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RNA virus populations will undergo processes of mutation and selection resulting in a mixed population of viral particles . High throughput sequencing of a viral population subsequently contains a mixed signal of the underlying clones . We would like to identify the underlying evolutionary structures . We utilize two s...	Any functional influenza virus particle is made up of eight distinct RNA segments . There can be in the order of 106 such particles per mL of infected tissue . Furthermore , on average , each new virus particle has a single mutation distinguishing the virus from its parent particle . The population of viruses thus cont...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Inferring the Clonal Structure of Viral Populations from Time Series Sequencing
Phosphatidylinositol-3-phosphate 5-kinase ( PIKfyve ) is a lipid kinase involved in endosome maturation that emerged from a haploid genetic screen as being required for Ebola virus ( EBOV ) infection . Here we analyzed the effects of apilimod , a PIKfyve inhibitor that was reported to be well tolerated in humans in pha...	The recent outbreak of Ebola virus ( EBOV ) disease in Western Africa highlights the urgent need to develop therapeutics to help quell this devastating hemorrhagic fever virus , especially in resource-limited areas around the globe . Here we show that apilimod , an investigational drug that was well-tolerated in phase ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "vesicles", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "drug", "screening", "viruses", "filoviruses", "clinical", "medicine", "rna", "viruses", ...	2017	The phosphatidylinositol-3-phosphate 5-kinase inhibitor apilimod blocks filoviral entry and infection
In nature , rabies virus ( RABV; genus Lyssavirus , family Rhabdoviridae ) represents an assemblage of phylogenetic lineages , associated with specific mammalian host species . Although it is generally accepted that RABV evolved originally in bats and further shifted to carnivores , mechanisms of such host shifts are p...	Host shifts of the rabies virus ( RABV ) from bats to carnivores are important for our understanding of viral evolution and emergence , and have significant public health implications , particularly for the areas where “terrestrial” rabies has been eliminated . In this study we addressed several rabies outbreaks in car...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "genome", "evolution", "microbiology", "convergent", "evolution", "veterinary", "science", "infectious", "diseases", "forms", "of", "evolution", "veterinary", "diseases", "epidemiology", "biology", "viral", "evolution...	2012	Molecular Inferences Suggest Multiple Host Shifts of Rabies Viruses from Bats to Mesocarnivores in Arizona during 2001–2009
σ factors provide RNA polymerase with promoter specificity in bacteria . Some σ factors require activation in order to interact with RNA polymerase and transcribe target genes . The Extra-Cytoplasmic Function ( ECF ) σ factor , σV , is encoded by several Gram-positive bacteria and is specifically activated by lysozyme ...	The exposed cell wall of Gram-positive bacteria renders them particularly susceptible to the innate immune defense enzyme lysozyme . Several Gram-positive bacteria activate lysozyme resistance via a signal transduction system , σV , which is induced by lysozyme . Here we report the co-structure of lysozyme with its bac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "bacillus", "microbiology", "enzymology", "vertebrates", "condensed", "matter", "physics", "animals", "mammal...	2016	The Anti-sigma Factor RsiV Is a Bacterial Receptor for Lysozyme: Co-crystal Structure Determination and Demonstration That Binding of Lysozyme to RsiV Is Required for σV Activation
Haploid germline nuclei of many filamentous fungi have the capacity to detect homologous nucleotide sequences present on the same or different chromosomes . Once recognized , such sequences can undergo cytosine methylation or cytosine-to-thymine mutation specifically over the extent of shared homology . In Neurospora c...	Recombination-independent pairing of homologous double-stranded DNA molecules is associated with many important biological processes including the alignment of homologous chromosomes in early meiosis , monoallelic gene expression in mammals , and somatic pairing of homologous chromosomes in Drosophila . The molecular m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "homologous", "chromosomes", "mutation", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "dna", "dna", "recombination", "homologous", "recombination", "research", "and", "analysis", "methods", "sequence", "analysis", "seq...	2016	Recombination-Independent Recognition of DNA Homology for Repeat-Induced Point Mutation (RIP) Is Modulated by the Underlying Nucleotide Sequence
Taenia solium cysticercosis affects millions of impoverished people worldwide and can cause neurocysticercosis , an infection of the central nervous system which is potentially fatal . Children may represent an especially vulnerable population to neurocysticercosis , due to the risk of cognitive impairment during forma...	The zoonotic tapeworm , Taenia solium , affects millions of impoverished people worldwide and can cause neurocysticercosis ( NCC ) , an infection of the central nervous system which is potentially fatal . Hypothetically , children may be a vulnerable population to infection as neurological problems and cognitive impair...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "education", "sociology", "tropical", "diseases", "vertebrates", "social", "sciences", "diet", "parasitic", "diseases", "animals", "mammals", "pediatrics", "animal", "products", "age", ...	2018	Prevalence and risk factors for Taenia solium cysticercosis in school-aged children: A school based study in western Sichuan, People’s Republic of China
Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities . This control can be exerted by metabolites acting as regulatory signals and/or a class of metabolic enzymes with dual functions as regulators of gene expression . However , little is know...	Metabolic control of gene expression coordinates the levels of specific gene products to meet cellular demand for their activities . This control can be exerted by metabolites acting as regulatory signals on a class of metabolic enzymes with dual functions as regulators of gene expression . However , little is known ab...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "plant", "biochemistry", "plant", "science", "model", "organisms", "plant", "biology", "plant", "cell", "biology", "botany", "biology", "molecular", "cell", "biology" ]	2013	Reciprocal Regulation of Protein Synthesis and Carbon Metabolism for Thylakoid Membrane Biogenesis
