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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Clock output pathways play a pivotal role by relaying timing information from the circadian clock to a diversity of physiological systems . Both cell-autonomous and systemic mechanisms have been implicated as clock outputs; however , the relative importance and interplay between these mechanisms are poorly understood ....	To guarantee normal growth and to avoid tumor formation , the timing of cell division must be under strict control . Remarkably , cells , from bacteria to man , often divide only at certain times of day , suggesting the influence of internal biological clocks . A central pacemaker structure in the brain controls diurna...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "animals", "cell", "biology", "danio", "(zebrafish)", "physiology", "diabetes", "and", "endocrinology", "vertebrates", "teleost", "fishes", "neuroscience", "molecular", "biology", "genetics", "and", "genomics" ]	2007	Glucocorticoids Play a Key Role in Circadian Cell Cycle Rhythms
Mechanism-based pharmacokinetic-pharmacodynamic ( PK/PD ) modelling is the standard computational technique for simulating drug treatment of infectious diseases with the potential to enhance our understanding of drug treatment outcomes , drug deployment strategies , and dosing regimens . Standard methodologies assume o...	Pharmacokinetic-pharmacodynamic ( PK/PD ) models of infectious diseases provide vital insights into the effectiveness of drug treatments ( including the optimal dosage level , frequency and duration ) by explicitly relating drug concentration after treatment to a pathogen kill rate , and ultimately the models describe ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "pharmacodynamics", "tropical", "diseases", "(non-neglected)", "population", "modeling", "drugs", "and", "devices", "infectious", "disease", "modeling", "biology", "malaria", "parasitic", "diseases", "computational", "biology", "pharmac...	2013	Improving Pharmacokinetic-Pharmacodynamic Modeling to Investigate Anti-Infective Chemotherapy with Application to the Current Generation of Antimalarial Drugs
Cutaneous leishmaniasis has various outcomes , ranging from self-healing reddened papules to extensive open ulcerations that metastasise to secondary sites and are often resistant to standard therapies . In the case of L . guyanensis ( L . g ) , about 5–10% of all infections result in metastatic complications . We rece...	Cutaneous leishmaniasis is a neglected parasitic disease particularly problematic in the South American tropics , where the parasites have an ability to migrate from the initial inoculation site in a process called “infectious metastasis” . Despite existing for centuries , the factors involved in parasite dissemination...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infographics", "medicine", "and", "health", "sciences", "animal", "models", "of", "disease", "tropical", "diseases", "microbiology", "basic", "cancer", "research", "parasitic", "diseases", "animal", "models", "oncology", "physiological", "processes", "model", "organism...	2016	Leishmaniavirus-Dependent Metastatic Leishmaniasis Is Prevented by Blocking IL-17A
Simple cells in primary visual cortex were famously found to respond to low-level image components such as edges . Sparse coding and independent component analysis ( ICA ) emerged as the standard computational models for simple cell coding because they linked their receptive fields to the statistics of visual stimuli ....	The statistics of our visual world is dominated by occlusions . Almost every image processed by our brain consists of mutually occluding objects , animals and plants . Our visual cortex is optimized through evolution and throughout our lifespan for such stimuli . Yet , the standard computational models of primary visua...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "visual", "system", "mathematics", "computational", "neuroscience", "statistics", "sensory", "systems", "biology", "computational", "biology", "neuroscience", "statistical", "methods", "probability", "theory", "coding", "mechanisms" ]	2013	Are V1 Simple Cells Optimized for Visual Occlusions? A Comparative Study
We characterized key components and major targets of the c-di-GMP signaling pathways in the foodborne pathogen Listeria monocytogenes , identified a new c-di-GMP-inducible exopolysaccharide responsible for motility inhibition , cell aggregation , and enhanced tolerance to disinfectants and desiccation , and provided fi...	Listeria monocytogenes is ubiquitously present in the environment , highly adaptable and tolerant to various stresses . L . monocytogenes is also a foodborne pathogen associated with the largest foodborne outbreaks in recent US history . Signaling pathways involving the second messenger c-di-GMP play important roles in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "genetics", "biology", "and", "life", "sciences", "microbiology" ]	2014	Cyclic di-GMP-dependent Signaling Pathways in the Pathogenic Firmicute Listeria monocytogenes
Consumer genomics enables genetic discovery on an unprecedented scale by linking very large databases of personal genomic data with phenotype information voluntarily submitted via web-based surveys . These databases are having a transformative effect on human genomics research , yielding insights on increasingly comple...	The genetic underpinnings of many phenotypic traits in domestic dogs remain undiscovered . Although two genetic loci are known to underlie blue eye color in dogs , these do not explain all cases of blue eyes . By examining > 3 , 000 dogs from the Embark Veterinary , Inc . customer database , representing the first geno...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "animal", "types", "medicine", "and", "health", "sciences", "vertebrates", "pets", "and", "companion", "animals", "dogs", "animals", "genetic", "mapping", "mammals", "alleles", "genome", "analysis", "mammalian", "genomics", "ey...	2018	Direct-to-consumer DNA testing of 6,000 dogs reveals 98.6-kb duplication associated with blue eyes and heterochromia in Siberian Huskies
Epithelial tubular morphogenesis leading to alteration of organ shape has important physiological consequences . However , little is known regarding the mechanisms that govern epithelial tube morphogenesis . Here , we show that inactivation of Sfrp1 and Sfrp2 leads to reduction in fore-stomach length in mouse embryos ,...	The gastrointestinal tract is generated from the primitive gut tube during embryogenesis . The primitive gut differentiates regionally along the cephalocaudal axis . Individual regions simultaneously acquire specific morphologies through morphogenetic mechanisms . The regional specification of the gut tube is controlle...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling", "cell", "biology/developmental", "molecular", "mechanisms", "developmental", "biology/pattern", "formation", "genetics", ...	2009	Sfrp Controls Apicobasal Polarity and Oriented Cell Division in Developing Gut Epithelium
DNA replication errors at certain sites in the genome initiate chromosome instability that ultimately leads to stable genomic rearrangements . Where instability begins is often unclear . And , early instability may form unstable chromosome intermediates whose transient nature also hinders mechanistic understanding . We...	Genomic instability forms unstable chromosomes that generate genomic rearrangements associated with human disease . Because unstable chromosomes are inherently dynamic and rarely observed , mechanisms of instability are often inferred from genomic sequencing of the end state . Longitudinal observation of events , from ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "networks", "chromosome", "structure", "and", "function", "dicentric", "chromosomes", "telomeres", "dna", "replication", "network", "analysis", "genome", "analysis", "dna", "recombination", "dna", "homologous", "recombination", "computer", "and", "information",...	2016	Ontogeny of Unstable Chromosomes Generated by Telomere Error in Budding Yeast
Evidence derived from human clinical studies and experimental animal models shows a causal relationship between adverse pregnancy and increased cardiovascular disease in the adult offspring . However , translational studies isolating mechanisms to design intervention are lacking . Sheep and humans share similar precoci...	Adverse conditions during pregnancy can increase the cardiovascular risk of the adult offspring . However , the mechanisms underlying these effects remain unclear , precluding the identification of candidate therapy . In this interventional study in sheep , a species of similar temporal developmental milestones to huma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "maternal", "health", "obstetrics", "and", "gynecology", "ruminants", "vertebrates", "organic", "compounds", "animals", "mammals", "women's", "health", "pregnancy", "hypoxia", "vitamin",...	2019	Intervention against hypertension in the next generation programmed by developmental hypoxia
Multiple transcripts encode for the cell cycle inhibitor p21Cip1 . These transcripts produce identical proteins but differ in their 5’ untranslated regions ( UTRs ) . Although several stresses that induce p21 have been characterized , the mechanisms regulating the individual transcript variants and their functional sig...	Cells sense nutrient levels in their environment in order to determine if conditions are favorable to divide . GCN2 is a protein that senses amino acids and responds to amino acid deficiency by suppressing protein synthesis and increasing the expression of genes involved in recovery from nutrient stress . Although GCN2...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Translational Upregulation of an Individual p21Cip1 Transcript Variant by GCN2 Regulates Cell Proliferation and Survival under Nutrient Stress
Global transcriptome studies can help pinpoint key cellular pathways exploited by viruses to replicate and cause pathogenesis . Previous data showed that laboratory-adapted HIV-1 triggers significant gene expression changes in CD4+ T cell lines and mitogen-activated CD4+ T cells from peripheral blood . However , HIV-1 ...	The gastrointestinal ( GI ) tract is a major site of early HIV-1 replication and death of CD4+ T cells . As HIV-1 replicates in the gut , the protective epithelial barrier gets disrupted , causing the entry of bacteria into the underlying tissue and the bloodstream , leading to inflammation and clinical complications e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell", "processes", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "bacter...	2017	The transcriptome of HIV-1 infected intestinal CD4+ T cells exposed to enteric bacteria
Carbon dioxide ( CO2 ) is a key molecule in many biological processes; however , mechanisms by which organisms sense and respond to high CO2 levels remain largely unknown . Here we report that acute CO2 exposure leads to a rapid cessation in the contraction of the pharynx muscles in Caenorhabditis elegans . To uncover ...	Carbon dioxide ( CO2 ) is a key molecule in many biological processes . High levels of CO2 in patients with pulmonary diseases are associated with worse outcomes . However , mechanisms by which organisms sense and respond to high CO2 levels remain largely unknown . Using Caenorhabditis elegans as a model system , we fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "cellular", "stress", "responses", "neurochemistry", "neural", "networks", "cell", "processes", "neuroscience", "cell", "signaling", "mutation", "model", "organisms", "neurotransmitters", "research", "and", "analysis", "methods", "mutagenesis", ...	2014	The Response to High CO2 Levels Requires the Neuropeptide Secretion Component HID-1 to Promote Pumping Inhibition
