in macrophages throughout infection . Nonetheless...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "flow", "cytometry", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animal", "models", "model", "organisms", "protozoans", "le...	2016	Characterization of Neutrophil Function in Human Cutaneous Leishmaniasis Caused by Leishmania braziliensis
The root epidermis of Arabidopsis provides an exceptional model for studying the molecular basis of cell fate and differentiation . To obtain a systems-level view of root epidermal cell differentiation , we used a genome-wide transcriptome approach to define and organize a large set of genes into a transcriptional regu...	A current challenge in the field of developmental biology is to define the composition and organization of gene networks that direct the pattern and differentiation of cells , tissues , and organs . In this study , we address this problem using Arabidopsis root epidermis development , a relatively simple model for stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "functional", "genomics", "plant", "growth", "and", "development", "cell", "differentiation", "gene", "function", "developmental", "biology", "molecular", "development", "plant", "genetics", "biology", "microarrays", "systems", "biology...	2012	A Gene Regulatory Network for Root Epidermis Cell Differentiation in Arabidopsis
The neural crest ( NC ) is a vertebrate-specific cell population that exhibits remarkable multipotency . Although derived from the neural plate border ( NPB ) ectoderm , cranial NC ( CNC ) cells contribute not only to the peripheral nervous system but also to the ectomesenchymal precursors of the head skeleton . To dat...	The evolution of the vertebrate head was made possible in large part by the emergence of a new cell population , the cranial neural crest . These cells contribute to diverse structures of the head , including most of the skull , yet how neural crest cells acquire such broad potential during development has remained a m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetic", "mutation", "genetic", "screens", "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "genetics", "genetics", "and", "genomics", "gene", "function" ]	2012	An Essential Role of Variant Histone H3.3 for Ectomesenchyme Potential of the Cranial Neural Crest
To become infectious , HIV-1 particles undergo a maturation process involving proteolytic cleavage of the Gag and Gag-Pol polyproteins . Immature particles contain a highly stable spherical Gag lattice and are impaired for fusion with target cells . The fusion impairment is relieved by truncation of the gp41 cytoplasmi...	The conformation of HIV-1 Env is of tremendous importance from an immunological standpoint . While several human monoclonal antibodies that exhibit broadly neutralizing activity have been identified , efforts to elicit such antibodies have met with minimal success . Here , we show that the conformation of Env is altere...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Maturation-Induced Cloaking of Neutralization Epitopes on HIV-1 Particles
Recent studies show that NK cells play important roles in murine biliary atresia ( BA ) , and a temporary immunological gap exists in this disease . In this study , we found high-mobility group box-1 ( HMGB1 ) and TLRs were overexpressed in human and rotavirus-induced murine BA . The overexpressed HMGB1 released from t...	Biliary atresia ( BA ) is the most common precipitating factor for liver transplantation in infants . BA is caused by the obstruction of hepatic bile ducts , leading to progressive obstructive jaundice and liver fibrosis . A well-recognized theory is that rotavirus injures biliary epithelia in a mouse model of BA , fol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "surgery", "immunology", "biology", "pediatric", "surgery", "immune", "response" ]	2014	HMGB1-Promoted and TLR2/4-Dependent NK Cell Maturation and Activation Take Part in Rotavirus-Induced Murine Biliary Atresia
Arabidopsis REVERSION-TO-ETHYLENE SENSITIVITY1 ( RTE1 ) represses ethylene hormone responses by promoting ethylene receptor ETHYLENE RESPONSE1 ( ETR1 ) signaling , which negatively regulates ethylene responses . To investigate the regulation of RTE1 , we performed a genetic screening for mutations that suppress ethylen...	The transcription and export of RNA is a dynamic and highly coordinated process . mRNA species that are selectively mediated by the THO/TRanscription EXport ( THO/TREX ) complex for their transcription and export remain to be identified . As well , the specific roles of complex components in transcription-coupled expor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	HYPER RECOMBINATION1 of the THO/TREX Complex Plays a Role in Controlling Transcription of the REVERSION-TO-ETHYLENE SENSITIVITY1 Gene in Arabidopsis