A fundamental step in the evolution of the visual system is the gene duplication of visual opsins and differentiation between the duplicates in absorption spectra and expression pattern in the retina . However , our understanding of the mechanism of expression differentiation is far behind that of spectral tuning of op...	Among vertebrates , fish may have the most advanced color vision . They have greatly varied repertoires of color sensors called visual opsins , possibly reflecting evolutionary adaptation to their diverse photic environments in water , and are an excellent model to study the evolution of vertebrate color vision . This ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "developmental", "biology/molecular", "development" ]	2010	A Single Enhancer Regulating the Differential Expression of Duplicated Red-Sensitive Opsin Genes in Zebrafish
The Cucumber mosaic virus ( CMV ) Y-satellite RNA ( Y-Sat ) has a small non-protein-coding RNA genome that induces yellowing symptoms in infected Nicotiana tabacum ( tobacco ) . How this RNA pathogen induces such symptoms has been a longstanding question . We show that the yellowing symptoms are a result of small inter...	Viral infections result in a variety of disease symptoms that vary in character and severity depending on the type of viral infection and individual host factors . Despite extensive research , the molecular basis of viral disease development has remained poorly understood . Both plant and animal viruses express 20–25 n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "plant", "pathogens", "plant", "pathology", "biology" ]	2011	Viral Small Interfering RNAs Target Host Genes to Mediate Disease Symptoms in Plants
Informed consent is one of the principal ethical requirements of conducting clinical research , regardless of the study setting . Breaches in the quality of the informed consent process are frequently described in reference to clinical trials conducted in developing countries , due to low levels of formal education , a...	Informed consent is an essential element of the ethical conduct of clinical trials of new vaccines , regardless of the study setting . However , the quality of informed consent is often suboptimal . Some research has suggested that the quality of the informed consent process may be reduced in resource-limited areas com...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "united", "states", "invertebrates", "medicine", "and", "health", "sciences", "health", "services", "research", "helminths", "immunology", "geographical", "locations", "hookworms", "animals", "health", "care", "vaccines", "preventive", "medicine", "research", "design", ...	2017	A Comparison of the Quality of Informed Consent for Clinical Trials of an Experimental Hookworm Vaccine Conducted in Developed and Developing Countries
Eukaryotic cells often use proteins localized to the ciliary membrane to monitor the extracellular environment . The mechanism by which proteins are sorted , specifically to this subdomain of the plasma membrane , is almost completely unknown . Previously , we showed that the IFT20 subunit of the intraflagellar transpo...	The primary cilium is a sensory organelle used by cells to monitor the extracellular environment . In mouse , severe defects in primary cilia lead to embryonic lethality while less severe defects cause a pleiotrophic phenotype that includes cystic kidney disease , retinal degeneration , obesity , and hydrocephaly , amo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "cell", "biology", "genetics", "and", "genomics" ]	2008	The Golgin GMAP210/TRIP11 Anchors IFT20 to the Golgi Complex
Genes are regulated because their expression involves a fitness cost to the organism . The production of proteins by transcription and translation is a well-known cost factor , but the enzymatic activity of the proteins produced can also reduce fitness , depending on the internal state and the environment of the cell ....	The levels of protein produced by an organism are likely to change its fitness , potentially driving the evolution of genetic regulation . Importantly , protein expression generates costs as well as benefits . Here , we use a model genetic system , the lac operon of Escherichia coli , to investigate different sources o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "mutation", "population", "genetics", "evolutionary", "selection", "microbiology", "mutation", "microbial", "evolution", "biology", "evolutionary", "theory", "evolutionary", "genetics", "systems", "biology", "natural", "selection", "evolutionary",...	2011	Nonlinear Fitness Landscape of a Molecular Pathway
Inner ear mechanosensory hair cells transduce sound and balance information . Auditory hair cells emerge from a Sox2-positive sensory patch in the inner ear epithelium , which is progressively restricted during development . This restriction depends on the action of signaling molecules . Fibroblast growth factor ( FGF ...	The ability of our brain to perceive sound depends on its conversion into electrical impulses within the cochlea of the inner ear . The cochlea has dedicated specialized cells , called inner ear hair cells , which register sound energy . Environmental effects , genetic disorders or just the passage of time can damage t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "morphogens", "medicine", "developmental", "biology", "cell", "fate", "determination", "developmental", "neuroscience", "neurogenesis", "otology", "signaling", "molecular", "development", "hearing", "disorders", "biology", "otorhinolaryngology", "neuroscience", "cell", "diffe...	2014	FGFR1-Frs2/3 Signalling Maintains Sensory Progenitors during Inner Ear Hair Cell Formation
At many promoters , transcription is regulated by simultaneous binding of a protein to multiple sites on DNA , but the structures and dynamics of such transcription factor-mediated DNA loops are poorly understood . We directly examined in vitro loop formation mediated by Escherichia coli lactose repressor using single-...	Some proteins that regulate DNA transcription do so by binding simultaneously to two separated sites on the DNA molecule , forming a DNA loop . Although such loops are common , many of their features are poorly characterized . Of particular interest is the question of how some proteins accommodate the formation of loop...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biophysics", "molecular", "biology" ]	2008	Interconvertible Lac Repressor–DNA Loops Revealed by Single-Molecule Experiments