The endosomal pathway in neuronal dendrites is essential for membrane receptor trafficking and proper synaptic function and plasticity . However , the molecular mechanisms that organize specific endocytic trafficking routes are poorly understood . Here , we identify GRIP-associated protein-1 ( GRASP-1 ) as a neuron-spe...	Neurons communicate with each other through specialized structures called synapses , and proper synapse function is fundamental for information processing and memory storage . The endosomal membrane trafficking pathway is crucial for the structure and function of synapses; however , the components of the neuronal endos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "neuroscience/neuronal", "and", "glial", "cell", "biology" ]	2010	Neuron Specific Rab4 Effector GRASP-1 Coordinates Membrane Specialization and Maturation of Recycling Endosomes
Environmental strain Burkholderia sp . DNT mineralizes the xenobiotic compound 2 , 4-dinitrotoluene ( DNT ) owing to the catabolic dnt genes borne by plasmid DNT , but the process fails to promote significant growth . To investigate this lack of physiological return of such an otherwise complete metabolic route , cells...	Many bacteria have acquired the capacity of metabolizing chemical compounds that have never been in the Biosphere before the onset of contemporary synthetic chemistry . However , the factors that shape the new metabolic properties of such microorganisms remain obscure . We examined the performance of a still-evolving m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Endogenous Stress Caused by Faulty Oxidation Reactions Fosters Evolution of 2,4-Dinitrotoluene-Degrading Bacteria
Drugs are often seen as ancillary to the purpose of fighting diseases . Here an alternative view is proposed in which they occupy a spearheading role . In this view , drugs are technologies with an inherent therapeutic potential . Once created , they can spread from disease to disease independently of the drug creator’...	The number of drug-like chemical and biological substances that can be constructed with current technologies is vast , yet the subset that can become an effective drug is far more restricted due to the many design constraints and the expense of development . Once developed , however , a drug can have multiple biologica...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "rheumatology", "medicine", "and", "health", "sciences", "immunology", "cancers", "and", "neoplasms", "oncology", "hematologic", "cancers", "and", "related", "disorders", "data", "management", "rheumatoid", "arthritis", "clinical", "medicine", "pharmacology", ...	2016	A Drug-Centric View of Drug Development: How Drugs Spread from Disease to Disease
Drug perturbations of human cells lead to complex responses upon target binding . One of the known mechanisms is a ( positive or negative ) feedback loop that adjusts the expression level of the respective target protein . To quantify this mechanism systems-wide in an unbiased way , drug-induced differential expression...	Many drug targets thought to be suitable for therapeutic purposes are subjected to positive or negative feedback loops upon chemical perturbations which might even account for the development of drug tolerance . In this study , we carried out the first systematic analysis of drug-induced differential expression of drug...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology/chemical", "biology", "of", "the", "cell", "computational", "biology/systems", "biology", "cell", "biology/gene", "expression" ]	2010	Drug-Induced Regulation of Target Expression
X-Chromosome Inactivation ( XCI ) is the process whereby one , randomly chosen X becomes transcriptionally silenced in female cells . XCI is governed by the Xic , a locus on the X encompassing an array of genes which interact with each other and with key molecular factors . The mechanism , though , establishing the fat...	In mammal female cells X-Chromosome Inactivation ( XCI ) is the vital process whereby one X , randomly chosen , is silenced to compensate dosage of X products with respect to males . XCI is governed by a region on the X , the X Inactivation Centre ( Xic ) , which undergoes a sequence of conformational modifications dur...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "physics", "statistical", "mechanics", "biology", "computational", "biology" ]	2011	Conformation Regulation of the X Chromosome Inactivation Center: A Model
Zika virus ( ZIKV ) is a newly-identified infectious cause of congenital disease . Transplacental transfer of maternal IgG to the fetus plays an important role in preventing many neonatal infections . However , antibody transfer may also have negative consequences , such as mediating enhancement of flavivirus infection...	In 2015 , a Zika virus ( ZIKV ) epidemic emerged in Latin America , where dengue virus ( DENV ) already was endemic . The ZIKV epidemic revealed an array of birth defects and neurodevelopmental abnormalities in newborns associated with maternal infection . ZIKV may now be co-endemic in Latin America with DENV . Antibod...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "children", "medicine", "and", "health", "sciences", "reproductive", "system", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "v...	2019	Efficient transplacental IgG transfer in women infected with Zika virus during pregnancy
A central issue in the study of the neural generation of respiratory rhythms is the role of the intrinsic pacemaking capabilities that some respiratory neurons exhibit . The debate on this issue has occurred in parallel to investigations of interactions among respiratory network neurons and how these contribute to resp...	Breathing movements in mammals are generated by brainstem respiratory central pattern generator ( CPG ) networks , which incorporate an excitatory oscillator located in the pre-Bötzinger Complex ( preBötC ) that can exhibit autorhythmic behavior . To understand how these autorhythmic properties impact CPG network dynam...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "knees", "medicine", "and", "health", "sciences", "legs", "neural", "networks", "population", "dynamics", "membrane", "potential", "electrophysiology", "neuroscience", "systems", "science", "mathematics", "network", "analysis", "body", "limbs", "population", "biology", ...	2019	Robustness of respiratory rhythm generation across dynamic regimes
In many mammals , including humans and mice , the zinc finger histone methyltransferase PRDM9 performs the first step in meiotic recombination by specifying the locations of hotspots , the sites of genetic recombination . PRDM9 binds to DNA at hotspots through its zinc finger domain and activates recombination by trime...	Genetic recombination is the meiotic process by which novel combinations of alleles are passed on to the next generation . This process accelerates evolution by creating genetic diversity , and is also essential for successful meiosis . In mammals , the enzyme PRDM9 initiates recombination and determines the subset of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "spermatocytes", "enzymes", "dna-binding", "proteins", "enzymology", "germ", "cells", "methylation", "immunoprecipitation", "epigenetics", "dna", "chromatin", "sperm", "research", "and", "analysis", "methods", "chromosome", "biology", "proteins", "animal", "cells", "gene"...	2016	The Meiotic Recombination Activator PRDM9 Trimethylates Both H3K36 and H3K4 at Recombination Hotspots In Vivo
The plant-specific RNA polymerases Pol IV and Pol V are essential to RNA–directed DNA methylation ( RdDM ) , which also requires activities from RDR2 ( RNA–Dependent RNA Polymerase 2 ) , DCL3 ( Dicer-Like 3 ) , AGO4 ( Argonaute ) , and DRM2 ( Domains Rearranged Methyltransferase 2 ) . RdDM is dedicated to the methylati...	In plant genomes , the RNA–directed DNA methylation ( RdDM ) process induces de novo methylation of cytosines at repeated sequences . The RNA polymerases Pol IV and Pol V are two key components of the RdDM pathway . Pol IV acts with RDR2 ( RNA–dependent RNA polymerase 2 ) and DCL3 ( Dicer-Like protein 3 ) to generate s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/gene", "expression" ]	2009	A Pol V–Mediated Silencing, Independent of RNA–Directed DNA Methylation, Applies to 5S rDNA
Drug resistance remains a major problem for the treatment of HIV . Resistance can occur due to mutations that were present before treatment starts or due to mutations that occur during treatment . The relative importance of these two sources is unknown . Resistance can also be transmitted between patients , but this pr...	For HIV patients who are treated with antiretroviral drugs , treatment usually works well . However , the virus can , and sometimes does , become resistant against one or more drugs . HIV drug resistance results from the acquisition of specific and well known mutations . It is currently unknown whether drug resistance ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "theoretical", "biology", "biology", "evolutionary", "biology" ]	2012	Standing Genetic Variation and the Evolution of Drug Resistance in HIV
Chemokines have been found to exert direct , defensin-like antimicrobial activity in vitro , suggesting that , in addition to orchestrating cellular accumulation and activation , chemokines may contribute directly to the innate host response against infection . No observations have been made , however , demonstrating d...	Innate immunity is critical to host defense and plays a central role in protecting the lungs from respiratory pathogens . Among the mediators important in the innate host response to pulmonary infection are chemokines , proteins originally described for their ability to regulate immune cell trafficking during an inflam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "respiratory", "medicine/respiratory", "infections", "immunology/immune", "response", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections", "microbiology/cell...	2010	Interferon-Inducible CXC Chemokines Directly Contribute to Host Defense against Inhalational Anthrax in a Murine Model of Infection
The high concentration of macromolecules in the crowded cellular interior influences different thermodynamic and kinetic properties of proteins , including their structural stabilities , intermolecular binding affinities and enzymatic rates . Moreover , various structural biology methods , such as NMR or different spec...	Protein behavior is strongly affected by highly crowded and interaction-rich environments , i . e . , typical conditions in both biologically relevant systems , such as the cellular interior , and solution-based structural experiments , including NMR and different spectroscopies . On the other hand , primarily because ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "macromolecular", "complex", "analysis", "biochemistry", "proteins", "protein", "structure", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "molecular", "biology", "macromolecular", "structure", "analysis", "biophysical", "simulations" ]	2014	Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?