Meiosis relies on the SPO11 endonuclease to generate the recombinogenic DNA double strand breaks ( DSBs ) required for homologous chromosome synapsis and segregation . The number of meiotic DSBs needs to be sufficient to allow chromosomes to search for and find their homologs , but not excessive to the point of causing...	Meiosis is a specialised type of cell division that occurs during sperm and egg development to reduce chromosome number prior to fertilisation . Recombination is a key step in meiosis as it facilitates the pairing of homologous chromosomes prior to their reductional division , and generates new combinations of genetic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "medicine", "and", "health", "sciences", "homologous", "chromosomes", "reproductive", "system", "spermatocytes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "germ", "cells", "dna", "sperm", "homologous", "recombination", "research", "an...	2017	Tex19.1 promotes Spo11-dependent meiotic recombination in mouse spermatocytes
The initial endemicity ( pre-control prevalence ) of onchocerciasis has been shown to be an important determinant of the feasibility of elimination by mass ivermectin distribution . We present the first geostatistical map of microfilarial prevalence in the former Onchocerciasis Control Programme in West Africa ( OCP ) ...	Onchocerciasis is a neglected tropical disease caused by Onchocerca volvulus and transmitted by Simulium blackflies . Operational between 1975 and 2002 , the Onchocerciasis Control Programme in West Africa ( OCP ) was one of the first large-scale intervention programmes ever implemented , and was successful in controll...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Model-Based Geostatistical Mapping of the Prevalence of Onchocerca volvulus in West Africa
The persistence of Mycobacterium leprae ( M . leprae ) infection is largely dependent on the types of host immune responses being induced . Macrophage , a crucial modulator of innate and adaptive immune responses , could be directly infected by M . leprae . We therefore postulated that M . leprae-infected macrophages m...	Macrophages play critical roles in modulating Mycobacterium leprae ( M . leprae ) infection . In this study , we investigated the immune status of macrophages stimulated with live M . leprae or killed M . leprae . We found that live M . leprae-infected macrophages polarized toward the regulatory M2-type , preferentiall...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Mycobacterium leprae-Infected Macrophages Preferentially Primed Regulatory T Cell Responses and Was Associated with Lepromatous Leprosy
Candida albicans is able to proliferate in environments that vary dramatically in ambient pH , a trait required for colonising niches such as the stomach , vaginal mucosal and the GI tract . Here we show that growth in acidic environments involves cell wall remodelling which results in enhanced chitin and β-glucan expo...	To be able to colonise a host or cause infection , microbes must be able to adapt and respond to changes in their environment . One of the most important environmental signals for opportunistic pathogens is ambient pH , with changes in external pH resulting in phenotypic , metabolic and physical changes in fungi and ba...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "walls", "chitin", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "fungi", "materials", "science", "experimental", "organism", "systems", "c...	2017	Adaptation of Candida albicans to environmental pH induces cell wall remodelling and enhances innate immune recognition
The increased sequencing of pathogen genomes and the subsequent availability of genome-scale functional datasets are expected to guide the experimental work necessary for target-based drug discovery . However , a major bottleneck in this has been the difficulty of capturing and integrating relevant information in an ea...	In cell-based drug development , researchers attempt to create drugs that kill a pathogen without necessarily understanding the details of how the drugs work . In contrast , target-based drug development entails the search for compounds that act on a specific intracellular target—often a protein known or suspected to b...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry/drug", "discovery", "genetics", "and", "genomics/functional", "genomics", "infectious", "diseases/neglected", "tropical", "diseases", "computational", "biology/comparative", "sequence", "analysis", "genetics", "and", "genomics/gene", "function", "computational", "...	2010	Identification of Attractive Drug Targets in Neglected-Disease Pathogens Using an In Silico Approach