Intrinsically disordered proteins play an important role in cellular signalling , mediated by their interactions with other biomolecules . A key question concerns the nature of their binding mechanism , and whether the bound structure is induced only by proximity to the binding partner . This is difficult to answer thr...	While many proteins have a specific ‘native’ conformation , so-called intrinsically disordered proteins ( IDPs ) adopt many different conformations in rapid succession—a characteristic that may be advantageous for rapid binding and promiscuous association . However , this characteristic also makes it very hard to make ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "protein", "folding", "biophysics", "theory", "biology", "biophysics", "simulations", "biophysics" ]	2012	A Preformed Binding Interface in the Unbound Ensemble of an Intrinsically Disordered Protein: Evidence from Molecular Simulations
Helminths express various carbohydrate-containing glycoconjugates on their surface , and they release glycan-rich excretion/secretion products that can be very important in their life cycles , infection and pathology . Recent evidence suggests that parasite glycoconjugates could play a role in the evasion of the immune...	Fasciola hepatica is a helminth that infects mainly ruminants , causing great economic losses worldwide . Importantly , fasciolosis is also considered an emerging zoonosis with an increasing number of human infections globally . As other helminths , F . hepatica is able to regulate the host immune response favoring par...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Glycans from Fasciola hepatica Modulate the Host Immune Response and TLR-Induced Maturation of Dendritic Cells
Toxoplasma gondii possesses sets of dense granule proteins ( GRAs ) that either assemble at , or cross the parasitophorous vacuole membrane ( PVM ) and exhibit motifs resembling the HT/PEXEL previously identified in a repertoire of exported Plasmodium proteins . Within Plasmodium spp . , cleavage of the HT/PEXEL motif ...	The opportunistic pathogen Toxoplasma gondii infects a large range of nucleated cells where it replicates intracellularly within a parasitophorous vacuole ( PV ) surrounded by a membrane ( PVM ) . Parasites constitutively secrete dense-granule proteins ( GRAs ) both into and beyond the PV which participate in remodelli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Fundamental Roles of the Golgi-Associated Toxoplasma Aspartyl Protease, ASP5, at the Host-Parasite Interface
The poxvirus life cycle , although physically autonomous from the host nucleus , is nevertheless dependent upon cellular functions . A requirement for de novo fatty acid biosynthesis was implied by our previous demonstration that cerulenin , a fatty acid synthase inhibitor , impaired vaccinia virus production . Here we...	Vaccinia virus , the prototypic poxvirus , is closely related to variola virus , the etiological agent of smallpox . A full understanding of the poxviral life cycle is imperative for the development of novel antiviral therapies , the design of new vaccines , and the effective and safe use of these viruses as oncolytic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "subcellular", "organelles", "protein", "metabolism", "enzymes", "microbiology", "oxygen", "metabolism", "protein", "synthesis", "dna", "replication", "dna", "bioenergetics", "lipid", "metabolism", "proteins", "metabolic", "pathways", "biology", ...	2014	De novo Fatty Acid Biosynthesis Contributes Significantly to Establishment of a Bioenergetically Favorable Environment for Vaccinia Virus Infection
Polypeptides exiting the ribosome must fold and assemble in the crowded environment of the cell . Chaperones and other protein homeostasis factors interact with newly translated polypeptides to facilitate their folding and correct localization . Despite the extensive efforts , little is known about the specificity of t...	In every cell , ribosomes translate the genetic instructions carried by messenger RNAs into the proteins they encode . Molecular midwives called chaperones often bind to nascent protein chains as they emerge from the ribosome to help them fold . Very little is known about this process . Do all proteins need chaperone a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "biochemistry", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	Defining the Specificity of Cotranslationally Acting Chaperones by Systematic Analysis of mRNAs Associated with Ribosome-Nascent Chain Complexes
White blood cell ( WBC ) count is a common clinical measure from complete blood count assays , and it varies widely among healthy individuals . Total WBC count and its constituent subtypes have been shown to be moderately heritable , with the heritability estimates varying across cell types . We studied 19 , 509 subjec...	WBC traits are highly variable , moderately heritable , and commonly assayed as part of clinical complete blood count ( CBC ) examinations . The counts of constituent cell subtypes comprising the WBC count measure are assayed as part of a standard clinical WBC differential test . In this study we employed meta-analytic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "medicine", "public", "health", "and", "epidemiology", "statistics", "applied", "mathematics", "immunology", "text", "mining", "mathematics", "population", "biology", "information", "technology", "epidemiology", "biology", "hematology", "computer", "science...	2011	Multiple Loci Are Associated with White Blood Cell Phenotypes
We propose a biologically plausible architecture for unsupervised ensemble learning in a population of spiking neural network classifiers . A mixture of experts type organisation is shown to be effective , with the individual classifier outputs combined via a gating network whose operation is driven by input timing dep...	Ensemble effects appear to be common in the nervous system . That is , there are many examples of where groups of neurons , or groups of neural circuits , act together to give better performance than is possible from a single neuron or single neural circuit . For instance , there is evidence that ensembles of spatially...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "learning", "and", "memory", "synaptic", "plasticity", "cognitive", ...	2016	Unsupervised Learning in an Ensemble of Spiking Neural Networks Mediated by ITDP