Tsetse flies undergo drastic fluctuations in their water content throughout their adult life history due to events such as blood feeding , dehydration and lactation , an essential feature of the viviparous reproductive biology of tsetse . Aquaporins ( AQPs ) are transmembrane proteins that allow water and other solutes...	Glossina sp . are responsible for transmission of African trypanosomes , the causative agents of sleeping sickness in humans and Nagana in cattle . Blood feeding and nutrient provisioning through lactation during intrauterine progeny development are periods when considerable water movement occurs within tsetse flies . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "animal", "physiology", "rna", "interference", "physiogenomics", "cell", "biology", "entomology", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "genomics", "molecular", "cell", "biology", "zoology", "parasitology" ]	2014	Aquaporins Are Critical for Provision of Water during Lactation and Intrauterine Progeny Hydration to Maintain Tsetse Fly Reproductive Success
The immune system must discriminate between pathogenic and nonpathogenic microbes in order to initiate an appropriate response . Toll-like receptors ( TLRs ) detect microbial components common to both pathogenic and nonpathogenic bacteria , whereas Nod-like receptors ( NLRs ) sense microbial components introduced into ...	The host immune system senses bacterial infection by recognizing conserved bacterial components . The host can differentiate between virulent and avirulent bacteria by detecting the activity of bacterial secretion systems that inject effector proteins into cells . How the host responds to such bacterial secretion syste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity", "microbiology/immunity", "to", "infections" ]	2008	Type IV Secretion-Dependent Activation of Host MAP Kinases Induces an Increased Proinflammatory Cytokine Response to Legionella pneumophila
When young suckle , they are rewarded intermittently with a let-down of milk that results from reflex secretion of the hormone oxytocin; without oxytocin , newly born young will die unless they are fostered . Oxytocin is made by magnocellular hypothalamic neurons , and is secreted from their nerve endings in the pituit...	When young suckle , they are rewarded intermittently with a let-down of milk that results from reflex secretion of the hormone oxytocin . Oxytocin is a neuropeptide made by specialised neurons in the hypothalamus , and is secreted from nerve endings in the pituitary gland . During suckling , every 5 min or so , each of...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "computational", "biology/systems", "biology", "computational", "biology/computational", "neuroscience", "computational", "biology" ]	2008	Emergent Synchronous Bursting of Oxytocin Neuronal Network
Do the frequencies of disease mutations in human populations reflect a simple balance between mutation and purifying selection ? What other factors shape the prevalence of disease mutations ? To begin to answer these questions , we focused on one of the simplest cases: recessive mutations that alone cause lethal diseas...	What determines the frequencies of disease mutations in human populations ? To begin to answer this question , we focus on one of the simplest cases: mutations that cause completely recessive , lethal Mendelian diseases . We first review theory about what to expect from mutation and selection in a population of finite ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "geographical", "locations", "alleles", "simulation", "and", "modeling", "mutation", "epigenetics", "population", "biology", "dna", "mutation", "databases", "chromatin", "dna", "methylation", "research", "and", "analysis", "methods", "chromosome", ...	2017	The population genetics of human disease: The case of recessive, lethal mutations
Dengue is one of the fastest spreading vector-borne diseases , caused by four antigenically distinct dengue viruses ( DENVs ) . Antibodies against DENVs are responsible for both protection as well as pathogenesis . A vaccine that is safe for and efficacious in all people irrespective of their age and domicile is still ...	Dengue is mosquito-borne viral disease which is currently a global public health problem . It is caused by four different types of dengue viruses . Nearly a 100 million people a year suffer from overt sickness , which may range from mild fever to potentially fatal disease . A virus-based dengue vaccine was launched for...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "serum", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "m...	2018	A tetravalent virus-like particle vaccine designed to display domain III of dengue envelope proteins induces multi-serotype neutralizing antibodies in mice and macaques which confer protection against antibody dependent enhancement in AG129 mice
Measles virus ( MeV ) is a highly contagious , re-emerging , major human pathogen . Replication requires a viral RNA-dependent RNA polymerase ( RdRP ) consisting of the large ( L ) polymerase protein complexed with the homo-tetrameric phosphoprotein ( P ) . In addition , P mediates interaction with the nucleoprotein ( ...	MeV belongs to the order of non-segmented negative polarity RNA viruses , which includes devastating human pathogens . While all feature encapsidated RNA genomes and P-L type polymerase complexes , insight into the intermolecular interactions within the polymerase hetero-oligomer and between the polymerase complex and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "interactions", "chemical", "compounds", "monomers", "engineering", "and", "technology", "aliphatic", "amino", "acids", "molecular", "probe", "techniques", "dna-binding", "proteins", "microbiology", "immunoblotting", "organic", "compounds", "polymerases", "amino"...	2019	Bipartite interface of the measles virus phosphoprotein X domain with the large polymerase protein regulates viral polymerase dynamics
Dengue is not well documented in Africa . In Cameroon , data are scarce , but dengue infection has been confirmed in humans . We conducted a study to document risk factors associated with anti-dengue virus Immunoglobulin G seropositivity in humans in three major towns in Cameroon . A cross sectional survey was conducte...	General awareness of dengue fever in Africa , and particularly in Cameroon , is weak . Many acute febrile illnesses are considered as malaria , although not laboratory confirmed , and the diagnosis of dengue fever is seldom evoked while its laboratory confirmation is even more seldom obtained . On the basis of anti-den...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "virology", "epidemiology", "dengue", "fever", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "population", "biology", "microbiology", ...	2014	Evidence of Dengue Virus Transmission and Factors Associated with the Presence of Anti-Dengue Virus Antibodies in Humans in Three Major Towns in Cameroon
Modeling plays a major role in policy making , especially for infectious disease interventions but such models can be complex and computationally intensive . A more systematic exploration is needed to gain a thorough systems understanding . We present an active learning approach based on machine learning techniques as ...	Mathematical models are used as pragmatic tools to inform policy makers on public health interventions and many non-health problems . Considerable efforts have been made to build realistic simulation models . Understanding the systems behavior and the effect of model assumptions and parameter values on the results befo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "chickenpox", "medicine", "and", "health", "sciences", "infectious", "disease", "epidemiology", "influenza", "epidemiological", "methods", "and", "statistics", "mathematics", "statistics", "(mathematics)", "population", "modeling", "economic", "epidemiology", "public", "and...	2014	Active Learning to Understand Infectious Disease Models and Improve Policy Making
The rigor to post-rigor transition in myosin , a consequence of ATP binding , plays an essential role in the Lymn–Taylor functional cycle because it results in the dissociation of the actomyosin complex after the powerstroke . On the basis of the X-ray structures of myosin V , we have developed a new normal mode superp...	Myosins are molecular motor proteins that interact with actin filaments to perform a wide range of cellular functions . They use the universal energy storage molecule adenosine triphosphate ( ATP ) . The functional cycle involves myosin binding to actin , a “powerstroke” leading to directed movement , and myosin releas...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry/protein", "chemistry", "biochemistry/membrane", "proteins", "and", "energy", "transduction", "biochemistry/macromolecular", "assemblies", "and", "machines", "biochemistry/theory", "and", "simulation" ]	2008	Allosteric Communication in Myosin V: From Small Conformational Changes to Large Directed Movements
Intra-host sequence data from RNA viruses have revealed the ubiquity of defective viruses in natural viral populations , sometimes at surprisingly high frequency . Although defective viruses have long been known to laboratory virologists , their relevance in clinical and epidemiological settings has not been establishe...	Defective viruses are viral particles with genetic mutations or deletions that eliminate essential functions , so that they cannot complete their life cycles independently . They can reproduce only by co-infecting host cells with functional viruses and ‘borrowing’ their functional elements . Defective viruses have been...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbiology", "emerging", "infectious", "diseases", "population", "modeling", "microbial", "evolution", "sequence", "analysis", "evolutionary", "modeling", "microbial", "pathogens", "biology", "population", "ecology", "viral", "evolution", "microbial", "ecology", "ecology...	2013	Phylodynamic Analysis of the Emergence and Epidemiological Impact of Transmissible Defective Dengue Viruses
Hair growth disorders often carry a major psychological burden . Therefore , more effective human hair growth–modulatory agents urgently need to be developed . Here , we used the hypertrichosis-inducing immunosuppressant , Cyclosporine A ( CsA ) , as a lead compound to identify new hair growth–promoting molecular targe...	Hair loss is a common disorder and can lead to psychological distress . Cyclosporine A , a fungal metabolite commonly used as an immunosuppressant , can potently induce hair growth in humans . However , it cannot be effectively used to restore hair growth because of its toxic profile . In this study , we used Cyclospor...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "skin", "medicine", "and", "health", "sciences", "hair", "growth", "integumentary", "system", "catagen", "phase", "scalp", "physiological", "processes", "immunologic", "techniques", "anagen", "phase", "research", "and", "analysis", "methods", "hair", "immunoassays", "...	2018	Identifying novel strategies for treating human hair loss disorders: Cyclosporine A suppresses the Wnt inhibitor, SFRP1, in the dermal papilla of human scalp hair follicles
Currently there are a dozen or so of new vaccine candidates in clinical trials for prevention of tuberculosis ( TB ) and each formulation attempts to elicit protection by enhancement of cell-mediated immunity ( CMI ) . In contrast , most approved vaccines against other bacterial pathogens are believed to mediate protec...	Vaccine design in the TB field has been driven by the imperative of attempting to elicit strong cell-mediated responses . However , in recent decades evidence has accumulated that humoral immunity can protect against many intracellular pathogens through numerous mechanisms . In this work , we demonstrate that immunizat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "immune", "cells", "spleen", "immunology", "drug", "delivery", "system", "preparation", "antigen", "encapsulation", "pharmaceutics", "antibodies", "immunolo...	2017	Enhanced control of Mycobacterium tuberculosis extrapulmonary dissemination in mice by an arabinomannan-protein conjugate vaccine
