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Chronic immune activation and progression to AIDS are observed after SIV infection in macaques but not in natural host primate species . To better understand this dichotomy , we compared acute pathogenic SIV infection in pigtailed macaques ( PTs ) to non-pathogenic infection in African green monkeys ( AGMs ) . SIVagm-i...	Natural infection by the simian immunodeficiency virus ( SIV ) in over 40 different species of African non-human primates is not accompanied by progression to acquired immunodeficiency syndrome ( AIDS ) . To understand this phenomenon , we have performed a detailed virologic , immunologic , and gene expression analysis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "immunology/immunity", "to", "infections", "virology/animal", "models", "of", "infection", "virology/host", "antiviral", "responses" ]	2009	Critical Loss of the Balance between Th17 and T Regulatory Cell Populations in Pathogenic SIV Infection
Cortical oscillations play a fundamental role in organizing large-scale functional brain networks . Noninvasive brain stimulation with temporally patterned waveforms such as repetitive transcranial magnetic stimulation ( rTMS ) and transcranial alternating current stimulation ( tACS ) have been proposed to modulate the...	Rhythms in the brain are believed to play an important role in cognition . Disruptions in these oscillations are associated with a number of neurological and psychiatric disorders . Therefore , noninvasive brain stimulation techniques that target these oscillations offer promise as therapeutic tools . In particular , t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "signal", "processing", "brain", "brain", "electrophysiology", "electrophysiology", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "transcranial", "alternating", "current",...	2016	Modulation of Cortical Oscillations by Low-Frequency Direct Cortical Stimulation Is State-Dependent
Bartonella bacilliformis is the causative agent of Carrion’s disease , a neglected illness with mortality rates of 40–85% in the absence of treatment . The lack of a diagnostic technique to overcome misdiagnosis and treat asymptomatic carriers is of note . This study aimed to identify new B . bacilliformis antigenic ca...	B . bacilliformis is a neglected pathogen causing Carrion’s disease , a febrile illness with two distinct phases , the acute so-called Oroya fever that can be life-threatening , and the chronic so-called Peruvian wart . This illness is currently limited to poor inhabitants of Andean valleys of Ecuador , Colombia and Pe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "body", "fluids", "pathogens", "immunology", "microbiology", "bacteria...	2016	Succinyl-CoA Synthetase: New Antigen Candidate of Bartonella bacilliformis
Recombinant KSAC and L110f are promising Leishmania vaccine candidates . Both antigens formulated in stable emulsions ( SE ) with the natural TLR4 agonist MPL® and L110f with the synthetic TLR4 agonist GLA in SE protected BALB/c mice against L . major infection following needle challenge . Considering the virulence of ...	Leishmaniasis is a neglected disease caused by the Leishmania parasite and transmitted by the bite of an infective sand fly . Despite the importance of this disease there is no vaccine available for humans . Studies have shown that vector-transmitted infections are more virulent , promoting parasite establishment and a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "immune", "cells", "proteins", "immunity", "immunology", "biology", "microbiology", "protozoology" ]	2012	KSAC, a Defined Leishmania Antigen, plus Adjuvant Protects against the Virulence of L. major Transmitted by Its Natural Vector Phlebotomus duboscqi
Three closely related bacterial species within the genus Neisseria are of importance to human disease and health . Neisseria meningitidis is a major cause of meningitis , while Neisseria gonorrhoeae is the agent of the sexually transmitted disease gonorrhea and Neisseria lactamica is a common , harmless commensal of ch...	The closely related bacterial species N . meningitidis , N . gonorrhoeae and N . lactamica exclusively colonise mucosal surfaces in humans . While N . gonorrhoeae leads to gonorrhea , the other two species persist mainly in their host in the absence of disease . N . meningitidis does occasionally cause severe , life th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "microbiology/microbial", "physiology", "and", "metabolism", "microbiology/microbial", "evolution", "and", "genomics", "microbiology", "microbiology/microbial", "growth", "and", "development" ]	2010	Structural Alterations in a Component of Cytochrome c Oxidase and Molecular Evolution of Pathogenic Neisseria in Humans
Sex differences in schizophrenia are well known , but their genetic basis has not been identified . We performed a genome-wide association scan for schizophrenia in an Ashkenazi Jewish population using DNA pooling . We found a female-specific association with rs7341475 , a SNP in the fourth intron of the reelin ( RELN ...	Schizophrenia is a complex mental disease , which includes symptoms of delusions , hallucinations , disorganized speech , aberrant behavior , lack of emotional expression , diminished motivation , and social withdrawal . The cause of schizophrenia is unknown , but there is extensive evidence that genetics play a signif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics", "neurological", "disorders" ]	2008	Genome-Wide Association Identifies a Common Variant in the Reelin Gene That Increases the Risk of Schizophrenia Only in Women
Staphylococcus aureus ( S . aureus ) pathogenesis is a complex process involving a diverse array of extracellular and cell wall components . ClfB , an MSCRAMM ( Microbial Surface Components Recognizing Adhesive Matrix Molecules ) family surface protein , described as a fibrinogen-binding clumping factor , is a key dete...	Staphylococcus aureus ( S . aureus ) , an important opportunistic pathogen , is a major threat to humans and animals , causing high morbidity and mortality worldwide . It is responsible for a variety of infections ranging from mild superficial infections to severe infections such as infective endocarditis , septic arth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "biology", "biophysics" ]	2012	Crystal Structures Reveal the Multi-Ligand Binding Mechanism of Staphylococcus aureus ClfB
Dietary , pharmacological and genetic interventions can extend health- and lifespan in diverse mammalian species . DNA methylation has been implicated in mediating the beneficial effects of these interventions; methylation patterns deteriorate during ageing , and this is prevented by lifespan-extending interventions . ...	Dietary , genetic and pharmacological interventions can extend lifespan in diverse organisms and represent good models for developing therapies against age-related diseases in humans . However , whether these longevity interventions act by slowing down the effects of ageing , or inducing novel phenotypes to cope better...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "dwarfism", "nucleotides", "organic", "compounds", "animal", "models", "model", "organisms", "methylation", "experimental", "organism", "systems", "pyrimidines", "epigenetics", "dna", "mammalian", "genomics...	2018	Hepatic gene body hypermethylation is a shared epigenetic signature of murine longevity
The forelimbs and hindlimbs of vertebrates are bilaterally symmetric . The mechanisms that ensure symmetric limb formation are unknown but they can be disrupted in disease . In Holt-Oram Syndrome ( HOS ) , caused by mutations in TBX5 , affected individuals have left-biased upper/forelimb defects . We demonstrate a role...	Externally , the human form appears bilaterally symmetric . For example , each of our pairs of arms and legs are the same length . This external symmetry masks many asymmetries found in internal organs . In most people the heart is found on the left side of the chest . The stomach , liver and spleen are also positioned...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "dna-binding", "proteins", "limbs", "(anatomy)", "thumbs", "somites", "animal", "models", "developmental", "biology", "model", "organisms", "organism", "development", "experimental", "organism", "systems", "embryos", "research", ...	2016	Tbx5 Buffers Inherent Left/Right Asymmetry Ensuring Symmetric Forelimb Formation
Mutations in genomes of species are frequently distributed non-randomly , resulting in mutation clusters , including recently discovered kataegis in tumors . DNA editing deaminases play the prominent role in the etiology of these mutations . To gain insight into the enigmatic mechanisms of localized hypermutagenesis th...	Genomes of tumors are heavily enriched with mutations . Some of these mutations are distributed non-randomly , forming mutational clusters . Editing cytosine deaminases from APOBEC superfamily are responsible for the formation of many of these clusters . We have expressed APOBEC enzyme in diploid yeast cells and found ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Disruption of Transcriptional Coactivator Sub1 Leads to Genome-Wide Re-distribution of Clustered Mutations Induced by APOBEC in Active Yeast Genes
Overfishing threatens the sustainability of coastal marine biodiversity , especially in tropical developing countries . To counter this problem , about 200 governments worldwide have committed to protecting 10%–20% of national coastal marine areas . However , associated impacts on fisheries productivity are unclear and...	Marine reserves are an important tool to conserve biodiversity but increasingly are relied upon also to benefit fisheries , specifically in diverse , unassessed , and otherwise unregulated systems . Whether the globally adopted Aichi Target 11 ( 10% “effective” protection of national coastal marine areas ) can help sus...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "ecology", "and", "environmental", "sciences", "biodiversity", "marine", "biology", "age", "groups", "developmental", "biology", "adults", "fisheries", "coral", "reefs", "marine", "and", "aquatic", "sciences", "life", "cycles", "reefs", "agriculture", "conservation", ...	2017	Marine Reserve Targets to Sustain and Rebuild Unregulated Fisheries
The whole-genome duplication ( WGD ) that occurred during yeast evolution changed the basal number of chromosomes from 8 to 16 . However , the number of chromosomes in post-WGD species now ranges between 10 and 16 , and the number in non-WGD species ( Zygosaccharomyces , Kluyveromyces , Lachancea , and Ashbya ) ranges ...	The number of chromosomes in organisms often changes over evolutionary time . To study how the number changes , we compare several related species of yeast that share a common ancestor roughly 150 million years ago and have varying numbers of chromosomes . By inferring ancestral genome structures , we examine the chang...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "telomeres", "genome", "evolution", "chromosome", "biology", "centromeres", "biology", "genomics", "comparative", "genomics", "genetics", "and", "genomics" ]	2011	Mechanisms of Chromosome Number Evolution in Yeast