While CD8+ T cells are clearly important in controlling virus replication during HIV and SIV infections , the mechanisms underlying this antiviral effect remain poorly understood . In this study , we assessed the in vivo effect of CD8+ lymphocyte depletion on the lifespan of productively infected cells during chronic S...	Despite overwhelming evidence that CD8+ T cells are important in controlling virus replication during HIV and simian immunodeficiency virus ( SIV ) infections , the mechanisms responsible for this antiviral effect in vivo remain poorly understood . This lack of knowledge represents a key obstacle to our efforts to deve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "pathology/pathophysiology", "pathology", "immunology/immune", "response", "infectious", "diseases/hiv", "infection", "and", "aids", "infectious", "diseases/viral", "infections", "immunology", "microbiology/parasitology", "pathology/immunology", "immunolog...	2010	CD8+ Lymphocytes Control Viral Replication in SIVmac239-Infected Rhesus Macaques without Decreasing the Lifespan of Productively Infected Cells
Loss of immune control over opportunistic infections can occur at different stages of HIV-1 ( HIV ) disease , among which mucosal candidiasis caused by the fungal pathogen Candida albicans ( C . albicans ) is one of the early and common manifestations in HIV-infected human subjects . The underlying immunological basis ...	HIV infection is closely associated with enhanced host susceptibility to various opportunistic infections ( OIs ) , among which mucosal candidiasis caused by the fungal pathogen Candida albicans ( C . albicans ) is an early and common manifestation . Even in the era of effective ART , mucosal candidiasis is still a cli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "hiv", "infections", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "pathogens", "immunology", "ce...	2016	Sequential Dysfunction and Progressive Depletion of Candida albicans-Specific CD4 T Cell Response in HIV-1 Infection
Despite the effectiveness of highly active antiretroviral therapy ( HAART ) in treating individuals infected with HIV , HAART is not a cure . A latent reservoir , composed mainly of resting CD4+T cells , drives viral rebound once therapy is stopped . Understanding the formation and maintenance of latently infected cell...	While HIV is a treatable disease due to effective antiviral therapies , these drugs do not cure HIV . When therapy is stopped , a pool of infected , long-lived , treatment resistant cells re-establishes infection . These latently infected cells , mainly resting CD4+T cells , are barriers to a cure . Studying and unders...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "hiv", "retrovirology", "and", "hiv", "immunopathogenesis", "viral", "diseases", "infectious", "disease", "modeling" ]	2012	Directly Infected Resting CD4+T Cells Can Produce HIV Gag without Spreading Infection in a Model of HIV Latency
DNA ligase IV ( Dnl4 in budding yeast ) is a specialized ligase used in non-homologous end joining ( NHEJ ) of DNA double-strand breaks ( DSBs ) . Although point and truncation mutations arise in the human ligase IV syndrome , the roles of Dnl4 in DSB repair have mainly been examined using gene deletions . Here , Dnl4 ...	Chromosomal rearrangements are common driver mutations in human genetic disease and cancer . The junctions observed at rearrangements typically show only a few base pairs in common between the partners , suggesting that they were formed by the end-to-end joining process , nonhomologous end joining ( NHEJ ) . However , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mutagenesis", "biochemistry", "genetic", "mutation", "enzyme", "classes", "nucleic", "acids", "enzymes", "genetics", "dna", "dna", "repair", "biology", "dna", "recombination", "ligases" ]	2013	Saccharomyces cerevisiae DNA Ligase IV Supports Imprecise End Joining Independently of Its Catalytic Activity
Important knowledge about the determinants of complex human phenotypes can be obtained from the estimation of heritability , the fraction of phenotypic variation in a population that is determined by genetic factors . Here , we make use of extensive phenotype data in Iceland , long-range phased genotypes , and a popula...	Phenotype is a function of a genome and its environment . Heritability is the fraction of variation in a phenotype determined by genetic factors in a population . Current methods to estimate heritability rely on the phenotypic correlations of closely related individuals and are potentially upwardly biased , due to the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "haplotypes", "mathematics", "genetic", "polymorphism", "heredity", "epidemiology", "statistics", "genetics", "population", "genetics", "population", "biology", "biology", "human", "genetics", "statistical", "methods", "genetic", "ep...	2013	Using Extended Genealogy to Estimate Components of Heritability for 23 Quantitative and Dichotomous Traits
Chromosome abnormalities are common in the human population , causing germ cell loss at meiotic prophase I and infertility . The mechanisms driving this loss are unknown , but persistent meiotic DNA damage and asynapsis may be triggers . Here we investigate the contribution of these lesions to oocyte elimination in mic...	Chromosome abnormalities , such as aneuploidies and structural variants ( i . e . translocations , inversions ) , are strikingly common in the human population , causing disorders such as Down syndrome and Turner syndrome . One important consequence of chromosome abnormalities in mammals is errors during meiosis , the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Histone H2AFX Links Meiotic Chromosome Asynapsis to Prophase I Oocyte Loss in Mammals