Bifunctional dihydrofolate reductase–thymidylate synthase ( DHFR-TS ) is a chemically and genetically validated target in African trypanosomes , causative agents of sleeping sickness in humans and nagana in cattle . Here we report the kinetic properties and sensitivity of recombinant enzyme to a range of lipophilic and...	There are few validated and fully characterised targets suitable for drug discovery against African trypanosomes , causative agents of sleeping sickness in humans and nagana in cattle . Here we report the biochemical properties of the bifunctional enzyme , dihydrofolate reductase–thymidylate synthase ( DHFR-TS ) , and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pyrimethamine", "chemical", "compounds", "enzymes", "drugs", "enzymology", "parasitic", "protozoans", "antimalarials", "protozoans", "pharmacology", "enzyme", "inhibitors", "thymidines", "proteins", "chemistry", "recombinant", "prot...	2016	Trypanosoma brucei DHFR-TS Revisited: Characterisation of a Bifunctional and Highly Unstable Recombinant Dihydrofolate Reductase-Thymidylate Synthase
During growth of multicellular organisms , identities of stem cells and differentiated cells need to be maintained . Cell fate is epigenetically controlled by the conserved Polycomb-group ( Pc-G ) proteins that repress their target genes by catalyzing histone H3 lysine 27 trimethylation ( H3K27me3 ) . Although H3K27me3...	All organs and differentiated tissues in multicellular organisms are derived from undifferentiated pluripotent stem cells . The evolutionarily conserved Polycomb-group ( Pc-G ) proteins control stem cell identity and maintenance , likely by repressing genes involved in differentiation processes . Pc-G proteins are epig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "growth", "and", "development", "plant", "biology", "cell", "differentiation", "developmental", "biology", "plant", "science", "model", "organisms", "stem", "cells", "plant", "genomics", "epigenetics", "arabidopsis", "thaliana", "plant", "genetics", "biology", ...	2011	Dynamic Regulation of H3K27 Trimethylation during Arabidopsis Differentiation
The type I interferon ( IFN ) response is imperative for the establishment of the early antiviral immune response . Here we report the identification of the first type I IFN antagonist encoded by murine cytomegalovirus ( MCMV ) that shuts down signaling following pattern recognition receptor ( PRR ) sensing . Screening...	The herpesvirus cytomegalovirus can cause severe morbidity in immunosuppressed people and poses a much greater global problem in the context of congenital infections than the Zika virus . To establish infection , cytomegalovirus needs to modulate the antiviral immune response of its host . One of the first lines of def...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "transfection", "luciferase", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "cells", "immune", "physiology", "enzymes", "spleen", "immunology", "enzymology", "fibroblasts", "immune", "receptor", "signaling", "membran...	2017	The murine cytomegalovirus M35 protein antagonizes type I IFN induction downstream of pattern recognition receptors by targeting NF-κB mediated transcription
Advances in single-cell ( SC ) genomics enable commensurate improvements in methods for uncovering lineage relations among individual cells , as determined by phylogenetic analysis of the somatic mutations harbored by each cell . Theoretically , complete and accurate knowledge of the genome of each cell of an individua...	A human cell lineage tree describes the entire developmental dynamics of a person starting from the zygote and ending with each and every extant cell . Fundamental open problems in biology and medicine are in fact questions about the human cell lineage tree: its structure and its dynamics in development , growth , rene...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "cycle", "and", "cell", "division", "cell", "processes", "simulation", "and", "modeling", "mutation", "phylogenetic", "analysis", "genome", "analysis", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "genomic", "signal", "proces...	2016	Accuracy of Answers to Cell Lineage Questions Depends on Single-Cell Genomics Data Quality and Quantity
Large-scale population sequencing studies provide a complete picture of human genetic variation within the studied populations . A key challenge is to identify , among the myriad alleles , those variants that have an effect on molecular function , phenotypes , and reproductive fitness . Most non-neutral variation consi...	A key challenge in human genetics is to identify , among the multitude of genetic differences between individuals , those that have an effect on traits . Even though new genetic variants arise through mutation in each generation , most are present only in a small proportion of individuals because they have slightly neg...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "mutation", "genetic", "polymorphism", "genome", "evolution", "natural", "selection", "genetics", "population", "genetics", "biology", "genomics", "genetics", "and", "genomics", "genetic", "drift" ]	2013	Deleterious Alleles in the Human Genome Are on Average Younger Than Neutral Alleles of the Same Frequency
Boid inclusion body disease ( BIBD ) is an often fatal disease affecting mainly constrictor snakes . BIBD has been associated with infection , and more recently with coinfection , by various reptarenavirus species ( family Arenaviridae ) . Thus far BIBD has only been reported in captive snakes , and neither the incubat...	Members of the genus Reptarenavirus are “newcomers” of the family Arenaviridae and have been associated with boid inclusion body disease ( BIBD ) , an economically important , fatal disease of captive boid snakes . Recently , we and others observed that snakes with BIBD commonly harbour several S and L segments ( arena...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "And", "Methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "sequencing", "techniques", "medicine", "and", "health", "sciences", "body", "fluids", "biological", "cultures", "brain", "vertebrates", "animals", "next-generation", "sequencing", "developmental", "biology", "rept...	2017	Co-infecting Reptarenaviruses Can Be Vertically Transmitted in Boa Constrictor
Telomerase serves a critical role in stem cell function and tissue homeostasis . This role depends on its ability to synthesize telomere repeats in a manner dependent on the reverse transcriptase ( RT ) function of its protein component telomerase RT ( TERT ) , as well as on a novel pathway whose mechanism is poorly un...	Stem cells and progenitor cells within a tissue are required to maintain tissue homeostasis and to repair tissues after injury by giving rise to differentiated daughter cells . Many progenitor cells express telomerase , a reverse transcriptase enzyme that adds DNA repeats to telomeres , the protective structures that c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mus", "(mouse)", "genetics", "and", "genomics", "developmental", "biology", "computational", "biology" ]	2008	TERT Promotes Epithelial Proliferation through Transcriptional Control of a Myc- and Wnt-Related Developmental Program
Developing and extending a biomedical ontology is a very demanding task that can never be considered complete given our ever-evolving understanding of the life sciences . Extension in particular can benefit from the automation of some of its steps , thus releasing experts to focus on harder tasks . Here we present a st...	Biomedical knowledge is complex and in constant evolution and growth , making it difficult for researchers to keep up with novel discoveries . Ontologies have become essential to help with this issue since they provide a standardized format to describe knowledge that facilitates its storing , sharing and computational ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "science", "ontology", "and", "logics", "bio-ontologies", "biology", "computational", "biology" ]	2012	Predicting the Extension of Biomedical Ontologies
HIV-1 replication normally requires Vif-mediated neutralization of APOBEC3 antiviral enzymes . Viruses lacking Vif succumb to deamination-dependent and -independent restriction processes . Here , HIV-1 adaptation studies were leveraged to ask whether viruses with an irreparable vif deletion could develop resistance to ...	APOBEC3G is a virus restriction factor that blocks the replication of Vif-deficient HIV-1 by deamination-dependent and -independent mechanisms . The HIV-1 accessary protein Vif counteracts APOBEC3G through a proteasome-mediated degradation pathway . However , viruses often possess multiple distinct mechanisms to evade ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "physiology", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "cells", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "immunology", "microbiology", "immunoblotting", "v...	2018	HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G
Cryptosporidiosis is an important cause for chronic diarrhea and death in HIV/AIDS patients . Among common Cryptosporidium species in humans , C . parvum is responsible for most zoonotic infections in industrialized nations . Nevertheless , the clinical significance of C . parvum and role of zoonotic transmission in cr...	The disease burden of Cryptosporidium parvum and role of zoonotic transmission in cryptosporidiosis epidemiology are poorly understood in developing countries . In this study , we examined the distribution and clinical manifestations of Cryptosporidium species and subtypes in HIV/AIDS patients in Addis Ababa , Ethiopia...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "cryptosporidiosis", "parasitic", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences" ]	2014	Distribution and Clinical Manifestations of Cryptosporidium Species and Subtypes in HIV/AIDS Patients in Ethiopia
Recombination has an evident impact on virus evolution and emergence of new pathotypes , and has generated an immense literature . However , the distribution of phenotypic effects caused by genome-wide random homologous recombination has never been formally investigated . Previous data on the subject have promoted the ...	Recombination creates new genome combinations by joining genome fragments of distinct “parental” origin . This phenomenon , frequent in viral populations , combines mutations originally present on distinct parental genomes , increasing genetic diversity and creating “offspring” with altered biological properties . Cons...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Acknowledgments" ]	[ "genome", "evolution", "viral", "transmission", "and", "infection", "plant", "biology", "emerging", "viral", "diseases", "microbiology", "plant", "science", "emerging", "infectious", "diseases", "microbial", "evolution", "plant", "pathology", "viral", "load", "biology",...	2011	Distribution of the Phenotypic Effects of Random Homologous Recombination between Two Virus Species
Transmission ratio distortion ( TRD ) by the mouse t-haplotype , a variant region on chromosome 17 , is a well-studied model of non-Mendelian inheritance . It is characterized by the high transmission ratio ( up to 99% ) of the t-haplotype from t/+ males to their offspring . TRD is achieved by the exquisite ability of ...	Exceptions to Gregor Mendel’s rules of inheritance have attracted geneticists over many decades . One of the best-studied cases in mammals is the extremely high transmission rate ( up to 99% ) of a chromosomal variant in mouse , called the t-haplotype , from t/+ heterozygous males to their offspring . Previous studies ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "reverse", "transcriptase-polymerase", "chain", "reaction", "meiosis", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "alleles", "reproductive", "physiology", ...	2019	Two isoforms of the RAC-specific guanine nucleotide exchange factor TIAM2 act oppositely on transmission ratio distortion by the mouse t-haplotype