Levels of G1 cyclins fluctuate in response to environmental cues and couple mitotic signaling to cell cycle entry . The G1 cyclin Cln3 is a key regulator of cell size and cell cycle entry in budding yeast . Cln3 degradation is essential for proper cell cycle control; however , the mechanisms that control Cln3 degradati...	Most cells only divide when they receive the proper cues . When a cell receives a signal to divide , levels of G1 cyclin proteins increase and drive entry into the cell division cycle . Overexpression of G1 cyclins can drive cells into the cell cycle inappropriately and thus may contribute to the hyperproliferation of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "molecular", "cell", "biology", "cell", "division", "cell", "biology", "genetics", "yeast", "and", "fungal", "models", "biology", "saccharomyces", "cerevisiae", "microbiology", "genetics", "and", "genomics", "cyclins" ]	2012	F-Box Protein Specificity for G1 Cyclins Is Dictated by Subcellular Localization
Information processing of the cerebellar granular layer composed of granule and Golgi cells is regarded as an important first step toward the cerebellar computation . Our previous theoretical studies have shown that granule cells can exhibit random alternation between burst and silent modes , which provides a basis of ...	Intensive studies of Pavlovian delay eyelid conditioning suggest that the cerebellum can memorize a passage-of-time ( POT ) from the onset of an external stimulus . To account for possible mechanisms of such POT representation , some network models have been proposed to show that granule cells ( grcs ) in the cerebella...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neural", "networks", "computational", "neuroscience", "biology", "neuroscience" ]	2011	Stimulus-Dependent State Transition between Synchronized Oscillation and Randomly Repetitive Burst in a Model Cerebellar Granular Layer
Meiotic recombination generates new genetic variation and assures the proper segregation of chromosomes in gametes . PRDM9 , a zinc finger protein with histone methyltransferase activity , initiates meiotic recombination by binding DNA at recombination hotspots and directing the position of DNA double-strand breaks ( D...	Sexually reproducing creatures need to produce germ cells , notably sperm and egg , and do so using a specialized cell division , termed meiosis . A hallmark of meiosis is the process of recombination , in which pieces of maternal and paternal genetic material are exchanged , creating new combinations that are inherite...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "genomics", "genetic", "polymorphism", "genome", "evolution", "chromosomal", "inheritance", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "molecular", "evolution", "computational", "biology", "evolutionary", ...	2015	PRDM9 Drives Evolutionary Erosion of Hotspots in Mus musculus through Haplotype-Specific Initiation of Meiotic Recombination
Phylogenetic trees are used to analyze and visualize evolution . However , trees can be imperfect datatypes when summarizing multiple trees . This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer , incomplete lineage sorting , and hybridization , as well as topologi...	Phylogenetic trees are the most common datatype by which we examine evolutionary patterns . However , biological and practical considerations require the exploration of other models . Here , we address a problem concerning the representation of conflicting and partially overlapping datasets in phylogenetics . We examin...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2013	Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs
CD8+ T-cell responses against latent viruses can cover considerable portions of the CD8+ T-cell compartment for many decades , yet their initiation and maintenance remains poorly characterized in humans . A key question is whether the clonal repertoire that is raised during the initial antiviral response can be maintai...	Several viruses have found ways to evade the human immune system and cause latent infections . Examples include HIV and herpes-viruses . Most humans carry these herpes-viruses . The human immune system mounts continuous responses against these viruses to prevent them from causing disease . If this balance is disturbed ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "immunity", "to", "infections", "immunology", "cytomegalovirus", "infection", "epstein-barr", "virus", "infectious", "mononucleosis", "adaptive", "immunity", "vaccination", "infectious", "diseases", "t", "cells", "clinical", "immunology", "i...	2012	Deep Sequencing of Antiviral T-Cell Responses to HCMV and EBV in Humans Reveals a Stable Repertoire That Is Maintained for Many Years
Visceral leishmaniasis ( VL ) is a life-threatening disease caused by protozoan parasites of the Leishmania donovani complex . Early case detection followed by adequate treatment is essential to the control of VL . However , the available diagnostic tests are either invasive and require considerable expertise ( parasit...	Visceral leishmaniasis is a neglected disease caused by different species of protozoan parasites of the genus Leishmania . The disease is endemic in 61 countries , and in many of them it poses a serious public health issue . As visceral leishmaniasis is fatal if left untreated , early diagnosis is essential for treatme...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Development of an Immunochromatographic Test for Diagnosis of Visceral Leishmaniasis Based on Detection of a Circulating Antigen
UBXN proteins likely participate in the global regulation of protein turnover , and we have shown that UBXN1 interferes with RIG-I-like receptor ( RLR ) signaling by interacting with MAVS and impeding its downstream effector functions . Here we demonstrate that over-expression of multiple UBXN family members decreased ...	A family of human genes termed UBXN is thought to control many cellular processes , including protein destruction . While working with these proteins , we noticed several profoundly blocked the production of human immunodeficiency virus ( HIV ) and other , similar viruses . We delved into the how this occurs , and it a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "vesicular", "stomatitis", "virus", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "293t", "cells", "pathogens", "biological", "cultures", ...	2017	Multiple UBXN family members inhibit retrovirus and lentivirus production and canonical NFκΒ signaling by stabilizing IκBα
Apicomplexan parasites cause devastating diseases including malaria and toxoplasmosis . They harbour a plastid-like , non-photosynthetic organelle of algal origin , the apicoplast , which fulfils critical functions for parasite survival . Because of its essential and original metabolic pathways , the apicoplast has bec...	Phosphatidyinositol 3-monophosphate ( PI3P ) is important for endocytic fusion events in eukaryotic cells . Despite the importance of this lipid in cell biology , its localization and function in apicomplexan parasites has not yet been extensively explored . In this study , we attribute for the first time a role for PI...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/parasitology" ]	2011	Phosphatidylinositol 3-Monophosphate Is Involved in Toxoplasma Apicoplast Biogenesis
The use of genetic data to reconstruct the transmission tree of infectious disease epidemics and outbreaks has been the subject of an increasing number of studies , but previous approaches have usually either made assumptions that are not fully compatible with phylogenetic inference , or , where they have based inferen...	With sequence data becoming available in increasing high volumes and at decreasing costs , there has been substantial recent interest in the possibility of using pathogen genome sequences as a means to retrace the spread of disease amongst the infected hosts in an epidemic . While several such methods exist , many of t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Epidemic Reconstruction in a Phylogenetics Framework: Transmission Trees as Partitions of the Node Set
Mycobacterium tuberculosis employs various virulence strategies to subvert host immune responses in order to persist and cause disease . Interaction of M . tuberculosis with mannose receptor on macrophages via surface-exposed lipoarabinomannan ( LAM ) is believed to be critical for cell entry , inhibition of phagosome-...	Mycobacterium tuberculosis is among the leading infectious causes of human death . A better understanding of its virulence mechanisms is needed to facilitate development of novel therapeutics and a preventative vaccine . Lipoarabinomannan ( LAM ) , an abundant surface-exposed lipoglycan , is believed to be a critical v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "diseases", "infectious", "diseases", "tuberculosis", "medicine", "and", "health", "sciences" ]	2014	LprG-Mediated Surface Expression of Lipoarabinomannan Is Essential for Virulence of Mycobacterium tuberculosis
Epigenetic regulatory mechanisms and their enzymes are promising targets for malaria therapeutic intervention; however , the epigenetic component of gene expression in P . falciparum is poorly understood . Dynamic or stable association of epigenetic marks with genomic features provides important clues about their funct...	Plasmodium falciparum is a unicellular pathogen that is responsible for the most severe form of malaria . Similar to other eukaryotic organisms , its genome is organized into chromosomes by proteins called histones . Modification or replacement of these histones has marked effects on the packaging grade of DNA and inst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/neglected", "tropical", "diseases", "microbiology/parasitology", "genetics", "and", "genomics/epigenetics", "molecular", "biology/translational", "regulation" ]	2010	H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3
Peptides presentation to T cells by MHC class II molecules is of importance in initiation of immune response to a pathogen . The level of MHC II expression directly influences T lymphocyte activation and is often targeted by various viruses . Kaposi's sarcoma-associated herpesvirus ( KSHV ) encoded LANA is known to eva...	Major histocompatibility complex ( MHC ) class II is critical for eliciting specific adaptive immune responses against a wide range of pathogenic agents . KSHV as a member of the herpesvirus family has been shown to encode viral proteins for deregulation of the MHC II signaling pathway . In this study , we discovered t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	IRF-4-Mediated CIITA Transcription Is Blocked by KSHV Encoded LANA to Inhibit MHC II Presentation
In mammals , the liver plays a central role in maintaining carbohydrate and lipid homeostasis by acting both as a major source and a major sink of glucose and lipids . In particular , when dietary carbohydrates are in excess , the liver converts them to lipids via de novo lipogenesis . The molecular checkpoints regulat...	After a meal , dietary glucose travels through the hepatic portal vein to the liver . A substantial part of this glucose is taken up by liver , which converts it to glycogen which is stored , and lipids which are in part stored and in part secreted as VLDL particles . The rest of the organs receive whatever glucose the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	PPP2R5C Couples Hepatic Glucose and Lipid Homeostasis