Little is known about the history and population structure of our closest living relatives , the chimpanzees , in part because of an extremely poor fossil record . To address this , we report the largest genetic study of the chimpanzees to date , examining 310 microsatellites in 84 common chimpanzees and bonobos . We i...	Common chimpanzees have been traditionally classified into three populations: western , central , and eastern . While the morphological or behavioral differences are very small , genetic studies of mitochondrial DNA and the Y chromosome have supported the geography-based designations . To obtain a crisp picture of chim...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "primates" ]	2007	Genetic Structure of Chimpanzee Populations
In fission yeast , the Swi5-Sfr1 complex plays an important role in homologous recombination ( HR ) , a pathway crucial for the maintenance of genomic integrity . Here we identify and characterize mammalian Swi5 and Sfr1 homologues . Mouse Swi5 and Sfr1 are nuclear proteins that form a complex in vivo and in vitro . Sw...	Our genome constantly undergoes DNA damage as a result of agents in the environment , as well as from metabolic processes . One method of repairing DNA damage is homologous recombination ( HR ) , in which genetic information from a duplicate sequence ( the sister chromatid ) is copied into the damaged site in DNA . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/cancer", "genetics", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/gene", "function" ]	2010	Role for the Mammalian Swi5-Sfr1 Complex in DNA Strand Break Repair through Homologous Recombination
The genetic background of complex diseases is proposed to consist of several low-penetrance risk loci . Addressing this complexity likely requires both large sample size and simultaneous analysis of different predisposing variants . We investigated the role of four thrombosis genes: coagulation factor V ( F5 ) , interc...	The genetic background of cardiovascular diseases is still largely unknown . As in other complex diseases , the genetic risk is thought to consist of several genetic variants and their possible interactions . Elucidation of the genetic component of any complex trait most likely requires simultaneous examination of vari...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics", "cardiovascular", "disorders" ]	2007	Combined Effects of Thrombosis Pathway Gene Variants Predict Cardiovascular Events
Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood . Volvocine algae include isogamous species such as Chlamydomonas reinhardtii , with two equal-sized mating types , and oogamous multicellular s...	Sexual differentiation in eukaryotes is manifested in two fundamentally different ways . Unicellular species may have mating types where gametes are morphologically identical but can only mate with those expressing a different mating type than their own , while multicellular species such as plants and animals have male...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organisms", "developmental", "biology", "sperm-egg", "interactions", "fertilization", "chlamydomonas", "reinhardtii", "haplontic", "life", "cycle", "life", "cycles", "biology", "and", "life", "sciences", "evolutionary", "biology", "plants", "algae", "cell", "fate", "de...	2014	Evolution of Sexes from an Ancestral Mating-Type Specification Pathway
SOX2 is a master regulator of both pluripotent embryonic stem cells ( ESCs ) and multipotent neural progenitor cells ( NPCs ) ; however , we currently lack a detailed understanding of how SOX2 controls these distinct stem cell populations . Here we show by genome-wide analysis that , while SOX2 bound to a distinct set ...	In mammals , a few thousand transcription factors regulate the differential expression of more than 20 , 000 genes to specify ∼200 functionally distinct cell types during development . How this is accomplished has been a major focus of biology . Transcription factors bind non-coding DNA regulatory elements , including ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "regulation", "cell", "differentiation", "histone", "modification", "developmental", "biology", "stem", "cells", "epigenetics", "molecular", "genetics", "embryonic", "stem", "cells", "biology", "microarrays", "neural", "stem", "cells", "genetics", "computational",...	2013	SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State