Polyploidy is frequent in nature and is a hallmark of cancer cells , but little is known about the strategy of DNA repair in polyploid organisms . We have studied DNA repair in the polyploid archaeon Haloferax volcanii , which contains up to 20 genome copies . We have focused on the role of Mre11 and Rad50 proteins , w...	Most organisms contain only one or two copies of their genome , but in some species multiple copies are found . The presence of multiple genome copies ( polyploidy ) has profound implications for DNA repair and is frequently seen in cancer cells . We have studied DNA repair in the archaeon Haloferax volcanii , which co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "microbiology/microbial", "growth", "and", "development", "molecular", "biology/dna", "repair" ]	2009	Mre11-Rad50 Promotes Rapid Repair of DNA Damage in the Polyploid Archaeon Haloferax volcanii by Restraining Homologous Recombination
Recent genomic data indicate that RNA polymerase II ( Pol II ) function extends beyond conventional transcription of primarily protein-coding genes . Among the five snRNAs required for pre-mRNA splicing , only the U6 snRNA is synthesized by RNA polymerase III ( Pol III ) . Here we address the question of how Pol II coo...	During transcription , RNA polymerases synthesize an RNA copy of a given gene . Human genes are transcribed by either RNA polymerase I , II , or III . Here , we focus on transcription of the U6 gene that encodes a small nuclear RNA ( snRNA ) , a non-coding RNA with unique activities in gene expression . The U6 snRNA is...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "genetics", "and", "genomics", "homo", "(human)" ]	2007	Extragenic Accumulation of RNA Polymerase II Enhances Transcription by RNA Polymerase III
Ebola virus ( EBOV ) infection in humans and non-human primates ( NHPs ) is highly lethal , and there is limited understanding of the mechanisms associated with pathogenesis and survival . Here , we describe a transcriptomic analysis of NHPs that survived lethal EBOV infection , compared to NHPs that did not survive . ...	Infection of humans and non-human primates ( NHPs ) with Ebola virus ( EBOV ) can cause viral hemorrhagic fever , an acute systemic illness which can lead to death . The high case fatality rates ( 25%–90% ) make EBOV a virus of significant concern from a biodefense perspective . To date , there are no FDA-approved post...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virus", "effects", "on", "host", "gene", "expression", "virology", "biology", "and", "life", "sciences", "microbiology", "computational", "biology" ]	2014	Transcriptional Correlates of Disease Outcome in Anticoagulant-Treated Non-Human Primates Infected with Ebolavirus
More than a third of the world's children are infected with intestinal nematodes . Current control approaches emphasise treatment of school age children , and there is a lack of information on the effects of deworming preschool children . We studied the effects on the heights and weights of 3 , 935 children , initially...	About one-third of children in poor communities globally are infected with intestinal worms . Treatment is effective and safe , and involves taking a pill once or twice a year . Most deworming programs are aimed at children of school age because most infections occur in this age group and schoolchildren are easy to rea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "pediatrics", "and", "child", "health/child", "development", "pediatrics", "and", "child", "health" ]	2008	Effects of Deworming on Malnourished Preschool Children in India: An Open-Labelled, Cluster-Randomized Trial
Nipah virus causes respiratory and neurologic disease with case fatality rates up to 100% in individual outbreaks . End stage lesions have been described in the respiratory and nervous systems , vasculature and often lymphoid organs in fatal human cases; however , the initial target organs of Nipah virus infection have...	Nipah virus is a highly fatal paramyxovirus that causes respiratory and neurologic disease with widespread vascular damage . Although end stage disease has been characterized in humans and in animal models , the early phase of infection has yet to be described . Thus , it is known where the virus replicates during the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "henipavirus", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "viruses", "respiratory", "system", "rna", "viruses", "respiratory", "physiology", "hamsters", "paramyxo...	2016	Identifying Early Target Cells of Nipah Virus Infection in Syrian Hamsters
The soil-dwelling Gram-negative bacterium Burkholderia pseudomallei is the cause of melioidosis . Extreme structuring of genotype and genotypic frequency has been demonstrated for B . pseudomallei in uncultivated land , but its distribution and genetic diversity in agricultural land where most human infections are prob...	Burkholderia pseudomallei is the cause of melioidosis , a serious human infection most commonly diagnosed in southeast Asia and northern Australia . The organism lives in the soil in a specific geographical distribution and infection results from bacterial inoculation , inhalation or ingestion . The purpose of this stu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "microbiology/environmental", "microbiology" ]	2009	Burkholderia pseudomallei Is Genetically Diverse in Agricultural Land in Northeast Thailand
There is an urgent need to develop new , safe and effective treatments for human African trypanosomiasis ( HAT ) because current drugs have extremely poor safety profiles and are difficult to administer . Here we report the discovery of 2 , 4-diaminopyrimidines , exemplified by 4-[4-amino-5- ( 2-methoxy-benzoyl ) -pyri...	The protozoan parasite Trypanosoma brucei is the causative agent of human African trypanosomiasis ( HAT ) or sleeping sickness , a fatal disease affecting nearly half a million people in sub-Saharan Africa . Current treatments for HAT have very poor safety profiles and are difficult to administer . There is an urgent n...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "chemical", "biology/small", "molecule", "chemistry", "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "microbiology/parasitology", "chemical", "biology/protein", "chemistry", "and", "proteomics", "biochemistry/drug", "discovery" ]	2011	2,4-Diaminopyrimidines as Potent Inhibitors of Trypanosoma brucei and Identification of Molecular Targets by a Chemical Proteomics Approach
Diets high in carbohydrates have long been linked to progressive heart dysfunction , yet the mechanisms by which chronic high sugar leads to heart failure remain poorly understood . Here we combine diet , genetics , and physiology to establish an adult Drosophila melanogaster model of chronic high sugar-induced heart d...	Heart disease remains the most common source of mortality in the American population . The Western diet has been implicated as an important factor , though the mechanisms by which high levels of dietary sugar and fat contribute to heart failure remain controversial . Here , we use the fruit fly Drosophila to explore th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "physiology", "genetics", "biology", "anatomy", "and", "physiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	A Drosophila Model of High Sugar Diet-Induced Cardiomyopathy
Toxocara canis ( Ascaridida: Nematoda ) , which parasitizes ( at the adult stage ) the small intestine of canids , can be transmitted to a range of other mammals , including humans , and can cause the disease toxocariasis . Despite its significance as a pathogen , the genetics , epidemiology and biology of this parasit...	Toxocara canis ( Nematoda: Ascaridida ) is the common roundworm of canids . This parasite is transmissible to humans as well as a range of other accidental or paratenic vertebrate hosts , in which ( after the oral ingestion of infective eggs ) the larvae of Toxocara canis invade the tissues and can cause different form...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry/structural", "genomics", "infectious", "diseases/helminth", "infections", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/genomics" ]	2008	The Mitochondrial Genome of Toxocara canis
Leishmania transmission occurs in the presence of insect saliva . Immunity to Phlebotomus papatasi or Lutzomyia longipalpis saliva or salivary components confers protection against an infection by Leishmania in the presence of the homologous saliva . However , immunization with Lutzomyia intermedia saliva did not prote...	Leishmaniasis , caused by parasitic protozoa Leishmania , is transmitted by bites of female sand flies that , during blood-feeding , inject humans with parasites and saliva . Sand fly saliva has been investigated as a potential vaccine candidate . It was previously shown that immunization with Lutzomyia longipalpis sal...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology", "biology" ]	2011	Lutzomyia longipalpis Saliva or Salivary Protein LJM19 Protects against Leishmania braziliensis and the Saliva of Its Vector, Lutzomyia intermedia
Transcription factors are key regulators of hematopoietic stem cells ( HSCs ) and act through their ability to bind DNA and impact on gene transcription . Their functions are interpreted in the complex landscape of chromatin , but current knowledge on how this is achieved is very limited . C/EBPα is an important transc...	Hematopoietic stem cells ( HSCs ) are required for the lifelong generation of blood cells . To fulfill this requirement HSCs carefully balance cell fate decisions such as self-renewal , differentiation , quiescence , proliferation and death . These features are regulated in part by transcription factors , which act by ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "developmental", "biology", "hematopoietic", "stem", "cells", "hematopoiesis", "stem", "cells", "gene", "expression", "genetics", "epigenetics", "biology", "hematology" ]	2014	C/EBPα Is Required for Long-Term Self-Renewal and Lineage Priming of Hematopoietic Stem Cells and for the Maintenance of Epigenetic Configurations in Multipotent Progenitors
Genome-wide associations have shown a lot of promise in dissecting the genetics of complex traits in humans with single variants , yet a large fraction of the genetic effects is still unaccounted for . Analyzing genetic interactions between variants ( epistasis ) is one of the potential ways forward . We investigated t...	The ultimate goal of genome-wide association studies ( GWAS ) is to explain the proportion of variation in a phenotypic trait that can be attributed to genetic factors . The past two years have seen a plethora of successes in this field , yet , for most traits , a large fraction of variation remains unexplained . Epist...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/population", "genetics", "genetics", "and", "genomics/medical", "genetics", "genetics", "and", "genomics/gene", "expression" ]	2008	Modifier Effects between Regulatory and Protein-Coding Variation
The disease course of human immunodeficiency virus ( HIV ) is often altered by existing or newly acquired coincident infections . To assess the influence of pre-existing Wuchereria bancrofti infection on HIV progression , we performed a case-controlled treatment study of HIV positive individuals with ( FIL+ ) or withou...	In people living with HIV infection , simultaneous infections can adversely affect HIV disease . This has been seen with bacterial ( tuberculosis ) , viral ( cytomegalovirus ) , and parasitic infections ( toxoplasmosis ) . Lymphatic filariasis is caused by a thin thread-like parasite that lives in the lymph vessels of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Treatment of W. bancrofti (Wb) in HIV/Wb Coinfections in South India