Extraparenchymal neurocysticercosis has an aggressive course because cysts in the cerebrospinal fluid compartments induce acute inflammatory reactions . The relationships between symptoms , imaging findings , lesion type and location remain poorly understood . In this retrospective clinical records-based study , we des...	Neurocysticercosis is caused by the accidental ingestion of eggs from Taenia solium whose larvae lodge in the central nervous system . In this study we found that cysts within the cerebrospinal fluid leaded to high rates of raised intracranial pressure , meningitis , seizures and headache . Imaging studies such as magn...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "inflammatory", "diseases", "medicine", "and", "health", "sciences", "body", "fluids", "diagnostic", "radiology", "pathology", "and", "laboratory", "medicine", "neurocysticercosis", "nervous", "system", "tropical", "diseases", "parasitic", "diseases", "migraine", "headach...	2016	Clinical Symptoms, Imaging Features and Cyst Distribution in the Cerebrospinal Fluid Compartments in Patients with Extraparenchymal Neurocysticercosis
Many proteins comprising of complex topologies require molecular chaperones to achieve their unique three-dimensional folded structure . The E . coli chaperone , GroEL binds with a large number of unfolded and partially folded proteins , to facilitate proper folding and prevent misfolding and aggregation . Although the...	Several non-native proteins require molecular chaperones for proper folding . Many unfolded proteins if not folded accurately , become causal factors in various types of misfolding or aggregation induced diseases such as Alzheimer′s , Huntington′s and several other neurodegenerative disorders . However , structural inf...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results" ]	[]	2015	Decoding Structural Properties of a Partially Unfolded Protein Substrate: En Route to Chaperone Binding
The voltage-sensitive sodium ( Na+ ) channel ( Vssc ) is the target site of pyrethroid insecticides . Pest insects develop resistance to this class of insecticide by acquisition of one or multiple amino acid substitution ( s ) in this channel . In Southeast Asia , two major Vssc types confer pyrethroid resistance in th...	Pyrethroids are one of the major classes of insecticides that is widely used to control mosquito vectors . The target site of pyrethroids is found in the voltage-sensitive Na+ channel ( Vssc ) consisting of about 2100 amino acid residues . In this study we generated several types of Vssc with a single or multiple mutat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neurotoxicology", "dengue", "virus", "medicine", "and", "health", "sciences", "flaviviruses", "viral", "transmission", "and", "infection", "medical", "microbiology", "virology", "viral", "pathogens", "entomology", "microbial", "pathogens", "epidemiology", "biology", "and...	2014	A Single Crossing-Over Event in Voltage-Sensitive Na+ Channel Genes May Cause Critical Failure of Dengue Mosquito Control by Insecticides
Metanephric kidney induction critically depends on mesenchymal–epithelial interactions in the caudal region of the nephric ( or Wolffian ) duct . Central to this process , GDNF secreted from the metanephric mesenchyme induces ureter budding by activating the Ret receptor expressed in the nephric duct epithelium . A fai...	In humans , kidney development originates during embryonic development by the sprouting of an epithelial bud—called the ureteric bud—from a simple epithelial structure—the nephric duct . The ureteric bud quickly grows and branches in a treelike fashion to form the kidney collecting duct system , while the emerging uret...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "developmental", "biology/cell", "differentiation", "nephrology/hereditary,", "genetic,", "and", "development", "nephrology", "developmental", "biology/organogenesis", "developmental", "biology/developmental", "molecular", "mechanisms", "cell", ...	2008	Gata3 Acts Downstream of β-Catenin Signaling to Prevent Ectopic Metanephric Kidney Induction
Amino acid sensing is an intracellular function that supports nutrient homeostasis , largely through controlled release of amino acids from lysosomal pools . The intracellular pathogen Leishmania resides and proliferates within human macrophage phagolysosomes . Here we describe a new pathway in Leishmania that specific...	Protozoa of the genus Leishmania are the causative agents of leishmaniasis in humans . These parasites cycle between promastigotes in the sand fly mid-gut and amastigotes in phagolysosome of mammalian macrophages . During infection , host cells up-regulate nitric oxide while/or parasites induce expression of host argin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "chemical", "compounds", "enzymes", "immunology", "microbiology", "enzymology", "parasitic", "diseases", "protozoan", "life", "cycles", "organic", "compounds", "parasitic", "protozoans", "deve...	2016	An Arginine Deprivation Response Pathway Is Induced in Leishmania during Macrophage Invasion
The protozoan Giardia lamblia differentiates into infectious cysts within the human intestinal tract for disease transmission . Expression of the cyst wall protein ( cwp ) genes increases with similar kinetics during encystation . However , little is known how their gene regulation shares common mechanisms . DNA topois...	Giardia lamblia becomes infective by differentiation into water-resistant cysts . During encystation , cyst wall proteins ( CWPs ) are highly synthesized and are targeted to the cyst wall . However , little is known about the regulation mechanisms of these genes . DNA topoisomerases can resolve the topological problems...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "developmental", "biology", "molecular", "cell", "biology", "chromosome", "biology", "chromosome", "structure", "and", "function", "gene", "expression", "parasitology", "protozoology", "microbial", "growth", "and", "development", "biology", "micr...	2013	DNA Topoisomerase II Is Involved in Regulation of Cyst Wall Protein Genes and Differentiation in Giardia lamblia
Knowledge about the distribution of mutational fitness effects ( DMFE ) is essential for many evolutionary models . In recent years , the properties of the DMFE have been carefully described for some microorganisms . In most cases , however , this information has been obtained only for a single environment , and very f...	Mutations are the raw material on which natural selection operates to optimize the fitness of populations . The occurrence of selection and its strength depend on the effect that mutations may have on the survival and reproduction of individuals: mutations can be lethal , deleterious , neutral , or beneficial . Thus , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "theoretical", "biology", "virology", "emerging", "viral", "diseases", "biology", "evolutionary", "biology", "microbiology", "host-pathogen", "interaction", "evolutionary", "genetics", "viral", "evolution" ]	2011	Effect of Host Species on the Distribution of Mutational Fitness Effects for an RNA Virus
Penetration of a male copulatory organ into a suitable mate is a conserved and necessary behavioral step for most terrestrial matings; however , the detailed molecular and cellular mechanisms for this distinct social interaction have not been elucidated in any animal . During mating , the Caenorhabditis elegans male cl...	Animal behaviors are generated when a sequence of muscle movements is coordinated by neural circuits . In complex invertebrates or lab-studied vertebrates , due to the large number of cells in their nervous systems and the complexities of their behaviors , it is difficult to address how circuits process information to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/sensory", "systems", "neuroscience/motor", "systems" ]	2011	A Cholinergic-Regulated Circuit Coordinates the Maintenance and Bi-Stable States of a Sensory-Motor Behavior during Caenorhabditis elegans Male Copulation
Post-transcriptional regulation is regarded as one of the major processes involved in the regulation of gene expression . It is mainly performed by RNA binding proteins and microRNAs , which target RNAs and typically affect their stability . Recent efforts from the scientific community have aimed at understanding post-...	All the cells in a given organism contain the same genome , yet their phenotype can be very diverse . The vast majority of this diversity arises from the differences in the expression of genes and proteins in them . One of the main mechanisms involved in controlling the protein and mRNA repertoire in cells is post-tran...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rna-binding", "proteins", "chemical", "characterization", "gene", "regulation", "messenger", "rna", "regulator", "genes", "micrornas", "post-transcriptional", "gene", "regulation", "gene", "types", "sequence", "motif", "analysis", "research", "and", "analysis", "methods"...	2017	Highly accessible AU-rich regions in 3’ untranslated regions are hotspots for binding of regulatory factors
Mobile group II introns retrohome by an RNP-based mechanism in which the intron RNA reverse splices into a DNA site and is reverse transcribed by the associated intron-encoded protein . The resulting intron cDNA is then integrated into the genome by cellular mechanisms that have remained unclear . Here , we used an Esc...	Mobile group II introns are bacterial retrotransposons that are evolutionarily related to introns and retroelements in higher organisms . They spread within and between genomes by a mechanism termed “retrohoming” in which the intron RNA inserts directly into a DNA site and is reverse transcribed by an intron-encoded re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "transposons", "retrotransposons", "dna", "replication", "nucleic", "acids", "genetics", "molecular", "genetics", "dna", "biology", "molecular", "cell", "biology", "rna", "stability" ]	2013	Genetic and Biochemical Assays Reveal a Key Role for Replication Restart Proteins in Group II Intron Retrohoming
In case-control studies , genetic associations for complex diseases may be probed either with single-locus tests or with haplotype-based tests . Although there are different views on the relative merits and preferences of the two test strategies , haplotype-based analyses are generally believed to be more powerful to d...	Methods of haplotype-based analysis and single-locus analysis are widely used in genetic association studies . There is no consensus as to the best strategy for the performance of the two methods . Although haplotype-based analysis is a powerful tool , the large number of distinct haplotypes may reduce its efficiency ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "haplotype", "cladistic", "analysis", "case", "control", "studies" ]	2007	Incorporating Single-Locus Tests into Haplotype Cladistic Analysis in Case-Control Studies
Adenovirus ( AdV ) morphogenesis is a complex process , many aspects of which remain unclear . In particular , it is not settled where in the nucleus assembly and packaging occur , and whether these processes occur in a sequential or a concerted manner . Here we use immunofluorescence and immunoelectron microscopy ( im...	Viruses assemble in particular locations inside infected cells where newly replicated genomes and capsids proteins meet , called viral factories . Virus genomes are packaged inside capsids by one of two mechanisms: concerted , where a protein shell is built around the genome , or sequential , where the genome is pumped...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "viral", "structure", "viruses", "dna", "replication", "dna", "viruses", "molecular", "biology", "techniques", "dna", "microbial", ...	2017	Localization of adenovirus morphogenesis players, together with visualization of assembly intermediates and failed products, favor a model where assembly and packaging occur concurrently at the periphery of the replication center