Vector-borne viruses are an important class of emerging and re-emerging pathogens; thus , an improved understanding of the cellular factors that modulate infection in their respective vertebrate and insect hosts may aid control efforts . In particular , cell-intrinsic antiviral pathways restrict vector-borne viruses in...	West Nile virus ( WNV ) is an insect-borne virus that has re-emerged globally and for which there are no specific therapeutics or vaccines . We set out to identify cellular factors that impact infection using Drosophila as a model insect . Using a genome-wide RNAi screen we identified a large number of genes that alter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "animal", "genetics", "functional", "genomics", "immunology", "host-pathogen", "interaction", "microbiology", "emerging", "infectious", "diseases", "neglected", "tropical", "diseases", "infectious", "diseases", "zoonoses", "biology", "vectors", "and", "hosts", ...	2014	Genome-Wide RNAi Screen Identifies Broadly-Acting Host Factors That Inhibit Arbovirus Infection
Striated muscle contraction is a highly cooperative process initiated by Ca2+ binding to the troponin complex , which leads to tropomyosin movement and myosin cross-bridge ( XB ) formation along thin filaments . Experimental and computational studies suggest skeletal muscle fiber activation is greatly augmented by coop...	In striated muscle myosin binds to actin and converts chemical energy from ATP hydrolysis into force , work , and power . Myosin cross-bridge binding is regulated by Ca2+ and the thin filament proteins troponin and tropomyosin . Cooperative interactions between actin , myosin , troponin , and tropomyosin greatly influe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "bioengineering", "biological", "systems", "engineering", "biology", "computational", "biology", "biophysics", "engineering" ]	2012	Filament Compliance Influences Cooperative Activation of Thin Filaments and the Dynamics of Force Production in Skeletal Muscle
The mammalian circadian clockwork is composed of a core PER/CRY feedback loop and additional interlocking loops . In particular , the ROR/REV/Bmal1 loop , consisting of ROR activators and REV-ERB repressors that regulate Bmal1 expression , is thought to “stabilize” core clock function . However , due to functional redu...	Circadian clocks in plants , fungi , insects , and mammals all share a common transcriptional network architecture . At the cellular level , the mammalian clockwork consists of a core Per/Cry negative feedback loop and additional interlocking loops . We wished to address experimentally the contribution of the interlock...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "genetics", "and", "genomics/gene", "function", "cell", "biology/gene", "expression" ]	2008	Redundant Function of REV-ERBα and β and Non-Essential Role for Bmal1 Cycling in Transcriptional Regulation of Intracellular Circadian Rhythms
Cofactor-independent phosphoglycerate mutase ( iPGAM ) is essential for the growth of C . elegans but is absent from humans , suggesting its potential as a drug target in parasitic nematodes such as Brugia malayi , a cause of lymphatic filariasis ( LF ) . iPGAM's active site is small and hydrophilic , implying that it ...	Parasitic worms like Brugia malayi cause widespread lymphatic filariasis ( LF ) in southeast Asia and sub-Saharan Africa . The adult worms causing most of the symptoms of LF are difficult to treat with existing drugs . As a possible step toward new LF drugs , we searched for inhibitors of the B . malayi cofactor-indepe...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "medicine", "biochemistry", "infectious", "diseases", "drug", "research", "and", "development", "drugs", "and", "devices", "enzymes", "neglected", "tropical", "diseases", "biology", "lymphatic", "filariasis", "drug", "discovery" ]	2014	Cofactor-Independent Phosphoglycerate Mutase from Nematodes Has Limited Druggability, as Revealed by Two High-Throughput Screens
Hepatocellular carcinoma ( HCC ) is one of the most lethal human cancers . The search for targeted treatments has been hampered by the lack of relevant animal models for the genetically diverse subsets of HCC , including the 20-40% of HCCs that are defined by activating mutations in the gene encoding β-catenin . To add...	Liver cancer is a leading cause of cancer-related death . Genetic analysis of liver cancer has enabled classification of these tumors into subsets with unique genetic , clinical , and prognostic features . The search for targeted liver cancer treatments has been hampered by the lack of relevant animal models for these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish
Neurons develop elaborate morphologies that provide a model for understanding cellular architecture . By studying C . elegans sensory dendrites , we previously identified genes that act to promote the extension of ciliated sensory dendrites during embryogenesis . Interestingly , the nonciliated dendrite of the oxygen-s...	Lewis Carroll's Alice told the Caterpillar , "Being so many different sizes in a day is very confusing . " Like Alice , the cells of our bodies face a problem in size control – they must become the right size and remain that way throughout the life of the organism . This problem is especially relevant for nerve cells (...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "nose", "face", "caenorhabditis", "oxygen", "neuroscience", "animals", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems", "cellular", "structures", "and", ...	2018	A neuronal MAP kinase constrains growth of a Caenorhabditis elegans sensory dendrite throughout the life of the organism