Small-angle X-ray scattering is an increasingly popular technique used to detect protein structures and ensembles in solution . However , the refinement of structures and ensembles against SAXS data is often ambiguous due to the low information content of SAXS data , unknown systematic errors , and unknown scattering c...	In solution , many proteins adopt ensembles of multiple distinct states . The relative concentrations of the states are tightly controlled by factors such as pH , phosphorylation , or ligand binding , and a misbalance between the states underlies diseases such as cancer or neurodegeneration . However , detecting protei...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "crystal", "structure", "condensed", "matter", "physics", "simulation", "and", "modeling", "mathematics", "statistics", "(mathematics)", "protein", "structure", "distribution", "curves", "crystallography", "research", "and", "analysis", "methods", "statistical", "distributi...	2017	Bayesian refinement of protein structures and ensembles against SAXS data using molecular dynamics
The lungs are a noted predilection site of acute , latent , and reactivated cytomegalovirus ( CMV ) infections . Interstitial pneumonia is the most dreaded manifestation of CMV disease in the immunocompromised host , whereas in the immunocompetent host lung-infiltrating CD8 T cells confine the infection in nodular infl...	Being strategically located beneath endothelial and epithelial surfaces , mast cells ( MC ) serve as sentinels for invading pathogens at host-environment boundaries as part of the innate defense against infection . Host genetic resistance against cytomegaloviruses ( CMV ) is largely determined by the innate immune resp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "microbiology", "cytomegalovirus", "infection", "population", "modeling", "infectious", "diseases", "white", "blood", "cells", "animal", "cells", ...	2014	Mast Cells Expedite Control of Pulmonary Murine Cytomegalovirus Infection by Enhancing the Recruitment of Protective CD8 T Cells to the Lungs
Neural network dynamics are governed by the interaction of spiking neurons . Stochastic aspects of single-neuron dynamics propagate up to the network level and shape the dynamical and informational properties of the population . Mean-field models of population activity disregard the finite-size stochastic fluctuations ...	In the brain , information about stimuli is encoded in the timing of action potentials produced by neurons . An understanding of this neural code is facilitated by the use of a well-established method called mean-field theory . Over the last two decades or so , mean-field theory has brought an important added value to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "partial", "differential", "equations", "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "population", "dynamics", "signal", "processing", "membrane", "potential", "electrophysiology", "neuroscience",...	2017	A stochastic-field description of finite-size spiking neural networks
Once transcribed , the nascent full-length RNA of HIV-1 must travel to the appropriate host cell sites to be translated or to find a partner RNA for copackaging to form newly generated viruses . In this report , we sought to delineate the location where HIV-1 RNA initiates dimerization and the influence of the RNA tran...	High genetic diversity of HIV-1 presents a difficult barrier for drug treatment and vaccine development . HIV-1 efficiently reassorts mutations in its genome by packaging two copies of RNA into one virion and using portions of each RNA as the template for DNA synthesis . Thus , a key to HIV-1's genetic diversity is how...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/medical", "microbiology" ]	2009	Probing the HIV-1 Genomic RNA Trafficking Pathway and Dimerization by Genetic Recombination and Single Virion Analyses
The largest ever recorded epidemic of the Chikungunya virus ( CHIKV ) broke out in 2004 and affected four continents . Acute symptomatic infections are typically associated with the onset of fever and often debilitating polyarthralgia/polyarthritis . In this study , a systems biology approach was adopted to analyze the...	The Chikungunya virus ( CHIKV ) has infected millions of people worldwide and presents a serious public health issue . Acute symptomatic infections caused by contracting this mosquito-transmitted arbovirus are typically associated with an abrupt onset of fever and often debilitating polyarthralgia/ polyarthritis , as w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rheumatology", "medicine", "and", "health", "sciences", "genetic", "networks", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "microbiology", "alphaviruses", "v...	2019	Systems analysis of subjects acutely infected with the Chikungunya virus
Metabolic cross-feeding interactions between microbial strains are common in nature , and emerge during evolution experiments in the laboratory , even in homogeneous environments providing a single carbon source . In sympatry , when the environment is well-mixed , the reasons why emerging cross-feeding interactions may...	Stable bacterial cross-feeding interactions , where one strain feeds on the waste of the other , are important to understand , as they can be a first step toward bacterial speciation . Their emergence is commonly observed in laboratory experiments using Escherichia coli as a model organism . Yet it is not clear how cro...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion" ]	[ "taxonomy", "organismal", "evolution", "dna", "metabolism", "ecology", "and", "environmental", "sciences", "ecological", "niches", "metabolic", "networks", "enzymology", "microbiology", "phylogenetics", "data", "management", "metabolites", "phylogenetic", "analysis", "netwo...	2017	Beware batch culture: Seasonality and niche construction predicted to favor bacterial adaptive diversification
Cryptosporidium is one of the most common parasitic diarrheal agents in the world and is a known zoonosis . We studied Cryptosporidium in people , livestock , and non-human primates in the region of Kibale National Park , Uganda . Land use change near the park has resulted in fragmented forest patches containing small ...	Cryptosporidium is a common gastrointestinal parasite known for its zoonotic potential . We found Cryptosporidium in 32 . 4% of people , 11 . 1% of non-human primates , and 2 . 2% of livestock in the region of Kibale National Park , Uganda . In people , infection rates were higher in one community than elsewhere , and ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "microbiology", "parasitology", "population", "biology", "veterinary", "science", "veterinary", "diseases", "disease", "ecology", "veterinary", "parasitology", "epidemiology", "b...	2012	Epidemiology and Molecular Relationships of Cryptosporidium spp. in People, Primates, and Livestock from Western Uganda
While circulating levels of soluble Intercellular Adhesion Molecule 1 ( sICAM-1 ) have been associated with diverse conditions including myocardial infarction , stroke , malaria , and diabetes , comprehensive analysis of the common genetic determinants of sICAM-1 is not available . In a genome-wide association study co...	Soluble Intercellular Adhesion Molecule 1 ( sICAM-1 ) is an inflammatory marker that has been associated with several common diseases such as diabetes , heart disease , stroke , and malaria . While it is known that blood concentrations of sICAM-1 are at least partially genetically determined , our current knowledge of ...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/complex", "traits", "cardiovascular", "disorders/cardiovascular", "diseases", "in", "women", "hematology/blood", "transfusion", "infectious", "diseases/tropical", "and", "t...	2008	Novel Association of ABO Histo-Blood Group Antigen with Soluble ICAM-1: Results of a Genome-Wide Association Study of 6,578 Women
The genetic basis of autoantibody production is largely unknown outside of associations located in the major histocompatibility complex ( MHC ) human leukocyte antigen ( HLA ) region . The aim of this study is the discovery of new genetic associations with autoantibody positivity using genome-wide association scan sing...	Autoantibodies are important markers for autoimmune diseases such as type 1 diabetes and Graves' disease . However , little is known about the genetic factors that control their production . To improve our understanding of this genetic basis , we measured four autoantibodies in a collection of up to 8 , 300 type 1 diab...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetics", "of", "the", "immune", "system", "genetics", "immunology", "biology", "autoimmunity", "genetics", "and", "genomics" ]	2011	Genome-Wide Association Analysis of Autoantibody Positivity in Type 1 Diabetes Cases
In the developing and adult brain , oligodendrocyte precursor cells ( OPCs ) are influenced by neuronal activity: they are involved in synaptic signaling with neurons , and their proliferation and differentiation into myelinating glia can be altered by transient changes in neuronal firing . An important question that h...	Oligodendrocytes are glial cells of the central nervous system . One of their major tasks is to enwrap neuronal axons with myelin , providing electrical insulation of axons and a dramatic increase in the speed of nerve impulse propagation . Oligodendrocytes develop from oligodendrocyte precursor cells ( OPCs ) . Self-r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "neurochemistry", "nervous", "system", "neuronal", "differentiation", "brain", "electrophysiology", "neuroscience", "surgical", "and", "invasive", "medical", "procedures", "cell", "differentiation", "developmental", "biology", "mathe...	2017	Different patterns of neuronal activity trigger distinct responses of oligodendrocyte precursor cells in the corpus callosum
Broadly neutralizing antibodies targeting the stalk region of influenza A virus ( IAV ) hemagglutinin ( HA ) are effective in blocking virus infection both in vitro and in vivo . The highly conserved epitopes recognized by these antibodies are critical for the membrane fusion function of HA and therefore less likely to...	IAV causes seasonal epidemics and periodic pandemics that result in significant morbidity and mortality worldwide . The effectiveness of influenza vaccines is highly variable because the virus evolves rapidly and causes antibody mismatch . The use of neuraminidase inhibitors , the current standard of treatment for IAV ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "flow", "cytometry", "cell", "physiology", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "hela", "cells", "enzymes", "pathogens", "immunology", "biological", "cultures", "microbiol...	2016	Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody
The enzyme activities catalysed by flavivirus non-structural protein 3 ( NS3 ) are essential for virus replication . They are distributed between the N-terminal protease domain in the first one-third and the C-terminal ATPase/helicase and nucleoside 5′ triphosphatase domain which forms the remainder of the 618-aa long ...	Dengue virus is the most prevalent mosquito transmitted infectious disease in humans and is responsible for febrile disease such as dengue fever , dengue hemorrhagic fever and dengue shock syndrome . Dengue non-structural protein 3 ( NS3 ) is an essential , multifunctional , viral enzyme with two distinct domains; a pr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/antigen", "processing", "and", "recognition", "virology/viral", "replication", "and", "gene", "regulation", "biochemistry/protein", "chemistry", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "infectious", "diseases/viral", "infecti...	2010	High Affinity Human Antibody Fragments to Dengue Virus Non-Structural Protein 3