The nematode Caenorhabditis elegans is a popular model system in genetics , not least because a majority of human disease genes are conserved in C . elegans . To generate a comprehensive inventory of its expressed proteome , we performed extensive shotgun proteomics and identified more than half of all predicted C . el...	Proteins are the active players that execute the genetic program of a cell , and their levels and interactions are precisely controlled . Routinely monitoring thousands of proteins is difficult , as they can be present at vastly different abundances , come with various sizes , shapes , and charge , and have a more comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "evolutionary", "biology" ]	2009	Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes
Sexually dimorphic phenotypes are a universal phenomenon in animals . In the model animal fruit fly Drosophila , males and females exhibit long- and short-sleep phenotypes , respectively . However , the mechanism is still a mystery . In this study , we showed that juvenile hormone ( JH ) is involved in regulation of se...	Sleep is a very important biological behavior in all animals and takes up around one third of the lifespan in many animals . In both insects and mammals ( including humans ) , sleep differences between male and female ( sexually dimorphic sleep ) have been described over the past decades . However , its internal regula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "sleep", "gene", "regulation", "neuroscience", "animals", "animal", "models", "physiological", "processes", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", ...	2018	Sexual dimorphism of sleep regulated by juvenile hormone signaling in Drosophila
The neural mechanisms determining the timing of even simple actions , such as when to walk or rest , are largely mysterious . One intriguing , but untested , hypothesis posits a role for ongoing activity fluctuations in neurons of central action selection circuits that drive animal behavior from moment to moment . To e...	The brain is never quiet . Even in the absence of environmental cues , neurons receive and produce an ongoing barrage of fluctuating signals . These fluctuations are well studied in the sensory periphery but their potential influence on central circuits and behavior are unknown . In particular , activity fluctuations i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Fluctuation-Driven Neural Dynamics Reproduce Drosophila Locomotor Patterns
Membrane bioenergetics are universal , yet the phospholipid membranes of archaea and bacteria—the deepest branches in the tree of life—are fundamentally different . This deep divergence in membrane chemistry is reflected in other stark differences between the two domains , including ion pumping and DNA replication . We...	The archaea and bacteria are the deepest branches of the tree of life . The two groups are similar in morphology and share some fundamental biochemistry , including the genetic code , but the differences between them are stark , and rank among the great unsolved problems in biology . The composition of cell membranes a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "astrobiology", "cell", "biology", "earth", "sciences", "genetics", "biology", "and", "life", "sciences", "chemistry", "microbiology", "computational", "biology", "evolutionary", "biology", "physical", "sciences", "biophysics", "geochemistry" ]	2014	A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria
The regulation of mucosal immune function is critical to host protection from enteric pathogens but is incompletely understood . The nervous system and the neurotransmitter acetylcholine play an integral part in host defense against enteric bacterial pathogens . Here we report that acetylcholine producing-T-cells , as ...	The nervous system is an active contributor to the regulation of immune responses . Prior studies have identified a unique CD4+ T-cell population that can relay signals from the sympathetic nervous system . These specialized T-cells express the enzyme choline acetyltransferase ( ChAT ) and produce acetylcholine ( ACh )...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2019	T-cell derived acetylcholine aids host defenses during enteric bacterial infection with Citrobacter rodentium
An increased prevalence of epilepsy has been reported in many onchocerciasis endemic areas . To determine the prevalence and distribution of epilepsy in an onchocerciasis endemic region in the Democratic Republic of the Congo ( DRC ) . An epilepsy prevalence study was carried out in 2014 , in two localities of the Bas-...	An increased prevalence of epilepsy has been reported in many onchocerciasis ( river blindness ) endemic areas . In 2014 , an epilepsy prevalence study was conducted in Dingila and Titule , two localities within the onchocerciasis endemic Orientale province of the Democratic Republic of Congo , both within the Bas-Uélé...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "onchocerca", "volvulus", "rivers", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "parasitic", "diseases", "animals", "onchoc...	2016	Prevalence of River Epilepsy in the Orientale Province in the Democratic Republic of the Congo
Human mobility plays a central role in shaping pathogen transmission by generating spatial and/or individual variability in potential pathogen-transmitting contacts . Recent research has shown that symptomatic infection can influence human mobility and pathogen transmission dynamics . Better understanding the complex r...	Dengue is the most important mosquito-borne viral disease of humans worldwide . Due to the limited mobility of the mosquitoes that transmit dengue virus , human mobility can be a key to both understanding an individual’s exposure to the virus and explaining the spread of dengue throughout a population . Accurate diseas...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "spatial", "epidemiology", "microbiology", "social", "sciences", "human", "...	2019	Dengue illness impacts daily human mobility patterns in Iquitos, Peru
The Government of Senegal has initiated the “Projet de lutte contre les glossines dans les Niayes” to remove the trypanosomosis problem from this area in a sustainable way . Due to past failures to sustainably eradicate Glossina palpalis gambiensis from the Niayes area , controversies remain as to the best strategy imp...	Tsetse flies transmit trypanosomes to humans ( sleeping sickness ) and animals ( nagana ) . Controlling these vectors is a very efficient way to contain these diseases . There are several strategies and methods that can be used for control , each being more or less efficient depending on several factors . The Governmen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2010	Population Genetics as a Tool to Select Tsetse Control Strategies: Suppression or Eradication of Glossina palpalis gambiensis in the Niayes of Senegal