The heart and head muscles share common developmental origins and genetic underpinnings in vertebrates , including humans . Parts of the heart and cranio-facial musculature derive from common mesodermal progenitors that express NKX2-5 , ISL1 , and TBX1 . This ontogenetic kinship is dramatically reflected in the DiGeorg...	Mutations in the regulatory genes encoding the transcription factors NKX2-5 and TBX1 , which govern heart and head muscle development , cause prevalent congenital defects . Recent studies using vertebrate models have shown that the heart and pharyngeal head muscle cells derive from common progenitors in the early embry...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	NK4 Antagonizes Tbx1/10 to Promote Cardiac versus Pharyngeal Muscle Fate in the Ascidian Second Heart Field
Mammalian cells rely on cellular uptake of the essential amino acid tryptophan . Tryptophan sequestration by up-regulation of the key enzyme for tryptophan degradation , indoleamine 2 , 3-dioxygenase ( IDO ) , e . g . , in cancer and inflammation , is thought to suppress the immune response via T cell starvation . Addi...	Although regulated suppression of the immune system prevents autoimmunity and is important during pregnancy to protect the fetus or after organ transplant to block graft rejection , it can be harmful if co-opted by tumors to escape detection . T cells of the immune system normally recognize and destroy abnormal cells ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biotechnology", "biochemistry", "cell", "biology", "physiology", "immunology" ]	2007	Nanosensor Detection of an Immunoregulatory Tryptophan Influx/Kynurenine Efflux Cycle
The initiation and propagation of action potentials ( APs ) places high demands on the energetic resources of neural tissue . Each AP forces ATP-driven ion pumps to work harder to restore the ionic concentration gradients , thus consuming more energy . Here , we ask whether the ionic currents underlying the AP can be p...	Neurons produce a myriad of action potentials with different shapes and varying heights and widths; underlying these action potentials are highly nonlinear , voltage-dependent ionic conductances with varying biophysical properties . Each action potential comes at a cost: the brain uses a substantial portion of its tota...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "mathematics", "biophysics/theory", "and", "simulation", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	Action Potential Energy Efficiency Varies Among Neuron Types in Vertebrates and Invertebrates
Mu is both a transposable element and a temperate bacteriophage . During lytic growth , it amplifies its genome by replicative transposition . During infection , it integrates into the Escherichia coli chromosome through a mechanism not requiring extensive DNA replication . In the latter pathway , the transposition int...	Transposon activity shapes genome structure and evolution . The movement of these elements generates target site duplications as a result of staggered cuts in the target made initially by the transposase . For replicative transposons , the single-stranded gaps generated after the initial strand transfer event are fille...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Mu Insertions Are Repaired by the Double-Strand Break Repair Pathway of Escherichia coli
The Rim101/PacC transcription factor acts in a fungal-specific signaling pathway responsible for sensing extracellular pH signals . First characterized in ascomycete fungi such as Aspergillus nidulans and Saccharomyces cerevisiae , the Rim/Pal pathway maintains conserved features among very distantly related fungi , wh...	Microorganisms that cause human disease use various cues to determine when they encounter a host . One of these signals is the slightly alkaline pH of human tissues . We have defined components of a pH-responsive signaling pathway in the human fungal pathogen Cryptococcus neoformans . This particular signaling pathway ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Cryptococcus neoformans Alkaline Response Pathway: Identification of a Novel Rim Pathway Activator
Following infection , virulent mycobacteria persist and grow within the macrophage , suggesting that the intrinsic activation of an innate antimicrobial response is subverted by the intracellular pathogen . For Mycobacterium leprae , the intracellular bacterium that causes leprosy , the addition of exogenous innate or ...	Our macrophages are equipped with the ability to detect and kill invading pathogens , and yet , these cells of the innate immune system are still subject to infection by intracellular bacterium . In particular , mycobacterium , the type of intracellular bacteria responsible for diseases such as tuberculosis and leprosy...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "immune", "cells", "chemical", "compounds", "immunology", "tropical", "diseases", "organic", "compounds", "bacterial", "diseases", "neglected", "tropical", "diseases", "bacteria", "inf...	2018	Intrinsic activation of the vitamin D antimicrobial pathway by M. leprae infection is inhibited by type I IFN
c-di-AMP is an important second messenger molecule that plays a pivotal role in regulating fundamental cellular processes , including osmotic and cell wall homeostasis in many Gram-positive organisms . In the opportunistic human pathogen Staphylococcus aureus , c-di-AMP is produced by the membrane-anchored DacA enzyme ...	c-di-AMP has recently emerged as an essential molecule in Gram-positive bacteria , controlling osmotic stress resistance and virulence . The molecule has also been linked to antibiotic resistance/sensitivity , as alterations in its levels have been shown to modulate the effect of cell wall-targeting antibiotics . c-di-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "condensed", "matter", "physics", "microbiology", "enzymology", "staphylococcus", "aureus", "pseudomonas", "aeruginosa", "materials", "sc...	2019	Inhibition of the Staphylococcus aureus c-di-AMP cyclase DacA by direct interaction with the phosphoglucosamine mutase GlmM
Comparisons of the DNA sequences of metazoa show an excess of transitional over transversional substitutions . Part of this bias is due to the relatively high rate of mutation of methylated cytosines to thymine . Postmutation processes also introduce a bias , particularly selection for codon-usage bias in coding region...	Some mutations occur more frequently than others . We need to understand these biases if we are to interpret the differences that have accumulated between species and individuals . Applications include estimating the time since evolutionary lineages diverged and detecting the signature of natural selection in DNA seque...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "insects" ]	2007	Transition-Transversion Bias Is Not Universal: A Counter Example from Grasshopper Pseudogenes
Virulent biofilms are responsible for a range of infections , including oral diseases . All biofilms harbor a microbial-derived extracellular-matrix . The exopolysaccharides ( EPS ) formed on tooth-pellicle and bacterial surfaces provide binding sites for microorganisms; eventually the accumulated EPS enmeshes microbia...	Virulent biofilms formed on surfaces are associated with many human infections . The disease dental caries , expressed as cavities , is a prime example of the consequences arising from interactions between bacteria and sugars on tooth-surfaces . When Streptococcus mutans metabolize sugars , they produce a glue-like pol...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "bacterial", "diseases", "infectious", "diseases", "oral", "medicine", "biology", "microbiology", "bacterial", "pathogens" ]	2012	The Exopolysaccharide Matrix Modulates the Interaction between 3D Architecture and Virulence of a Mixed-Species Oral Biofilm
Identifying driver mutations and their functional consequences is critical to our understanding of cancer . Towards this goal , and because domains are the functional units of a protein , we explored the protein domain-level landscape of cancer-type-specific somatic mutations . Specifically , we systematically examined...	Extensive tumor genome sequencing has provided raw material to understand mutational processes and identify cancer-associated somatic variants . However , fundamental problems remain to: i ) separate ‘driver’ from ‘passenger’ mutations , ii ) further understand the functional mechanisms and consequences of driver mutat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Protein Domain-Level Landscape of Cancer-Type-Specific Somatic Mutations
The loss of functional redundancy is the key process in the evolution of duplicated genes . Here we systematically assess the extent of functional redundancy among a large set of duplicated genes in Saccharomyces cerevisiae . We quantify growth rate in rich medium for a large number of S . cerevisiae strains that carry...	Gene duplication is the primary source of new genes . To persist , duplicated genes must lose some of the original redundancy either by partitioning the ancestral function ( subfunctionalization ) or by gaining new non-redundant functions ( neofunctionalization ) . The extent to which these processes shape the evolutio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/functional", "genomics", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics" ]	2008	Pervasive and Persistent Redundancy among Duplicated Genes in Yeast
The coagulation system is characterized by the sequential and highly localized activation of a series of serine proteases , culminating in the conversion of fibrinogen into fibrin , and formation of a fibrin clot . Here we show that C-terminal peptides of thrombin , a key enzyme in the coagulation cascade , constitute ...	Wounding of the skin and other epithelial barriers represents an ever-present challenge and poses a potential threat for invasive infection and sepsis . Therefore , it is not surprising that evolutionary pressure has maintained and developed multiple host defense systems , involving initial hemostasis and fibrin format...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dermatology", "infectious", "diseases", "immunology", "microbiology" ]	2010	Proteolysis of Human Thrombin Generates Novel Host Defense Peptides
Neurological involvement occurs throughout the leprosy clinical spectrum and is responsible for the most feared consequences of the disease . Ultrasonography ( US ) provides objective measurements of nerve thickening and asymmetry . We examined leprosy patients before beginning multi-drug therapy aiming to describe dif...	Leprosy is an infectious disease that affects the peripheral nerves , leading to nerve thickening , asymmetry and dysfunction; therefore , early detection of leprosy neuropathy is important for preventing deformities and disabilities . We examined peripheral nerve involvement using ultrasonography ( US ) in 96 leprosy ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Asymmetric Nerve Enlargement: A Characteristic of Leprosy Neuropathy Demonstrated by Ultrasonography