E-cadherin-mediated cell-cell adhesion is critical for naive pluripotency of cultured mouse embryonic stem cells ( mESCs ) . E-cadherin-depleted mESC fail to downregulate their pluripotency program and are unable to initiate lineage commitment . To further explore the roles of cell adhesion molecules during mESC differ...	Disease may be due to either excess of undesirable cells , like in cancer or autoimmune disease , or by progressive loss of vital cells . The latter , for instance , causes neurodegenerative diseases such as Alzheimer’s disease . Stem-cell based therapy holds great potential to cure devastating diseases with cell loss ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blastocysts", "cell", "physiology", "fluorescence", "imaging", "cell", "differentiation", "cell", "polarity", "developmental", "biology", "embryos", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "specimen", "preparation", "and",...	2016	p120 Catenin-Mediated Stabilization of E-Cadherin Is Essential for Primitive Endoderm Specification
The clinical studies were approved by the Human Ethics Committee at Lund University ( approval numbers LU106-02 , LU236-99 and Clinical Trial Registration RTP-A2003 , International Committee of Medical Journal Editors , www . clinicaltrials . gov ) . Acute cystitis is rapidly becoming a therapeutic enigma , as antibiot...	Infections continue to threaten human health as pathogenic organisms outsmart available therapies with remarkable genetic versatility . Fortunately , microbial versatility is matched by the flexibility of the host immune system which provide a rich source of novel therapeutic concepts . Emerging therapeutic solutions i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "urology", "medicine", "and", "health", "sciences", "body", "fluids", "bladder", "and", "ureteric", "disorders", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "bladder", "urine", "animal", "models", "bacterial", "di...	2016	Molecular Basis of Acute Cystitis Reveals Susceptibility Genes and Immunotherapeutic Targets
It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes . The repertoire of naturally occurring cytosine modifications , however , extends beyond 5-methylcytosine to include its oxidation derivatives , notably 5-hydroxy...	Most cytosines that occur in a CpG context in mammalian genomes are methylated . Methylation has important functional consequences in the cell but also affects genome evolution . Notably , methylated cytosines are prone to deaminate and constitute mutational hotspots in mammalian genomes . Recently , a series of other ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "microevolution", "genomics", "genome", "evolution", "evolutionary", "biology", "evolutionary", "processes", "genetics", "biology", "and", "life", "sciences", "dna", "computational", "biology", "dna", "modification", "comparative", "genomics", "epigenomics",...	2014	Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates
Pruritic scabies lesions caused by Sarcoptes scabiei burrowing in the stratum corneum of human skin facilitate opportunistic bacterial infections . Emerging resistance to current therapeutics emphasizes the need to identify novel targets for protective intervention . We have characterized several protein families locat...	The gut of most invertebrates is lined by a protective layer of chitin and glycoproteins , often designated as a peritrophic matrix . Previous research suggests that it forms a barrier that may protect the midgut epithelium from abrasive food particles and pathogens . Parasitic invertebrates ingesting vertebrate plasma...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "dermatology", "complement", "system", "infectious", "diseases", "skin", "infections", "scabies", "neglected", "tropical", "diseases", "immunology", "biology", "parasitic", "diseases", "immune", "system" ]	2011	Scabies Mite Peritrophins Are Potential Targets of Human Host Innate Immunity
Due to geographic overlap of malaria and visceral leishmaniasis ( VL ) , co-infections may exist but have been poorly investigated . To describe prevalence , features and risk factors for VL-malaria co-infections , a case-control analysis was conducted on data collected at Amudat Hospital , Uganda ( 2000–2006 ) by Méde...	Visceral leishmaniasis ( VL ) and malaria are two major parasitic diseases sharing a similar demographic and geographical distribution . In areas where both diseases are endemic , such as Sudan , Uganda , India and Bangladesh , co-infection cases have been reported , but features and risk factors associated with these ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "health", "screening", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "leishmaniasis", "neglected", "tropical", "diseases", "malaria", "protozoan", "infections", ...	2012	Prevalence, Features and Risk Factors for Malaria Co-Infections amongst Visceral Leishmaniasis Patients from Amudat Hospital, Uganda