Praziquantel ( PZQ ) is the treatment of choice for infections with the liver fluke Opisthorchis viverrini , a major health problem in Southeast Asia . However , pharmacokinetic ( PK ) studies investigating the disposition of PZQ enantiomers ( R- and S-PZQ ) and its main metabolite , R-trans-4-OH-PZQ , in diseased pati...	Opisthorchiasis , caused by the food-borne trematode Opisthorchis viverrini , affects more than 8 million people in Southeast Asia , and in its chronic phase it might lead to cholangiocarcinoma . Praziquantel ( PZQ ) is the sole drug available to treat the disease and is administered as a racemic mixture of R and S ena...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "stereoisomers", "chemical", "compounds", "tropical", "diseases", "parasitic", "diseases", "isomerism", "foodborne", "trematodiases", "metabolites", "pharmaceutics", "neglected", "tropical", "diseases", "pharmacolog...	2016	Pharmacokinetic Study of Praziquantel Enantiomers and Its Main Metabolite R-trans-4-OH-PZQ in Plasma, Blood and Dried Blood Spots in Opisthorchis viverrini-Infected Patients
Phenotypic plasticity is associated with non-genetic drug tolerance in several cancers . Such plasticity can arise from chromatin remodeling , transcriptomic reprogramming , and/or protein signaling rewiring , and is characterized as a cell state transition in response to molecular or physical perturbations . This , in...	Cancer cells exhibit varied degrees of phenotypic heterogeneity . These phenotypes , each of them with unique molecular and functional profiles , display dynamic interconversion in response to drug perturbations , and can evolve to form new drug-tolerant phenotypes . Such phenotypic plasticity , in turn , renders tumor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "medicine", "and", "health", "sciences", "population", "dynamics", "biological", "cultures", "pharmaceutics", "genome", "analysis", "cell", "cultures", "population", "biology", "melanoma", "cells", "thermodynamics", "research", "and", "analysis", "m...	2019	Phenotypic heterogeneity and evolution of melanoma cells associated with targeted therapy resistance
Mycobacterium ulcerans disease , or Buruli ulcer ( BU ) , is an indolent , necrotizing infection of skin , subcutaneous tissue and , occasionally , bones . It is the third most common human mycobacteriosis worldwide , after tuberculosis and leprosy . There is evidence that M . ulcerans is an environmental pathogen tran...	Mycobacterium ulcerans infection , or Buruli ulcer , is the third most common mycobacteriosis of humans worldwide , after tuberculosis and leprosy . Buruli ulcer is a neglected , devastating , necrotizing disease , sometimes producing massive , disfiguring ulcers , with huge social impact . Buruli ulcer occurs predomin...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	First Cultivation and Characterization of Mycobacterium ulcerans from the Environment
In October 2017 , a blood sample from a resident of Kween District , Eastern Uganda , tested positive for Marburg virus . Within 24 hour of confirmation , a rapid outbreak response was initiated . Here , we present results of epidemiological and laboratory investigations . A district task force was activated consisting...	Marburg virus disease ( MVD ) is caused by the virus that belongs to the same family as that of Ebola Virus disease . The disease is characterized by severe clinical symptoms such as high fever , diarrhoea and vomiting , and severe bleeding from most body openings . On average , 54% of the people who get infected with ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "marburg", "virus", "uganda", "geographical", "locations", "vertebrates", "animals", "mammals", "viruses", "filoviruses", "rna", "viruses", "signs", "and", "...	2019	Marburg virus disease outbreak in Kween District Uganda, 2017: Epidemiological and laboratory findings
Human strongyloidiasis varies from a chronic but limited infection in normal hosts to hyperinfection in patients treated with corticosteroids or with HTLV-1 co-infection . Regulatory T cells dampen immune responses to infections . How human strongyloidiasis is controlled and how HTLV-1 infection affects this control ar...	Human strongyloidiasis varies from a mild , controlled infection to a severe frequently fatal disseminated infection depending on the hosts . Patients infected with the retrovirus HTLV-1 have more frequent and more severe forms of strongyloidiasis . It is not clear how human strongyloidiasis is controlled by the immune...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "virology/immunodeficiency", "viruses", "immunology", "immunology/immune", "response" ]	2009	Regulatory T Cell Expansion in HTLV-1 and Strongyloidiasis Co-infection Is Associated with Reduced IL-5 Responses to Strongyloides stercoralis Antigen
Paired Immunoglobulin-like Type 2 Receptor Alpha ( PILRA ) is a cell surface inhibitory receptor that recognizes specific O-glycosylated proteins and is expressed on various innate immune cell types including microglia . We show here that a common missense variant ( G78R , rs1859788 ) of PILRA is the likely causal alle...	Alzheimer’s disease ( AD ) is a devastating neurodegenerative disorder resulting from a complex interaction of environmental and genetic risk factors . Despite considerable progress in defining the genetic component of AD risk , understanding the biology of common variant associations is a challenge . We find that PILR...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "flow", "cytometry", "cell", "physiology", "blood", "cells", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "cells", "neurodegenerative", "diseases", "293t", "cells", "biological", "cultures", "immunology", "alzheim...	2018	Paired Immunoglobulin-like Type 2 Receptor Alpha G78R variant alters ligand binding and confers protection to Alzheimer's disease
The intracellular bacterial pathogen Shigella infects and spreads through the human intestinal epithelium . Effector proteins delivered by Shigella into cells promote infection by modulating diverse host functions . We demonstrate that the effector protein OspB interacts directly with the scaffolding protein IQGAP1 , a...	During infection , Shigella spp . deliver into the cytoplasm of cells effector proteins that manipulate host cell processes in ways that promote infection and bacterial spread . We have discovered that the Shigella effector protein OspB interacts with the cellular scaffolding protein IQGAP1 . OspB induces increased cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Shigella Effector OspB Activates mTORC1 in a Manner That Depends on IQGAP1 and Promotes Cell Proliferation