Cholera toxin ( CT ) enters and intoxicates host cells after binding cell surface receptors via its B subunit ( CTB ) . We have recently shown that in addition to the previously described binding partner ganglioside GM1 , CTB binds to fucosylated proteins . Using flow cytometric analysis of primary human jejunal epithe...	The disease cholera , caused by cholera toxin produced by Vibrio cholerae , is responsible for over 100 000 deaths every year . When taken up by cells in the intestine , the toxin causes diarrhea , and the ganglioside GM1 ( a glycolipid ) has long been considered the main receptor for cholera toxin . We here present da...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "blood", "cells", "cell", "physiology", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "epithelial", "cells", "granulocytes", "glycoproteins", "digestive", "system", "research", "and", "analysis", "met...	2018	GM1 ganglioside-independent intoxication by Cholera toxin
This report presents a systematic review of scientific literature published between 1990–2010 relating to the frequency of human brucellosis , commissioned by WHO . The objectives were to identify high quality disease incidence data to complement existing knowledge of the global disease burden and , ultimately , to con...	Brucellosis is a bacterial disease transmitted to humans by consumption of infected , unpasteurised animal milk or through direct contact with infected animals , particularly aborted foetuses . The livestock production losses resulting from these abortions have a major economic impact on individuals and communities . I...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "veterinary", "epidemiology", "epidemiology", "public", "health", "veterinary", "science" ]	2012	Global Burden of Human Brucellosis: A Systematic Review of Disease Frequency
Genotypic variation , environmental variation , and their interaction may produce variation in the developmental process and cause phenotypic differences among individuals . Developmental noise , which arises during development from stochasticity in cellular and molecular processes when genotype and environment are fix...	The observable characteristics of an organism make up its phenotype . Variation among phenotypes is due to genetic differences , environmental factors and developmental noise ( effects due to inherent stochasticity ) during development . We used mathematical models to investigate the contributions of variation of the d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "population", "genetics", "vertebrates", "animals", "mammals", "simulation", "and", "modeling", "developmental", "biology", "morphometry", "molecular", "development", "population", "biology", "morphogenesis", "pattern", "formation", "research", "and", "analysis", "methods",...	2019	Isolating and quantifying the role of developmental noise in generating phenotypic variation
Protein–protein interaction ( PPI ) networks are commonly explored for the identification of distinctive biological traits , such as pathways , modules , and functional motifs . In this respect , understanding the underlying network structure is vital to assess the significance of any discovered features . We recently ...	A protein–protein interaction network represents the set of pair-wise associations that have been discerned between the constituent proteins of an organism . There are three main types of such networks: ( i ) those determined from a single high-throughput experiment; ( ii ) curated , where interactions are compiled fro...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics", "computer", "science", "computational", "biology" ]	2008	Probing the Extent of Randomness in Protein Interaction Networks
Organogenesis requires coordinated regulation of cellular differentiation and morphogenesis . Cartilage cells in the vertebrate skeleton form polarized stacks , which drive the elongation and shaping of skeletal primordia . Here we show that an atypical cadherin , Fat3 , and its partner Dachsous-2 ( Dchs2 ) , control p...	Little is known about the mechanisms of cell-cell communication necessary to assemble skeletal elements of appropriate size and shape . In this study , we investigate the roles of genetic factors belonging to a developmental pathway that affects skeletal progenitor behavior: the atypical cadherins Fat3 and Dachsous2 ( ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "embryology", "developmental", "biology", "biology", "and", "life", "sciences", "morphogenesis", "cell", "differentiation" ]	2014	Fat-Dachsous Signaling Coordinates Cartilage Differentiation and Polarity during Craniofacial Development
Messenger RNA acts as an informational molecule between DNA and translating ribosomes . Emerging evidence places mRNA in central cellular processes beyond its major function as informational entity . Although individual examples show that specific structural features of mRNA regulate translation and transcript stabilit...	Messenger RNA ( mRNA ) is intrinsically prone to form higher order structures which is optimized for mRNA stability in the cell . We took advantage of recent developments in high throughput sequencing technologies and coupled them with RNA structure-probing approaches to provide a high resolution view of the mRNA secon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Secondary Structure across the Bacterial Transcriptome Reveals Versatile Roles in mRNA Regulation and Function
The poly ( A ) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export , stability and translational efficiency , and changes in its length can strongly impact gene expression . The Arabidopsis thaliana genome encodes three canonical nuclear poly ( A ) polymerases , PAPS1 , PAPS2 and PAPS4 . As shown by their...	The poly ( A ) tail of eukaryotic mRNAs promotes export from the nucleus , translation in the cytoplasm and stability of the mRNA , and changes in poly ( A ) -tail length can strongly impact on gene expression . The Arabidopsis thaliana genome encodes three nuclear canonical poly ( A ) polymerases ( PAPS1 , PAPS2 , PAP...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Wide Analysis of PAPS1-Dependent Polyadenylation Identifies Novel Roles for Functionally Specialized Poly(A) Polymerases in Arabidopsis thaliana
An isolate of the methicillin-resistant Staphylococcus aureus ( MRSA ) clone USA300 with reduced susceptibility to vancomycin ( SG-R ) ( i . e , vancomycin-intermediate S . aureus , VISA ) and its susceptible “parental” strain ( SG-S ) were recovered from a patient at the end and at the beginning of an unsuccessful van...	The extensive use of antibiotics has led to the selection of methicillin-resistant S . aureus ( MRSA ) strains that are resistant to most antimicrobial agents and a treatment of choice against such strains is vancomycin . However , during the last decade reports of treatment failure with vancomycin non-susceptible MRSA...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "evolutionary", "biology" ]	2012	Genetic Pathway in Acquisition and Loss of Vancomycin Resistance in a Methicillin Resistant Staphylococcus aureus (MRSA) Strain of Clonal Type USA300
Stochastic signals with pronounced oscillatory components are frequently encountered in neural systems . Input currents to a neuron in the form of stochastic oscillations could be of exogenous origin , e . g . sensory input or synaptic input from a network rhythm . They shape spike firing statistics in a characteristic...	We explore how a neuron responds to a special type of input signal which is oscillatory but noisy ( narrow-band noise ) . These fluctuations could be due to sensory input , due to oscillatory activity of a surrounding network , or due to a natural stimulus . We study theoretically the effects of noisy oscillations on a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "single", "neuron", "function", "sensory", "systems", "biology", "neuroscience" ]	2013	Characteristic Effects of Stochastic Oscillatory Forcing on Neural Firing: Analytical Theory and Comparison to Paddlefish Electroreceptor Data
The study of endemic dengue transmission is essential for proposing alternatives to impact its burden . The traditional paradigm establishes that transmission starts around cases , but there are few studies that determine the risk . To assess the association between the peridomestic dengue infection and the exposure to...	The study of dengue transmission is essential for proposing alternatives to diminish the cases and the cost of dengue treatment and control . The traditional paradigm establishes that transmission chain starts around a case , but there are few studies that determine the risk , therefore , we studied if to live around a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Peridomestic Infection as a Determining Factor of Dengue Transmission
Learning complex ordering relationships between sensory events in a sequence is fundamental for animal perception and human communication . While it is known that rhythmic sensory events can entrain brain oscillations at different frequencies , how learning and prior experience with sequencing relationships affect neoc...	While natural environments constantly change , certain events can predict the future occurrence of others . Learning ordering relationships is vital for animal perception and human communication , yet how such learning and prior experience affect the brain remains poorly understood . We set out to understand how learni...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "auditory", "cortex", "acoustics", "medicine", "and", "health", "sciences", "linguistics", "brain", "vertebrates", "social", "sciences", "neuroscience", "animals", "mammals", "primates", "computational", "neuroscience", "old", "world", "monkeys", "research", "and", "ana...	2017	Sequence learning modulates neural responses and oscillatory coupling in human and monkey auditory cortex
In vivo two-photon microscopy was used to image in real time dendrites and their spines in a mouse photothrombotic stroke model that reduced somatosensory cortex blood flow in discrete regions of cortical functional maps . This approach allowed us to define relationships between blood flow , cortical structure , and fu...	The brain is critically dependent on an adequate supply of energy as it consumes up to 20% of the oxygen we breathe . Here we determine the distance scale over which interruptions in blood flow affect synaptic hard wiring and brain function . High-resolution microscopy of live mice was used to image cerebral cortex syn...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders", "mus", "(mouse)", "radiology", "and", "medical", "imaging", "neuroscience", "hematology", "cardiovascular", "disorders" ]	2007	Imaging the Impact of Cortical Microcirculation on Synaptic Structure and Sensory-Evoked Hemodynamic Responses In Vivo
Using human brain microvascular endothelial cells ( HBMECs ) as an in vitro model for how African trypanosomes cross the human blood-brain barrier ( BBB ) we recently reported that the parasites cross the BBB by generating calcium activation signals in HBMECs through the activity of parasite cysteine proteases , partic...	Human African trypanosomiasis , or sleeping sickness , occurs when single-cell trypanosome protozoan parasites spread from the blood to brain over the blood-brain barrier ( BBB ) . This barrier is composed of brain microvascular endothelial cells ( BMECs ) especially designed to keep pathogens out . Safe drugs for trea...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2009	Protease Activated Receptor Signaling Is Required for African Trypanosome Traversal of Human Brain Microvascular Endothelial Cells