Rabies is a fatal neurologic disease caused by lyssavirus infection . People are infected through contact with infected animals . The relative increase of human rabies acquired from bats calls for a better understanding of lyssavirus infections in their natural hosts . So far , there is no experimental model that mimic...	Rabies is a neurologic disease that causes severe suffering and is almost always fatal . The disease is caused by infection with a virus of the genus Lyssavirus , of which 16 species are known . These viruses replicate in neurons , are excreted in the mouth , and are transmitted by bites . Dogs are the most important s...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "neuroscience", "animals", "mammals", "motor", "neurons", "viruses", "rna", "viruses", "fruit", "bats", "digestive", "system", "rabies", ...	2018	Pathogenesis of bat rabies in a natural reservoir: Comparative susceptibility of the straw-colored fruit bat (Eidolon helvum) to three strains of Lagos bat virus
The establishment of latent infections in sensory neurons is a remarkably effective immune evasion strategy that accounts for the widespread dissemination of life long Herpes Simplex Virus type 1 ( HSV1 ) infections in humans . Periodic reactivation of latent virus results in asymptomatic shedding and transmission of H...	Although mouse models have been very useful in studies of HSV1 latency , the inability to efficiently reactivate latent HSV1 in vivo has impeded studies of reactivation . Reasoning that reactivation would be much more efficient in the absence of T cells , we exploited IVIG to promote survival of latently infected Rag m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Establishment of HSV1 Latency in Immunodeficient Mice Facilitates Efficient In Vivo Reactivation
Hepatitis C virus ( HCV ) nonstructural protein ( NS ) 5A is a RNA-binding protein composed of a N-terminal membrane anchor , a structured domain I ( DI ) and two intrinsically disordered domains ( DII and DIII ) interacting with viral and cellular proteins . While DI and DII are essential for RNA replication , DIII is...	Hepatitis C virus ( HCV ) nonstructural protein ( NS ) 5A is an enigmatic RNA-binding protein that appears to regulate the different steps from RNA replication to the assembly of infectious virus particles by yet unknown mechanisms . Assembly requires delivery of the viral RNA genome from the replication machinery to t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Coordination of Hepatitis C Virus Assembly by Distinct Regulatory Regions in Nonstructural Protein 5A
Eukaryotic cell cycle involves a number of protein kinases important for the onset and progression through mitosis , most of which are well characterized in the budding and fission yeasts and conserved in other fungi . However , unlike the model yeast and filamentous fungi that have a single Cdc2 essential for cell cyc...	In the model yeasts and filamentous fungi , CDC2 is an essential gene that encodes the only CDK essential for mitotic cell cycle progression . However , the wheat scab fungus F . graminearum contains two CDC2 orthologs . The cdc2A and cdc2B deletion mutants had no defects in vegetative growth but deletion of both is le...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Two Cdc2 Kinase Genes with Distinct Functions in Vegetative and Infectious Hyphae in Fusarium graminearum
DNA methylation is an epigenetic modification that plays a crucial role in normal mammalian development , retrotransposon silencing , and cellular reprogramming . Although methylation mainly occurs on the cytosine in a CG site , non-CG methylation is prevalent in pluripotent stem cells , brain , and oocytes . We previo...	Methylation of cytosine bases in DNA is an epigenetic modification crucial for normal development , retrotransposon silencing , and cellular reprogramming . In mammals , the vast majority of 5-methylcytosine occurs at CG dinucleotides , and thus most studies to date have focused on this dinucleotide . However , recent ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "epigenetics", "biology" ]	2013	Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases
The gradient of Bicoid ( Bcd ) is key for the establishment of the anterior-posterior axis in Drosophila embryos . The gradient properties are compatible with the SDD model in which Bcd is synthesized at the anterior pole and then diffuses into the embryo and is degraded with a characteristic time . Within this model ,...	Understanding the mechanisms by which equivalent cells develop into different body parts is a fundamental question in biology . One well-studied example is the patterning along the anterior-posterior axis of Drosophila melanogaster embryos for which the spatial gradient of the protein Bicoid is determinant . The locali...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "developmental", "biology", "biophysics", "theory", "biology", "and", "life", "sciences", "chemistry", "physical", "sciences", "chemical", "physics", "biophysics" ]	2014	Messages Do Diffuse Faster than Messengers: Reconciling Disparate Estimates of the Morphogen Bicoid Diffusion Coefficient
Modern computational methods are revealing putative transcription-factor ( TF ) binding sites at an extraordinary rate . However , the major challenge in studying transcriptional networks is to map these regulatory element predictions to the protein transcription factors that bind them . We have developed a microarray-...	Specific interactions between protein transcription factors ( TFs ) and their DNA recognition sites are central to the regulation of gene expression . Inter-species conservation of these TF binding sites ( TFBS ) , and their statistical enrichment in sets of co-expressed genes , facilitates their large-scale prediction...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/transcription", "and", "translation", "biotechnology", "molecular", "biology", "genetics", "and", "genomics" ]	2009	Microarray Profiling of Phage-Display Selections for Rapid Mapping of Transcription Factor–DNA Interactions
Pancreatic islets manage elevations in blood glucose level by secreting insulin into the bloodstream in a pulsatile manner . Pulsatile insulin secretion is governed by islet oscillations such as bursting electrical activity and periodic Ca2+ entry in β-cells . In this report , we demonstrate that although islet oscilla...	A global shift throughout the last century toward excessive nutrient intake relative to energy expenditure has fueled a dramatic increase in the incidence of diabetes in humans . The epidemic is primarily of type 2 diabetes , a disease characterized by the inability of the body to effectively control blood glucose leve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "engineering", "and", "technology", "diabetic", "endocrinology", "bifurcation", "theory", "carbohydrates", "organic", "compounds", "glucose", "hormones", "endocrine", "physiology", "glucos...	2016	Glucose Oscillations Can Activate an Endogenous Oscillator in Pancreatic Islets
Recent advances in long-range Hi-C contact mapping have revealed the importance of the 3D structure of chromosomes in gene expression . A current challenge is to identify the key molecular drivers of this 3D structure . Several genomic features , such as architectural proteins and functional elements , were shown to be...	Chromosomal DNA is tightly packed up in 3D such that around 2 meters of this long molecule fits into the microscopic nucleus of every cell . The genome packing is not random , but instead structured in 3D domains that are essential to numerous key processes in the cell , such as for the regulation of gene expression or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "functional", "genomics", "computational", "biology", "dna-binding", "proteins", "enzymology", "animals", "invertebrate", "genomics", "animal", "models", "insulators", "drosophila", "melanogaster", "model", "organisms", "materials", "science", "genome", "an...	2016	Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation
Domains are the building blocks of proteins and play a crucial role in protein–protein interactions . Here , we propose a new approach for the analysis and prediction of domain–domain interfaces . Our method , which relies on the representation of domains as residue-interacting networks , finds an optimal decomposition...	Proteins are built by domains , which mediate protein–protein interactions involved in different biological activities . A challenging problem in computational biology is the understanding of the domain–domain interaction mechanism . Here , we propose a new approach for the analysis and prediction of domain–domain bind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "caenorhabditis", "computational", "biology", "drosophila", "biophysics", "molecular", "biology", "animals", "saccharomyces" ]	2007	The Modular Organization of Domain Structures: Insights into Protein–Protein Binding
Candida albicans is a prevalent fungal pathogen amongst the immunocompromised population , causing both superficial and life-threatening infections . Since C . albicans is diploid , classical transmission genetics can not be performed to study specific aspects of its biology and pathogenesis . Here , we exploit the dip...	Candida albicans is the principal human fungal pathogen responsible for life-threatening fungal infections . Despite an urgent need for more efficacious antifungal agents , the pace of discovery has waned using the traditional approaches . In part , this reflects the longstanding limitation of performing mechanism-of-a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "infectious", "diseases", "genetics", "and", "genomics", "yeast", "and", "fungi" ]	2007	Genome-Wide Fitness Test and Mechanism-of-Action Studies of Inhibitory Compounds in Candida albicans
Cellular signal transduction generally involves cascades of post-translational protein modifications that rapidly catalyze changes in protein-DNA interactions and gene expression . High-throughput measurements are improving our ability to study each of these stages individually , but do not capture the connections betw...	The ways in which cells respond to changes in their environment are controlled by networks of physical links among the proteins and genes . The initial signal of a change in conditions rapidly passes through these networks from the cytoplasm to the nucleus , where it can lead to long-term alterations in cellular behavi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "biochemistry", "genomics", "regulatory", "networks", "biology", "computational", "biology", "signaling", "networks", "proteomics" ]	2013	Linking Proteomic and Transcriptional Data through the Interactome and Epigenome Reveals a Map of Oncogene-induced Signaling
Malignant brain tumour ( MBT ) domain proteins are transcriptional repressors that function within Polycomb complexes . Some MBT genes are tumour suppressors , but how they prevent tumourigenesis is unknown . The Caenorhabditis elegans MBT protein LIN-61 is a member of the synMuvB chromatin-remodelling proteins that co...	The genome is continually under threat from exogenous sources of DNA damage , as well as from sources that originate within the cell . DNA double-strand breaks ( DSBs ) are arguably the most problematic type of damage as they can cause dangerous chromosome rearrangements , which can lead to cancer , as well as mutation...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "molecular", "cell", "biology", "nucleic", "acids", "dna", "biology", "dna", "repair", "molecular", "biology" ]	2013	A Role for the Malignant Brain Tumour (MBT) Domain Protein LIN-61 in DNA Double-Strand Break Repair by Homologous Recombination
Persistent activation of NF-κB by the Human T-cell leukemia virus type 1 ( HTLV-1 ) oncoprotein , Tax , is vital for the development and pathogenesis of adult T-cell leukemia ( ATL ) and HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . K63-linked polyubiquitinated Tax activates the IKK complex in...	HTLV-1 infection leads to the development of Adult T-cell Leukemia ( ATL ) or HTLV-1 associated myelopathy/ tropical spastic paraparesis ( HAM/TSP ) . One of the major causes responsible for the development of HTLV-1 associated diseases is chronic inflammation directed by NF-kappaB ( NF-κB ) . NF-κB activation in respo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Human T-Cell Leukemia Virus Type 1 (HTLV-1) Tax Requires CADM1/TSLC1 for Inactivation of the NF-κB Inhibitor A20 and Constitutive NF-κB Signaling