During vertebrate craniofacial development , neural crest cells ( NCCs ) contribute to most of the craniofacial pharyngeal skeleton . Defects in NCC specification , migration and differentiation resulting in malformations in the craniofacial complex are associated with human craniofacial disorders including Treacher-Co...	Here , we describe the identification and characterization of a novel zebrafish craniofacial mutant , fantome ( fan ) , caused by a point mutation in the wdr43 gene . Although previously characterized as UTP5 in yeast , a nucleolar protein functioning in ribosome biogenesis , here we show that Wdr43 also regulates earl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "genomics", "neuroscience" ]	2014	Tissue Specific Roles for the Ribosome Biogenesis Factor Wdr43 in Zebrafish Development
Populations of Human Immunodeficiency Virus type 1 ( HIV-1 ) undergo a surprisingly large amount of genetic drift in infected patients despite very large population sizes , which are predicted to be mostly deterministic . Several models have been proposed to explain this phenomenon , but all of them implicitly assume t...	Genetic drift can be a strong evolutionary force , especially in small populations . Studies of HIV evolution within a single infected patient suggest that genetic drift plays an important role in the evolution of the virus , despite the large size of the viral population . The factors responsible for the high genetic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virus", "evolution", "and", "symbiosis", "molecular", "biology/molecular", "evolution", "virology/immunodeficiency", "viruses", "virology", "genetics", "and", "genomics/population", "genetics" ]	2009	Genetic Drift of HIV Populations in Culture
Military conflict has been a major challenge in the detection and control of emerging infectious diseases such as malaria . It poses issues associated with enhancing emergence and transmission of infectious diseases by destroying infrastructure and collapsing healthcare systems . The Orakzai agency in Pakistan has witn...	The malaria epidemic and endemic in Pakistan is a present and ongoing threat to public health which could have an impact in the nearby regions as well . For the first time , we report a clinical assessment of malaria endemicity in the Orakzai Agency , which is Pakistan’s most neglected area due to Talibanization and wa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Epidemiology and Clinical Burden of Malaria in the War-Torn Area, Orakzai Agency in Pakistan
The polarization of nascent embryonic fields and the endowment of cells with organizer properties are key to initiation of vertebrate organogenesis . One such event is antero-posterior ( AP ) polarization of early limb buds and activation of morphogenetic Sonic Hedgehog ( SHH ) signaling in the posterior mesenchyme , w...	During early limb bud development , posterior mesenchymal cells are selected to express Sonic Hedgehog ( Shh ) , which controls antero-posterior ( AP ) limb axis formation ( axis from thumb to little finger ) . We generated a conditional loss-of-function Hand2 allele to inactivate Hand2 specifically in mouse limb buds ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "developmental", "biology", "developmental", "biology/morphogenesis", "and", "cell", "biology", "developmental", "biology/pattern", "formation", "genetics", "and", "genomics/gene", "function", "developmental", "biology/molecular", "developme...	2010	Distinct Roles of Hand2 in Initiating Polarity and Posterior Shh Expression during the Onset of Mouse Limb Bud Development
A new methodology termed Single Amino Acid Mutation based change in Binding free Energy ( SAAMBE ) was developed to predict the changes of the binding free energy caused by mutations . The method utilizes 3D structures of the corresponding protein-protein complexes and takes advantage of both approaches: sequence- and ...	Developing methods for accurate prediction of effects of amino acid substitutions on protein-protein affinity is important for both understanding disease-causing mechanism of missense mutations and guiding protein engineering . For both purposes , there is a need for accurate methods primarily based on first principle ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[]	2015	Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
Microalgae are promising microorganisms for the production of numerous molecules of interest , such as pigments , proteins or triglycerides that can be turned into biofuels . Heterotrophic or mixotrophic growth on fermentative wastes represents an interesting approach to achieving higher biomass concentrations , while ...	Most existing metabolic modeling tools are not suitable for studying diauxic growth with dynamic substrate shifts . This paper describes a successful modeling of Chlorella sorokiniana metabolism , based on 172 reactions and validated by nine independent dynamic experiments ( nine experiments were used for its calibrati...	[ "Abstract", "Introduction", "Model", "Results/Discussion" ]	[ "carbohydrate", "metabolism", "protein", "metabolism", "chemical", "compounds", "metabolic", "networks", "carbohydrates", "organic", "compounds", "plant", "science", "metabolites", "network", "analysis", "photosynthesis", "computer", "and", "information", "sciences", "chemi...	2017	Dynamic metabolic modeling of heterotrophic and mixotrophic microalgal growth on fermentative wastes
The mosquito Aedes aegypti ( L . ) is a major vector of viral diseases like dengue fever , Zika and chikungunya . Aedes aegypti exhibits high morphological and behavioral variation , some of which is thought to be of epidemiological significance . Globally distributed domestic Ae . aegypti have often been grouped into ...	Aedes aegypti , the most important vector of dengue and Zika , greatly varies in body color and behavior . Two domestic forms of this mosquito , the very pale queenslandensis and the browner type , are often found together in populations around the globe . Knowing how freely they interbreed is important for the control...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "&", "Discussion", "Conclusion" ]	[ "biogeography", "invertebrates", "plant", "anatomy", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "population", "genetics", "geographical", "locations", "animals", "wolbachia", "singapore", "plant", "science", "mitochondria", "bi...	2016	The queenslandensis and the type Form of the Dengue Fever Mosquito (Aedes aegypti L.) Are Genomically Indistinguishable