Base composition is highly variable among and within plant genomes , especially at third codon positions , ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones ( particularly Monocots ) . Consequently , synonymous codon usage is biased in most species , even when base composition is rel...	In protein coding genes , base composition strongly varies within and among plant genomes , especially at positions where changes do not alter the coded protein ( synonymous variations ) . Some species , such as the model plant Arabidopsis thaliana , are relatively GC-poor and homogeneous while others , such as grasses...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Materials", "&", "methods" ]	[ "biotechnology", "taxonomy", "plant", "genomes", "plant", "taxonomy", "mutation", "substitution", "mutation", "plant", "science", "data", "management", "phylogenetics", "genome", "analysis", "plant", "genomics", "plants", "flowering", "plants", "computer", "and", "infor...	2017	Evolutionary forces affecting synonymous variations in plant genomes
Host selection by vector mosquitoes is a critical component of virus proliferation , particularly for viruses such as West Nile ( WNV ) that are transmitted enzootically to a variety of avian hosts , and tangentially to dead-end hosts such as humans . Culex tarsalis is a principal vector of WNV in rural areas of wester...	West Nile virus ( WNV ) is transmitted from one vertebrate host to another by the bite of a mosquito . The virus is maintained primarily in birds , but can also be transmitted to mammals such as horses and humans which may suffer severe neurological disease . Culex tarsalis is a primary mosquito vector of WNV in the we...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "flavivirus", "population", "biology", "veterinary", "science", "infectious", "diseases", "disease", "ecology", "epidemiology", "biology", "vectors", "and", "hosts", "public", "health", "mosquitoes", "ecology", "tro...	2011	Mosquito Host Selection Varies Seasonally with Host Availability and Mosquito Density
Hypertension is one of the most common age-related chronic disorders , and by predisposing individuals for heart failure , stroke , and kidney disease , it is a major source of morbidity and mortality . Its etiology remains enigmatic despite intense research efforts over many decades . By use of empirically well-constr...	Hypertension is highly age-related and affects more than 1 billion people worldwide . It is a major source of morbidity and mortality as it makes us more prone to experience heart failure , stroke , and kidney disease . Despite intense research efforts over several decades , there is still no consensus on what are the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "medicine", "and", "health", "sciences", "medical", "physics", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Arterial Stiffening Provides Sufficient Explanation for Primary Hypertension
Dengue is a mosquito-borne disease that threatens over half of the world’s population . Despite being endemic to more than 100 countries , government-led efforts and tools for timely identification and tracking of new infections are still lacking in many affected areas . Multiple methodologies that leverage the use of ...	As communicable diseases spread in our societies , people frequently turn to the Internet to search for medical information . In recent years , multiple research teams have investigated how to utilize Internet users’ search activity to track infectious diseases around our planet . In this article , we show that a metho...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "geographical", "locations", "north", "america", "singapore", "internet", "infectious", "disease", "control", "infectious", "diseases", "computer", "and", "information", "sciences", "taiwan", "south", "america", "epidemiology", "...	2017	Advances in using Internet searches to track dengue
Active trachoma is not uniformly distributed in endemic areas , and local environmental factors influencing its prevalence are not yet adequately understood . Determining whether clustering is a consistent phenomenon may help predict likely modes of transmission and help to determine the appropriate level at which to t...	Active trachoma is not uniformly distributed in endemic areas , and local environmental factors influencing its prevalence are not yet adequately understood . Determining whether clustering is a consistent phenomenon may help predict likely modes of transmission and help to determine the appropriate level at which to t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health", "public", "health", "and", "epidemiology/environmental", "health", "ecology/spatial", "and", "landscape", "ecology" ]	2010	Active Trachoma among Children in Mali: Clustering and Environmental Risk Factors