Gene transfer agents ( GTAs ) randomly transfer short fragments of a bacterial genome . A novel putative GTA was recently discovered in the mouse-infecting bacterium Bartonella grahamii . Although GTAs are widespread in phylogenetically diverse bacteria , their role in evolution is largely unknown . Here , we present a...	Viruses are selfish genetic elements that replicate and transfer their own DNA , often killing the host cell in the process . Unlike viruses , gene transfer agents ( GTAs ) transfer random pieces of the bacterial genome rather than their own DNA . GTAs are widespread in bacterial genomes , but it is not known whether t...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "microbiology", "biology", "genomics" ]	2013	A Gene Transfer Agent and a Dynamic Repertoire of Secretion Systems Hold the Keys to the Explosive Radiation of the Emerging Pathogen Bartonella
THO/TREX connects transcription with genome integrity in yeast , but a role of mammalian THO in these processes is uncertain , which suggests a differential implication of mRNP biogenesis factors in genome integrity in yeast and humans . We show that human THO depletion impairs transcription elongation and mRNA export ...	THO/TREX is an eukaryotic conserved complex , first identified in budding yeast , that acts at the interface between transcription and mRNP ( ribonucleoprotein ) export . In yeast , THO mutants show gene expression defects and a transcription-associated recombination phenotype . Despite the structural conservation of T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetics", "molecular", "genetics", "biology", "genetics", "and", "genomics" ]	2011	Genome Instability and Transcription Elongation Impairment in Human Cells Depleted of THO/TREX
The Esperanza Window Trap ( EWT ) baited with CO2 and human sweat compounds is attractive to Simulium ochraceum s . l . , the primary vector of Onchocerca volvulus in the historically largest endemic foci in México and Guatemala . The ability of the EWT to locally reduce numbers of questing S . ochraceum s . l . was ev...	The Esperanza window trap ( EWT ) , when used in large numbers ( 3-4/household and >90% coverage ) and baited with human sweat compounds and CO2 , can be used to collect epidemiologically significant numbers of Simulium ochraceum s . l . , the primary vector of Onchocerca volvulus in the historically largest endemic fo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "onchocerca", "volvulus", "education", "helminths", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "random", "variables", "teachers", "parasitic", "diseases", "animals", "on...	2017	The esperanza window trap reduces the human biting rate of Simulium ochraceum s.l. in formerly onchocerciasis endemic foci in Southern Mexico
Melanoma is the most fatal skin cancer , but the etiology of this devastating disease is still poorly understood . Recently , the transcription factor Sox10 has been shown to promote both melanoma initiation and progression . Reducing SOX10 expression levels in human melanoma cells and in a genetic melanoma mouse model...	For the development of future cancer therapies it is imperative to understand the molecular processes underlying tumor initiation and expansion . Many key factors involved in these processes have been identified based on cell culture and transplantation experiments , but their relevance for tumor formation and disease ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Antagonistic Cross-Regulation between Sox9 and Sox10 Controls an Anti-tumorigenic Program in Melanoma
Central obesity , measured by waist circumference ( WC ) or waist-hip ratio ( WHR ) , is a marker of body fat distribution . Although obesity disproportionately affects minority populations , few studies have conducted genome-wide association study ( GWAS ) of fat distribution among those of predominantly African ances...	Central obesity is a marker of body fat distribution and is known to have a genetic underpinning . Few studies have reported genome-wide association study ( GWAS ) results among individuals of predominantly African ancestry ( AA ) . We performed a collaborative meta-analysis in order to identify genetic loci associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "genetics", "biology", "metabolic", "disorders" ]	2013	Genome-Wide Association of Body Fat Distribution in African Ancestry Populations Suggests New Loci
Stable integration of HIV proviral DNA into host cell chromosomes , a hallmark and essential feature of the retroviral life cycle , establishes the infection permanently . Current antiretroviral combination drug therapy cannot cure HIV infection . However , expressing an engineered HIV-1 long terminal repeat ( LTR ) si...	Current antiretroviral combination therapy can efficiently suppress virus replication , but cannot eliminate HIV . Therefore , no cure for HIV exists . A main hurdle for virus eradication is seen in the existence of resting cells that contain integrated replication-competent , but temporarily silenced , HIV genomes . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Highly Significant Antiviral Activity of HIV-1 LTR-Specific Tre-Recombinase in Humanized Mice
The presence of bottlenecks in the transmission cycle of many RNA viruses leads to a severe reduction of number of virus particles and this occurs multiple times throughout the viral transmission cycle . Viral replication is then necessary for regeneration of a diverse mutant swarm . It is now understood that any pertu...	RNA viruses replicate with a high mutation rate , giving them the ability to generate mutations that might be beneficial under different selection pressures . Any perturbation of the accumulation of mutations has been shown to result in severe attenuation of the virus . However , the mechanism of this attenuation is st...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "microbial", "mutation", "medicine", "and", "health", "sciences", "insertion", "mutation", "microbiology", "vertebrates", "cloning", "animals", "viruses", "mutation", "rna", "viruses", "molecular", "biology", "techniques", "insect", "vectors", "microbial"...	2019	Viral RNA-dependent RNA polymerase mutants display an altered mutation spectrum resulting in attenuation in both mosquito and vertebrate hosts
Members of the species Rickettsia are obligate intracellular , gram-negative , arthropod-borne pathogens of humans and other mammals . The life-threatening character of diseases caused by many Rickettsia species and the lack of reliable protective vaccine against rickettsioses strengthens the importance of identifying ...	Several rickettsiae are pathogenic to humans by causing severe infections , including epidemic typhus ( Rickettsia prowazekii ) , Rocky Mountain spotted fever ( Rickettsia rickettsii ) , and Mediterranean spotted fever ( Rickettsia conorii ) . Progress in correlating rickettsial genes and gene functions has been greatl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "gram", "negative", "bacteria", "biochemistry", "hydrolases", "enzymes", "bacterial", "genes", "biology", "and", "life", "sciences", "proteases", "enzymology", "biochemical", "activity", "microbiology", "pepsins", "aspartate", "proteases" ]	2014	RC1339/APRc from Rickettsia conorii Is a Novel Aspartic Protease with Properties of Retropepsin-Like Enzymes
Given the widespread distribution of Plasmodium and helminth infections , and similarities of ecological requirements for disease transmission , coinfection is a common phenomenon in sub-Saharan Africa and elsewhere in the tropics . Interactions of Plasmodium falciparum and soil-transmitted helminths , including immuno...	In sub-Saharan Africa , parasitic worms ( helminths ) are among the most common chronic infections , malaria among the most deadly , and coinfection is the norm rather than the exception . Infections with hookworm and Plasmodium can decrease the level of hemoglobin and are therefore associated with anemia . Previous st...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "tropical", "diseases", "(non-neglected)", "neglected", "tropical", "diseases", "parasitic", "diseases", "anemia", "hematology" ]	2012	Interactions and Potential Implications of Plasmodium falciparum-Hookworm Coinfection in Different Age Groups in South-Central Côte d'Ivoire
Several reports suggest obesity and bipolar disorder ( BD ) share some physiological and behavioural similarities . For instance , obese individuals are more impulsive and have heightened reward responsiveness , phenotypes associated with BD , while bipolar patients become obese at a higher rate and earlier age than pe...	The World Health Organization suggests obesity is a major cause of poor health and is becoming the leading public health concern . Likewise , mood-based disorders , such as bipolar disorder , are one of the top ten causes of disability worldwide . There is evidence that obesity and bipolar disorder may be linked and th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "body", "weight", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "nervous", "system", "dopaminergics", "bipolar", "disorder", "neuroscience", "animals", "organic", "compounds", "hormones", "animal", "models", "drosophi...	2016	The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder
The Alanine-Serine-Cysteine transporter ASCT2 ( SLC1A5 ) is a membrane protein that transports neutral amino acids into cells in exchange for outward movement of intracellular amino acids . ASCT2 is highly expressed in peripheral tissues such as the lung and intestines where it contributes to the homeostasis of intrace...	ASCT2 is a membrane protein that imports neutral amino acids into cells in exchange for intracellular amino acids . ASCT2 is highly expressed in peripheral tissues such as the lung , where it contributes to the homeostasis of intracellular concentrations of neutral amino acids . Recently , ASCT2 has been shown to be im...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening
Horizontal gene transfer ( HGT ) is an important mode of adaptation and diversification of prokaryotes and eukaryotes and a major event underlying the emergence of bacterial pathogens and mutualists . Yet it remains unclear how complex phenotypic traits such as the ability to fix nitrogen with legumes have successfully...	Horizontal gene transfer has an extraordinary impact on microbe evolution and diversification , by allowing exploration of new niches such as higher organisms . This is the case for rhizobia , a group of phylogenetically diverse bacteria that form a nitrogen-fixing symbiotic relationship with most leguminous plants . W...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "ecology", "and", "environmental", "sciences" ]	2014	Transient Hypermutagenesis Accelerates the Evolution of Legume Endosymbionts following Horizontal Gene Transfer
Meiotic chromosomes are organized into linear looped chromatin arrays by a protein axis localized along the loop-bases . Programmed remodelling of the axis occurs during prophase I of meiosis . Structured illumination microscopy ( SIM ) has revealed dynamic changes in the chromosome axis in Arabidopsis thaliana and Bra...	In the reproductive cells of many eukaryotes , a process called meiosis generates haploid gametes . During meiosis , homologous parental chromosomes ( homologs ) recombine forming crossovers ( CO ) that provide genetic variation . CO formation generates physical links called chiasmata , which are essential for accurate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers

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