Soil-transmitted helminths ( STHs ) affect more than 1 . 5 billion people . The global strategy to control STH infections requires periodic mass drug administration ( MDA ) based on prevalence among populations at risk determined by diagnostic testing . Widely used copromicroscopy methods to detect infection , however ...	Soil-transmitted helminths affect more than 1 . 5 billion people , mostly in very poor regions without proper sanitation . To control infections , countries periodically give deworming drugs to populations at risk , such as school-age children , based on the results of diagnostic testing to determine the prevalence of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "education", "decision", "making", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "neuroscience", "cognitive", "psychology", "cognition", "neglected", "tropical", "diseases", "extraction", "tech...	2019	Formative research to inform development of a new diagnostic for soil-transmitted helminths: Going beyond the laboratory to ensure access to a needed product
Polygenic risk scores ( PRS ) are designed to serve as single summary measures that are easy to construct , condensing information from a large number of genetic variants associated with a disease . They have been used for stratification and prediction of disease risk . The primary focus of this paper is to demonstrate...	In the study of genetically complex diseases , polygenic risk scores ( PRS ) synthesize information from multiple genetic risk factors to provide insight into a patient’s inherited risk of developing a disease based on his/her genetic profile . These risk scores can be explored in conjunction with health and disease in...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "dermatology", "medicine", "and", "health", "sciences", "carcinomas", "cancers", "and", "neoplasms", "oncology", "skin", "neoplasms", "genome", "analysis", "malignant", "skin", "neoplasms", "skin", "diseases", "basal", "cell", ...	2019	Exploring various polygenic risk scores for skin cancer in the phenomes of the Michigan genomics initiative and the UK Biobank with a visual catalog: PRSWeb
Curly , described almost a century ago , is one of the most frequently used markers in Drosophila genetics . Despite this the molecular identity of Curly has remained obscure . Here we show that Curly mutations arise in the gene dual oxidase ( duox ) , which encodes a reactive oxygen species ( ROS ) generating NADPH ox...	Fruit fly geneticists rely on a handful of dominant mutations that modify adult morphology in a way that is easy to spot , like changing the shape of the fly’s wings , eyes or bristles . One of the first such mutants identified in the early days of fly genetics and to this day likely the most widely used mutation , is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Curly Encodes Dual Oxidase, Which Acts with Heme Peroxidase Curly Su to Shape the Adult Drosophila Wing
Large parts of South Sudan are thought to be trachoma-endemic but baseline data are limited . This study aimed to estimate prevalence for planning trachoma interventions in Unity State , to identify risk factors and to investigate the effect of different sampling approaches on study conclusions . The survey area was de...	Large parts of South Sudan are thought to be trachoma endemic but baseline data , required to initiate interventions , are few . District-by-district surveys , currently recommended by the World Health Organization ( WHO ) , are often not financially or logistically viable . We therefore adapted existing WHO guidelines...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "disease", "mapping", "infectious", "diseases", "survey", "methods", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "trachoma" ]	2012	Prevalence of Trachoma in Unity State, South Sudan: Results from a Large-Scale Population-Based Survey and Potential Implications for Further Surveys
Several genetic variants associated with platelet count and mean platelet volume ( MPV ) were recently reported in people of European ancestry . In this meta-analysis of 7 genome-wide association studies ( GWAS ) enrolling African Americans , our aim was to identify novel genetic variants associated with platelet count...	The majority of the variation in platelet count and mean platelet volume between individuals is heritable . We performed genome-wide association studies in more than 16 , 000 African American participants from seven population-based cohorts to identify genetic variants that correlate with variation in platelet count an...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "genetics", "genetics", "and", "genomics", "biology", "hematology" ]	2012	A Meta-Analysis and Genome-Wide Association Study of Platelet Count and Mean Platelet Volume in African Americans
Mutations in the neuron-specific α3 isoform of the Na+/K+-ATPase are found in patients suffering from Rapid onset Dystonia Parkinsonism and Alternating Hemiplegia of Childhood , two closely related movement disorders . We show that mice harboring a heterozygous hot spot disease mutation , D801Y ( α3+/D801Y ) , suffer a...	The neurological spectrum associated with mutations in the ATP1A3 gene , encoding the α3 isoform of the Na+/K+-ATPase , is complex and still poorly understood . To elucidate the disease-specific pathophysiology , we examined a mouse model harboring the mutation D801Y , which was originally found in a patient with Rapid...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "medicine", "and", "health", "sciences", "swimming", "pathology", "and", "laboratory", "medicine", "neurodegenerative", "diseases", "neuroscience", "biological", "locomotion", "animal", "models", "model", "organisms", "physiological", "parameters", "signs", "and", "sympto...	2017	Hypothermia-induced dystonia and abnormal cerebellar activity in a mouse model with a single disease-mutation in the sodium-potassium pump
Mitochondrion-related organelles , mitosomes and hydrogenosomes , are found in a phylogenetically broad range of organisms . Their components and functions are highly diverse . We have previously shown that mitosomes of the anaerobic/microaerophilic intestinal protozoan parasite Entamoeba histolytica have uniquely evol...	The mitochondrion and its related organelles are ubiquitous in all extant eukaryotic cells . The mitochondria are believed to have originated from the endosymbiosis of α-proteobacteria in an ancestral eukaryote , and show diverse structures , contents , and functions . Evolution and diversification of mitochondrion-rel...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "organismal", "evolution", "microbial", "metabolism", "giardiasis", "microbiology", "parasitic", "diseases", "parasitology", "parastic", "protozoans", "amebiasis", "microsporidiosis", "microbial", "evolution", "cryptosporidiosis", "infectious", "diseases", "microbia...	2011	Sulfate Activation in Mitosomes Plays an Important Role in the Proliferation of Entamoeba histolytica