Recent technological advancements have made time-resolved , quantitative , multi-omics data available for many model systems , which could be integrated for systems pharmacokinetic use . Here , we present large-scale simulation modeling ( LASSIM ) , which is a novel mathematical tool for performing large-scale inferenc...	There are excellent methods to mathematically model time-resolved biological data on a small scale using accurate mechanistic models . Despite the rapidly increasing availability of such data , mechanistic models have not been applied on a genome-wide level due to excessive runtimes and the non-identifiability of model...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Data", "access" ]	[ "blood", "cells", "t", "helper", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "immunology", "cell", "differentiation", "optimization", "developmental", "biology", "regulator", "genes", "mathematics", "genome", "analysis", ...	2017	LASSIM—A network inference toolbox for genome-wide mechanistic modeling
Dynamic models in disease ecology have historically evaluated vaccination strategies under the assumption that they are implemented homogeneously in space and time . However , this approach fails to formally account for operational and logistical constraints inherent in the distribution of vaccination to the population...	It has long been recognized that an epidemic of infectious disease can be prevented if a sufficient proportion of the susceptible population is vaccinated in advance . This logic also holds for vaccine-based outbreak response to stop an outbreak of a novel , or re-emerging pathogen , but with an important caveat . If v...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "vaccines", "public", "and", "occupational", "health", "preventive", "medicine", "population", "metrics", "infectious", "diseases", "medicine", "and", "health", "sciences", "cholera", "vaccines", "immunity", "epidemiology", "disease", "dynamics", "biology", "and", "life...	2018	Logistical constraints lead to an intermediate optimum in outbreak response vaccination
During mammalian development , left-right ( L-R ) asymmetry is established by a cilia-driven leftward fluid flow within a midline embryonic cavity called the node . This ‘nodal flow’ is detected by peripherally-located crown cells that each assemble a primary cilium which contain the putative Ca2+ channel PKD2 . The in...	Vertebrates exhibit left-right ( L-R ) asymmetry in positioning and patterning their internal organs and associated vasculature; abnormal L-R asymmetry can result in birth defects such as congenital heart disease . The earliest known event in mammalian L-R patterning is a leftward fluid flow across a transient embryoni...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "classical", "mechanics", "fluid", "mechanics", "population", "genetics", "social", "sciences", "neuroscience", "isomerism", "developmental", "biology", "mutation", "population", "biology", "embryos", "cellular", "structures", "and", "organelles", "embryology", "chemistry",...	2016	Genetic Analysis Reveals a Hierarchy of Interactions between Polycystin-Encoding Genes and Genes Controlling Cilia Function during Left-Right Determination
Many human parasites and pathogens have closely related counterparts among non-human primates . For example , non-human primates harbour several species of malaria causing parasites of the genus Plasmodium . Studies suggest that for a better understanding of the origin and evolution of human malaria parasites it is imp...	Non-human primates are our closest relatives and with them we share many of our disease-causing pathogens . Malaria is one such example where the parasite ( Plasmodium ) causing malaria in humans has originated from non-human primate populations . To understand origin and evolution of human malaria parasites it is impo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "taxonomy", "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "tropical", "diseases", "geographical", "locations", "vertebrates", "india", "parasitic", "diseases", "parasitic", "protozoans", "animals", "mammals", "parasitology", "primates", "api...	2018	Reinvestigating the status of malaria parasite (Plasmodium sp.) in Indian non-human primates
Heterozygous mutations in the tumor suppressor BRCA2 confer a high risk of breast and other cancers in humans . BRCA2 maintains genome stability in part through the regulation of Rad51-dependent homologous recombination . Much about its precise function in the DNA damage responses is , however , not yet known . We have...	Breast cancer can arise due to inherited mutations in a few well-defined breast cancer susceptibility genes . BRCA2 is one of two known human genes in which common mutations are associated with high breast cancer risk . A known function of BRCA2 is the repair of damaged DNA using the homologous recombination repair pat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "cell", "biology", "molecular", "biology", "drosophila", "genetics", "and", "genomics" ]	2008	Drosophila brca2 Is Required for Mitotic and Meiotic DNA Repair and Efficient Activation of the Meiotic Recombination Checkpoint
Helicobacter pylori ( Hp ) intimately interacts with the gastric epithelial surface and translocates the virulence factor CagA into host cells in a contact-dependent manner . To study how Hp benefits from interacting with the cell surface , we developed live-cell microscopy methods to follow the fate of individual bact...	Helicobacter pylori ( Hp ) is a bacterium that chronically infects the human stomach , in some cases leading to diseases such as stomach cancer and ulcers . The bacteria live in close proximity to the epithelial lining and can adhere directly to the host cell membrane and deliver toxins . We utilized live-cell imaging ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis" ]	2009	Helicobacter pylori Usurps Cell Polarity to Turn the Cell Surface into a Replicative Niche
Heat-shock protein 90 ( Hsp90 ) inhibitors exhibit activity against human cancers . We evaluated a series of new , oral bioavailable , chemically diverse Hsp90 inhibitors ( PU-H71 , AUY922 , BIIB021 , NVP-BEP800 ) against Kaposi sarcoma ( KS ) . All Hsp90 inhibitors exhibited nanomolar EC50 in culture and AUY922 reduce...	Heat shock proteins , such as Hsp90 , aid the folding of proteins . They seem to be essential to sustain the growth of cancer cells . Hsp90 inhibitors are in clinical trials for many cancers but with mixed results , presumably since these proteins have many clients . The mechanism for drug efficacy and tumor-type varia...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "oncology", "medicine", "infectious", "diseases", "basic", "cancer", "research", "virology", "oncology", "agents", "biology", "microbiology", "host-pathogen", "interaction", "viral", "diseases" ]	2012	Hsp90 Inhibitors Are Efficacious against Kaposi Sarcoma by Enhancing the Degradation of the Essential Viral Gene LANA, of the Viral Co-Receptor EphA2 as well as Other Client Proteins
The natural maintenance cycles of many mosquito-borne pathogens require establishment of persistent non-lethal infections in the invertebrate host . The mechanism by which this occurs is not well understood , but we have previously shown that an antiviral response directed by small interfering RNAs ( siRNAs ) is import...	Mosquitoes defend themselves against viral infection with an innate immune response . Thus , mosquito-borne viral diseases like West Nile fever , dengue fever , and chikungunya fever are transmitted to humans only when the pathogen overcomes these defenses . Despite this , relatively little is known about the immune pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "interference", "viral", "transmission", "and", "infection", "immunology", "microbiology", "host-pathogen", "interaction", "viral", "vectors", "biology", "pathogenesis", "molecular", "biology", "immune", "response", "biochemistry", "rna", "mosquitoes", "nucleic", "...	2012	Production of Virus-Derived Ping-Pong-Dependent piRNA-like Small RNAs in the Mosquito Soma
Fibronectin ( FN ) exists in two forms—plasma FN ( pFN ) and cellular FN ( cFN ) . Although the role of FN in embryonic blood vessel development is well established , its function and the contribution of individual isoforms in early postnatal vascular development are poorly understood . Here , we employed a tamoxifen-d...	Fibronectin is a protein that exists in vertebrates in two distinct forms: one present in the blood and the other in blood vessel walls . In mammals , fibronectin is important for the development of blood vessels before birth , but whether it is continuously required for blood vessel homeostasis from birth to adulthood...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "biological", "cultures", "collagens", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "cell", "cultures", "cellular", "structures", "and", "organelles", "elastin", "r...	2018	Roles of fibronectin isoforms in neonatal vascular development and matrix integrity
Degeneration and loss of lower motor neurons is the major pathological hallmark of spinal muscular atrophy ( SMA ) , resulting from low levels of ubiquitously-expressed survival motor neuron ( SMN ) protein . One remarkable , yet unresolved , feature of SMA is that not all motor neurons are equally affected , with some...	Selective vulnerability of particular cell types is a prominent , unresolved feature of many neurodegenerative diseases . In SMA , motor neurons are the most affected cell type , but not all motor neuron pools are affected at the same rate . Some pools degenerate early in disease and others remain resistant . Understan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "population", "genetics", "vertebrates", "neuroscience", "animals", "gene", "pool", "motor", "neurons", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "experimental", "o...	2017	Bioenergetic status modulates motor neuron vulnerability and pathogenesis in a zebrafish model of spinal muscular atrophy
The Greatwall kinase/Mastl is an essential gene that indirectly inhibits the phosphatase activity toward mitotic Cdk1 substrates . Here we show that although Mastl knockout ( MastlNULL ) MEFs enter mitosis , they progress through mitosis without completing cytokinesis despite the presence of misaligned chromosomes , wh...	Cdk1 phosphorylates many substrates in mitosis and simultaneoulsy reduces the activity of the corresponding phosphatase PP2A through the Greatwall kinase/Mastl . When Mastl is deleted , cells progress through mitosis with missegregated chromosomes , which become unraveled . However , the molecular mechansims by which M...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "cell", "physiology", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "phosphatases", "biochemical", "analysis", "mitosis", "in", "vitro", "kinase", "assay", "enzyme", "assays", "immunoprecipitation", "bioassa...	2016	Loss of the Greatwall Kinase Weakens the Spindle Assembly Checkpoint
Multiple epigenetic marks have been proposed to contribute to the regulation of antigen receptor gene assembly via V ( D ) J recombination . Here we provide a comprehensive view of DNA methylation at the immunoglobulin heavy chain ( IgH ) gene locus prior to and during V ( D ) J recombination . DNA methylation did not ...	DNA methylation at CpG dinucleotides is implicated in the regulation of gene expression in mammals . However , the regulation of DNA methylation itself is less clear despite recent advances in identifying enzymes that add or remove methyl groups . We have investigated the dynamics of DNA methylation during genome rearr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Localized DNA Demethylation at Recombination Intermediates during Immunoglobulin Heavy Chain Gene Assembly