The genetic adaptation of pathogens in host tissue plays a key role in the establishment of chronic infections . While whole genome sequencing has opened up the analysis of genetic changes occurring during long-term infections , the identification and characterization of adaptive traits is often obscured by a lack of k...	Here we investigate the molecular function of the important cyclic-di-GMP signaling system YfiBNR in the opportunistic pathogen Pseudomonas aeruginosa and demonstrate its importance for the evolution of persistent small colony variant ( SCV ) morphotypes in chronic cystic fibrosis ( CF ) lung infections . Previously we...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "organismal", "evolution", "cellular", "stress", "responses", "genetic", "mutation", "microbiology", "bacterial", "biochemistry", "bacterial", "diseases", "developmental", "biology", "molecular", "cell", "biology", "microbial", "evolution", "pseu...	2012	The YfiBNR Signal Transduction Mechanism Reveals Novel Targets for the Evolution of Persistent Pseudomonas aeruginosa in Cystic Fibrosis Airways
The epidemiology of dengue fever is characterized by highly seasonal , multi-annual fluctuations , and the irregular circulation of its four serotypes . It is believed that this behaviour arises from the interplay between environmental drivers and serotype interactions . The exact mechanism , however , is uncertain . C...	The fluctuations of multi-serotype infectious diseases are often highly irregular and hard to predict . Previous theoretical approaches have attempted to disentangle the drivers that may underlie this behaviour in dengue dynamics with variable success . Here , we examine the role of such drivers using a pattern-oriente...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "infectious", "disease", "epidemiology", "immunology", "tropical", "diseases", "simulation", "and", "modeling", "multivariate", "analysis", "mathematics", "statistics", "(mathematics)", "neglected", "tropical"...	2016	The Role of Serotype Interactions and Seasonality in Dengue Model Selection and Control: Insights from a Pattern Matching Approach
Acinetobacter baumannii is an important nosocomial pathogen that accounts for up to 20 percent of infections in intensive care units worldwide . Furthermore , A . baumannii strains have emerged that are resistant to all available antimicrobials . These facts highlight the dire need for new therapeutic strategies to com...	Acinetobacter baumannii is a bacterium responsible for an increasing number of infections in the hospital setting . These infections are particularly challenging because most strains of A . baumannii are resistant to commonly used antibiotics . Unfortunately , there is relatively little known about this organism and ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "acinetobacter", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "bacterial", "diseases", "bacterial", "pneumonia", "bacterial", "pathogens", "infectious", "diseases", "biology", "pathogenesis", "immune", "response", "ba...	2012	Identification of an Acinetobacter baumannii Zinc Acquisition System that Facilitates Resistance to Calprotectin-mediated Zinc Sequestration
Computational prediction of nucleic acid binding sites in proteins are necessary to disentangle functional mechanisms in most biological processes and to explore the binding mechanisms . Several strategies have been proposed , but the state-of-the-art approaches display a great diversity in i ) the definition of nuclei...	Nucleic acid binding sites in proteins are functionally important in a majority of biological processes . Computationally predicting these binding sites can help the biological community in understanding the nucleic acid binding proteins in the very first step . The emergence of nucleic acid binding site prediction pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Large-Scale Assessment of Nucleic Acids Binding Site Prediction Programs
Genotoxic agents that cause double-strand breaks ( DSBs ) often generate damage at the break termini . Processing enzymes , including nucleases and polymerases , must remove damaged bases and/or add new bases before completion of repair . Artemis is a nuclease involved in mammalian nonhomologous end joining ( NHEJ ) , ...	Chromosomal DSBs caused by replication fork disruption , environmental factors , or endogenous nucleases are common yet potentially dangerous DNA lesions in all organisms . If they are repaired by homologous recombination ( HR ) , the integrity of the genome is usually maintained . However , if the broken ends undergo ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair" ]	2008	Proofreading Activity of DNA Polymerase Pol2 Mediates 3′-End Processing during Nonhomologous End Joining in Yeast

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