In addition to detecting novel transcripts and higher dynamic range , a principal claim for RNA-sequencing has been greater replicability , typically measured in sample-sample correlations of gene expression levels . Through a re-analysis of ENCODE data , we show that replicability of transcript abundances will provide...	RNA-sequencing has become a popular means to detect the expression levels of genes . However , quality control is still challenging , requiring both extreme measures and rules which are set in stone from extensive previous analysis . Instead of relying on these rules , we show that co-expression can be used to measure ...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "interactions", "engineering", "and", "technology", "rna", "analysis", "experimental", "design", "research", "design", "industrial", "engineering", "quality", "control", "bioassays", "and", "physiological", "analysis", "molecular", "biology", "techniques", "res...	2016	AuPairWise: A Method to Estimate RNA-Seq Replicability through Co-expression
A substantial number of mutations have been identified in voltage-gated sodium channel genes that result in various forms of human epilepsy . SCN1A mutations result in a spectrum of severity ranging from mild febrile seizures to Dravet syndrome , an infant-onset epileptic encephalopathy . Dravet syndrome patients exper...	Epilepsy is a neurological disorder affecting approximately 3 million Americans and 1% of the worldwide population . Approximately 70% of patients diagnosed with epilepsy have a genetic basis for their disease . The same genetic mutation can result in epilepsy with varying clinical severity in some individuals . This s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chromosome", "5", "medicine", "and", "health", "sciences", "body", "fluids", "alleles", "animal", "models", "model", "organisms", "research", "and", "analysis", "methods", "epilepsy", "chromosome", "biology", "mouse", "models", "chromosome", "pairs", "blood", "plas...	2016	Fine Mapping of a Dravet Syndrome Modifier Locus on Mouse Chromosome 5 and Candidate Gene Analysis by RNA-Seq
Highly pathogenic avian influenza virus ( HPAI , such as H5N1 ) infection causes severe cytokine storm and fatal respiratory immunopathogenesis in human and animal . Although TGF-β1 and the integrin CD103 in CD8+ T cells play protective roles in H5N1 virus infection , it is not fully understood which key signaling prot...	Infection of avian influenza virus , especially the highly pathogenic strain H5N1 , is a serious threat to public health worldwide , which causes severe fatal respiratory disease and excessive levels of inflammation . It has been reported that both transforming growth factor-beta 1 ( TGF-β1 ) and the integrin CD103 ind...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Immune Adaptor ADAP Regulates Reciprocal TGF-β1-Integrin Crosstalk to Protect from Influenza Virus Infection
The importance of regulated necrosis in pathologies such as cerebral stroke and myocardial infarction is now fully recognized . However , the physiological relevance of regulated necrosis remains unclear . Here , we report a conserved role for p53 in regulating necrosis in Drosophila and mammalian spermatogenesis . We ...	Cell death allows elimination of supernumerary cells during development or of abnormal cells throughout life . Physiological cell death is tightly regulated to prevent pathologies such as degenerative diseases or cancers , which often occur due to excessive or absent cell death , respectively . Understanding the mechan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "spermatogo...	2017	p53-dependent programmed necrosis controls germ cell homeostasis during spermatogenesis
Neuroimaging and neurophysiology have revealed that multiple areas in the prefrontal cortex ( PFC ) are activated in a specific memory task , but severity of impairment after PFC lesions is largely different depending on which activated area is damaged . The critical relationship between lesion sites and impairments ha...	Patients with lesions in the front part of the brain’s frontal lobe—the prefrontal cortex—suffer from severe memory deficits . Neuroimaging and neurophysiology studies have revealed that multiple areas in the prefrontal cortex are activated during a specific memory task . However , the severity of the memory deficit af...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dynamically Allocated Hub in Task-Evoked Network Predicts the Vulnerable Prefrontal Locus for Contextual Memory Retrieval in Macaques
Opisthorchis viverrini ( Ov ) is a complex-life-cycle trematode affecting 10 million people in SEA ( Southeast Asia ) . Human infection occurs when infected cyprinid fish are consumed raw or undercooked . Ov requires three hosts and presents two free-living parasitic stages . As a consequence Ov transmission and infect...	Opisthorchis viverrini ( Ov ) is a fish-borne parasite infecting humans when they consume raw or undercooked fish . Ov is endemic in Southeast Asia , particularly in rural parts of Northeast Thailand , Lao PDR , Cambodia and Vietnam . The Ov lifecycle includes three different hosts: snails , fish and humans . Transmiss...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "surface", "water", "pathology", "and", "laboratory", "medicine", "vertebrates", "parasitic", "diseases", "animals", "freshwater", "fish", "gastropods", "aquatic", "...	2016	Seasonal and Spatial Environmental Influence on Opisthorchis viverrini Intermediate Hosts, Abundance, and Distribution: Insights on Transmission Dynamics and Sustainable Control
The global burden of diarrhea is a leading cause of morbidity and mortality worldwide . In montane areas of South-East Asia such as northern Laos , recent changes in land use have induced increased runoff , soil erosion and in-stream suspended sediment loads , and potential pathogen dissemination . To our knowledge , f...	Aiming to identify the most critical drivers of diarrhea epidemics in montane areas of South-East Asia , we conducted a retrospective time series analysis of diarrhea reported cases and of hydro-meteorological variables measured in two contrasted river basins in northern Laos , together with socio-behavioral practices ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "surface", "water", "pathology", "and", "laboratory", "medicine", "rivers", "atmospheric", "science", "geographical", "locations", "health", "care", "diarrhea",...	2016	Hydrological Regime and Water Shortage as Drivers of the Seasonal Incidence of Diarrheal Diseases in a Tropical Montane Environment
Signaling pathways enable cells to sense and respond to their environment . Many cellular signaling strategies are conserved from fungi to humans , yet their activity and phenotypic consequences can vary extensively among individuals within a species . A systematic assessment of the impact of naturally occurring geneti...	Wild yeast strains differ in phenotypes that are controlled by highly conserved signaling pathways . Yet it remains unknown how naturally occurring genetic variants influence signaling pathways in yeast . We have developed an approach to facilitate the mapping of genetic variants that underlie these phenotypic differen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "fungal", "genomes", "quantitative", "trait", "loci", "fungal", "genetics", "population", "genetics", "alleles", "genome", "analysis", "trait", "locus", "analysis", "genetic", "interactions", "genetic", "loci", "signal", "transduction", "fungal...	2015	Genetic Mapping of MAPK-Mediated Complex Traits Across S. cerevisiae
In mammals , observations of rapid shifts in mitochondrial DNA ( mtDNA ) variants between generations have led to the creation of the bottleneck theory for the transmission of mtDNA . The bottleneck could be attributed to a marked decline of mtDNA content in germ cells giving rise to the next generation , to a small ef...	Mutations of mtDNA are responsible for many types of mitochondrial diseases in humans , including myopathy and neurological disorders . Females carrying a mixture of mutant and wild-type mtDNA variants transmit a variable amount of mutant mtDNA to each offspring . The proportion of mutated mtDNA inherited from the moth...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics" ]	2009	New Evidence Confirms That the Mitochondrial Bottleneck Is Generated without Reduction of Mitochondrial DNA Content in Early Primordial Germ Cells of Mice
Purkinje neurons play an important role in cerebellar computation since their axons are the only projection from the cerebellar cortex to deeper cerebellar structures . They have complex internal dynamics , which allow them to fire spontaneously , display bistability , and also to be involved in network phenomena such ...	How neurons generate output spikes in response to various combinations of inputs is a central issue in contemporary neuroscience . Due to their large dendritic tree and complex intrinsic properties , cerebellar Purkinje cells are an important model system to study this input-output transformation . Here we examine how ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "brain", "electrophysiology", "neuroscience", "materials", "science", "cerebellum", "neuronal", "dendrites", "research", "and", "analysis", "methods", "curve", "fitting", "mathematic...	2016	Inverse Stochastic Resonance in Cerebellar Purkinje Cells
In October of 2010 , an outbreak of cholera was confirmed in Haiti for the first time in more than a century . A single clone of toxigenic Vibrio cholerae O1 biotype El Tor serotype Ogawa strain was implicated as the cause . Five years after the onset of cholera , in October , 2015 , we have discovered a major switch (...	For the first time in 100 years , in October 2010 , cholera caused by toxigenic strains of V . cholerae was introduced in Haiti . Conventional and genetic analysis revealed that a single clone of V . cholerae O1 biotype El Tor , serotype Ogawa strain was brought to Haiti by Nepalese Peace-Keeping troops . These troops ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "deletion", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "vibrio", "tropical", "diseases", "microbiology", "geographical", "locations", "organic", "compounds", "north", "america", ...	2016	Major Shift of Toxigenic V. cholerae O1 from Ogawa to Inaba Serotype Isolated from Clinical and Environmental Samples in Haiti
The prevalence of bacteremia caused by Gram negative non-fermentative ( GNNF ) bacteria has been increasing globally over the past decade . Many studies have investigated their epidemiology but focus on the common GNNF including Pseudomonas aeruginosa and Acinetobacter baumannii . Knowledge of the uncommon GNNF bactere...	Infections caused by Gram negative non fermentative bacteria ( GNNF ) , other than the more commonly described Pseudomonas aeruginosa and Acinetobacter baumannii , constitute an emerging problem . They are not only isolated in nosocomial settings , mainly affecting immunocomprised hosts , but also are opportunistic inf...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Disclaimers" ]	[ "bacteriology", "antimicrobials", "taxonomy", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "genomic", "databases", "data", "management", "antibiotics", "genome", "analysis", ...	2019	Identification of Gram negative non-fermentative bacteria: How hard can it be?
Infectious prions cause diverse clinical signs and form an extraordinary range of structures , from amorphous aggregates to fibrils . How the conformation of a prion dictates the disease phenotype remains unclear . Mice expressing GPI-anchorless or GPI-anchored prion protein exposed to the same infectious prion develop...	Prions cause fatal neurodegenerative disease in humans and animals and there is currently no treatment available . The cellular prion protein is normally tethered to the outer leaflet of the plasma membrane by a glycophosphatidyl inositol ( GPI ) anchor . A rare stop codon mutation in the PRNP gene leads to the product...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases", "neurology", "neurodegenerative", "diseases", "prion", "diseases" ]	2013	Defining the Conformational Features of Anchorless, Poorly Neuroinvasive Prions
Although BCG has been found to impart protection against leprosy in many populations , the utility of repeat or booster BCG vaccinations is still unclear . When a policy of giving a second BCG dose to school children in Brazil was introduced , a trial was conducted to assess its impact against tuberculosis , and a lepr...	BCG is a vaccine developed and used to protect against tuberculosis , but it can also protect against leprosy . In Brazil , children receive BCG at birth , and since 1996 a trial has been conducted to find out if a second dose of BCG administered to schoolchildren gives additional protection against tuberculosis . We u...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/immunization" ]	2008	BCG Revaccination Does Not Protect Against Leprosy in the Brazilian Amazon: A Cluster Randomised Trial
The main criterion for treatment effectiveness in Chagas Disease has been the seronegative conversion , achieved many years post-treatment . One of the main limitations in evaluating treatment for chronic Chagas disease is the lack of reliable tests to ensure parasite clearance and to examine the effects of treatment ....	The main criterion for treatment effectiveness in Chagas Disease has been the seronegative conversion of previously reactive serology , generally achieved many years post-treatment . The lack of reliable tests to ensure parasite clearance and to examine the effect of treatment is the main difficulty in evaluating treat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2011	Impact of Aetiological Treatment on Conventional and Multiplex Serology in Chronic Chagas Disease
In this study , we present a theoretical framework combining experimental characterizations and analytical calculus to capture the firing rate input-output properties of single neurons in the fluctuation-driven regime . Our framework consists of a two-step procedure to treat independently how the dendritic input transl...	Neocortical processing of sensory input relies on the specific activation of subpopulations within the cortical network . Though specific circuitry is thought to be the primary mechanism underlying this functional principle , we explore here a putative complementary mechanism: whether diverse biophysical features in si...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "dendritic", "structure", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "ganglion", "cells", "neuronal", "dendrites", "animal", "cells", "biophysics", "physics", "cellula...	2017	Heterogeneous firing responses predict diverse couplings to presynaptic activity in mice layer V pyramidal neurons
Clp ATPases are powerful ring shaped nanomachines which participate in the degradation pathway of the protein quality control system , coupling the energy from ATP hydrolysis to threading substrate proteins ( SP ) through their narrow central pore . Repetitive cycles of sequential intra-ring ATP hydrolysis events induc...	Cell survival is critically dependent on tightly regulated protein quality control , which includes chaperone-mediated folding and degradation . In the degradation pathway , AAA+ nanomachines , such as bacterial Clp proteases , use ATP-driven mechanisms to mechanically unfold , translocate , and destroy excess or defec...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[]	2016	Coarse-Grained Simulations of Topology-Dependent Mechanisms of Protein Unfolding and Translocation Mediated by ClpY ATPase Nanomachines
The Down syndrome cell adhesion molecule , also known as Dscam , is a member of the immunoglobulin super family . Dscam plays an essential function in neuronal wiring and appears to be involved in innate immune reactions in insects . The deduced amino acid sequence of Dscam in the crustacean Pacifastacus leniusculus ( ...	Invertebrate animals lack an adaptive immune system and have no antibodies . Vertebrate antibodies belong to the immunoglobulin super family of proteins , and one other member of this large family is the Down syndrome cell adhesion molecule or Dscam . Of specific interest is that Dscam proteins in invertebrates show a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology" ]	2011	Bacteria-Induced Dscam Isoforms of the Crustacean, Pacifastacus leniusculus
Severe Plasmodium falciparum malaria is a major cause of global mortality , yet the immunological factors underlying progression to severe disease remain unclear . CD4+CD25+ regulatory T cells ( Treg cells ) are associated with impaired T cell control of Plasmodium spp infection . We investigated the relationship betwe...	Malaria is a major global health problem responsible for more than 1 million deaths annually . Severity of malaria disease is associated with the inability of host immune cells to efficiently eliminate malaria parasites from the blood . Little is known about immune regulatory factors controlling the onset of severe and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunomodulation", "infectious", "diseases/protozoal", "infections" ]	2009	Parasite-Dependent Expansion of TNF Receptor II–Positive Regulatory T Cells with Enhanced Suppressive Activity in Adults with Severe Malaria
Ciliogenesis is a fundamental biological process central to human health . Precisely how this process is coordinated with the cell cycle remains an open question . We report that nephrocystin-5 ( NPHP5/IQCB1 ) , a positive regulator of ciliogenesis , is a stable and low turnover protein subjected to cycles of ubiquitin...	Centrosomes are non-membrane bound organelles that modulate a variety of cellular processes including cell division and formation of hair-like protrusions called primary cilia . Primary cilia function as cellular antennae to sense a wide variety of signals important for growth , development and differentiation . Defect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "centrosomes", "nuclear", "staining", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "immunoprecipitation", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "small", "interfering", "rnas", ...	2017	USP9X counteracts differential ubiquitination of NPHP5 by MARCH7 and BBS11 to regulate ciliogenesis
The henipaviruses , represented by Hendra ( HeV ) and Nipah ( NiV ) viruses are highly pathogenic zoonotic paramyxoviruses with uniquely broad host tropisms responsible for repeated outbreaks in Australia , Southeast Asia , India and Bangladesh . The high morbidity and mortality rates associated with infection and lack...	Since their initial emergence , henipaviruses have continued to cause spillover events in both human and livestock populations , posing significant biothreats . Currently there are no licensed or approved therapies for treatment of henipavirus infection and the human case mortality rates average >70% . We used X-ray cr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Crystal Structure of the Hendra Virus Attachment G Glycoprotein Bound to a Potent Cross-Reactive Neutralizing Human Monoclonal Antibody
The kinase PINK1 and the E3 ubiquitin ( Ub ) ligase Parkin participate in mitochondrial quality control . The phosphorylation of Ser65 in Parkin's ubiquitin-like ( UBl ) domain by PINK1 stimulates Parkin activation and translocation to damaged mitochondria , which induces mitophagy generating polyUb chain . However , P...	Parkinson's disease is a neurodegenerative disorder caused by degeneration of the midbrain dopaminergic system in addition to other nervous systems . PINK1 and parkin , which encode mitochondrial protein kinase and cytosolic Ub ligase , respectively , were identified as the genes responsible for the autosomal recessive...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "biochemical", "analysis", "in", "vitro", "kinase", "assay", "enzyme", "assays", "mitochondria", "molecular", "genetics", "bioenergetics", "bioassays", "and", "physiological", "analysis", "cellular", "structures", "and", "organelles", "mitochondrial"...	2014	Phosphorylation of Mitochondrial Polyubiquitin by PINK1 Promotes Parkin Mitochondrial Tethering
Brazil is a tropical country that is largely covered by rainforests and other natural ecosystems , which provide ideal conditions for the existence of many arboviruses . However , few analyses have examined the associations between environmental factors and arboviral diseases . Thus , based on the hypothesis of correla...	The Oropouche , Mayaro , Saint Louis , and Rocio viruses are neglected emerging mosquito-borne viruses that are spreading and causing wide-scale epidemics in South America . However , under-reporting of these cases is possible , as the symptoms are shared with other endemic diseases . Moreover , little is known regardi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "atmospheric", "science", "geographical", "locations", "animals", "viruses", "animal", "behavior", "infectious", "disease", "control", "insect", "vectors", "zoology", "climate", "change", "infectious", "diseases", ...	2017	Impact of environmental factors on neglected emerging arboviral diseases
HEI10 was first described in human as a RING domain-containing protein that regulates cell cycle and cell invasion . Mice HEI10mei4 mutant displays no obvious defect other than meiotic failure from an absence of chiasmata . In this study , we characterize rice HEI10 by map-based cloning and explore its function during ...	Meiosis is a specialized cell division that is essential for sexual reproduction . Errors in meiosis are the leading cause of both infertility and birth defects . Most meiotic genes and their functions seem to be highly conserved among different species . HEI10 was first identified to regulate cell cycle and cell invas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2012	The Role of Rice HEI10 in the Formation of Meiotic Crossovers
Central corneal thickness ( CCT ) is one of the most heritable ocular traits and it is also a phenotypic risk factor for primary open angle glaucoma ( POAG ) . The present study uses the BXD Recombinant Inbred ( RI ) strains to identify novel quantitative trait loci ( QTLs ) modulating CCT in the mouse with the potenti...	Glaucoma is a complex group of diseases with several known causal mutations and many known risk factors . One well-known risk factor for developing primary open angle glaucoma is the thickness of the central cornea . The present study leverages a unique blend of systems biology methods using BXD recombinant inbred mice...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ocular", "anatomy", "neuroscience", "glaucoma", "ganglion", "cells", "eye", "diseases", "mammalian", "genomics", "eyes", "genomics", "animal", "cells", "head", "animal", "genomics", "genetic", "loci", "cellular", "neuroscience...	2018	Genomic locus modulating corneal thickness in the mouse identifies POU6F2 as a potential risk of developing glaucoma

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