The dynamics of the PPi release during the transcription elongation of bacterial RNA polymerase and its effects on the Trigger Loop ( TL ) opening motion are still elusive . Here , we built a Markov State Model ( MSM ) from extensive all-atom molecular dynamics ( MD ) simulations to investigate the mechanism of the PPi...	Pyrophosphate ion ( PPi ) release is a critical step in the nucleotide addition cycle of transcription elongation . Despite extensive experimental studies , the kinetic mechanism of the PPi release in bacterial RNA polymerases ( RNAP ) still remains largely a mystery . As a cellular machine , RNAP contains more than 30...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "computational", "chemistry", "chemistry", "theoretical", "chemistry", "biology", "computational", "biology", "biophysics" ]	2013	A Two-State Model for the Dynamics of the Pyrophosphate Ion Release in Bacterial RNA Polymerase
Helicobacter pylori are gram-negative bacteria notable for their high level of genetic diversity and plasticity , features that may play a key role in the organism's ability to colonize the human stomach . Homeologous natural transformation , a key contributor to genomic diversification , has been well-described for H ...	Helicobacter pylori are gram-negative bacteria that have been implicated in human diseases after decades of persistence in the stomach . Known for its high level of genetic diversity , H . pylori is competent to undergo natural transformation , a process in which donor DNA is integrated into the recipient chromosome . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/recombination", "microbiology/microbial", "evolution", "and", "genomics", "infectious", "diseases/gastrointestinal", "infections" ]	2009	Natural Transformation of Helicobacter pylori Involves the Integration of Short DNA Fragments Interrupted by Gaps of Variable Size
Effective antiretroviral therapy ( ART ) dramatically reduces AIDS-related complications , yet the life expectancy of long-term ART-treated HIV-infected patients remains shortened compared to that of uninfected controls , due to increased risk of non-AIDS related morbidities . Many propose that these complications resu...	While antiretroviral therapy for HIV-infected patients is remarkably effective in suppressing viral replication and preventing progression to AIDS , treated patients still have a shorter life expectancy due to increased risks for non-AIDS associated morbidities . Recent data showed that these complications are associat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "hiv", "immunopathogenesis", "immunology", "microbiology", "epithelial", "cells", "immunodeficiency", "viruses", "gastroenterology", "and", "hepatology", "digestive", "system", "infectious", "diseases", "medical", "microbiology", "hi...	2014	Progressive Proximal-to-Distal Reduction in Expression of the Tight Junction Complex in Colonic Epithelium of Virally-Suppressed HIV+ Individuals
The extensive genetic regulatory flows underlying specification of different neuronal subtypes are not well understood at the molecular level . The Nplp1 neuropeptide neurons in the developing Drosophila nerve cord belong to two sub-classes; Tv1 and dAp neurons , generated by two distinct progenitors . Nplp1 neurons ar...	The nervous system contains a myriad of different cell types . These are specified by elaborate transcription factor cascades , starting with early factors that provide spatial and temporal information , to late factors that dictate final cell identity . The molecular nature of such cascades is poorly understood in any...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "invertebrates", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "neuroscience", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental"...	2017	Neuronal cell fate specification by the molecular convergence of different spatio-temporal cues on a common initiator terminal selector gene
Metagenomic sequencing projects from environments dominated by a small number of species produce genome-wide population samples . We present a two-site composite likelihood estimator of the scaled recombination rate , ρ = 2Nec , that operates on metagenomic assemblies in which each sequenced fragment derives from a dif...	At a broad scale , the exchange of genetic material through homologous recombination ( i . e . what happens in animals during sex ) increases the potential rate of adaptation . Bacteria often reproduce clonally , without recombination , by making exact copies of their genomes , but they also have mechanisms analogous t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/metagenomics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2009	Inference of Microbial Recombination Rates from Metagenomic Data
Soil-transmitted helminths ( STH ) are the most common parasitic infections in impoverished communities , particularly among children . Current STH control is through school-based mass drug administration ( MDA ) , which in the Philippines is done twice annually . As expected , MDA has decreased the intensity and preva...	Worldwide , two billion people are estimated to be infected with soil-transmitted helminths ( STH ) . These infections are primarily found in low resource settings and can result in cognitive impairment and growth stunting in children . The current control method is by chemotherapy , usually during large-scale mass dru...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "schoolchildren", "medicine", "and", "health", "sciences", "education", "helminths", "sociology", "tropical", "diseases", "hookworms", "social", "sciences", "parasitic", "diseases", "animals", "necator", "americanus", "ascaris", "ascaris", "lumbricoides", ...	2017	Status of soil-transmitted helminth infections in schoolchildren in Laguna Province, the Philippines: Determined by parasitological and molecular diagnostic techniques
Pre-mRNA splicing is a critical step of gene expression in eukaryotes . Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins . The retention and splicing ( RES ) complex is formed by three different proteins ( Bud13p , Pml1...	RES complex is essential for splicing in yeast but its function and role during vertebrate development are unknown . Here , we combined genetic loss-of-function mutants with transcriptomic analysis and found that a subset of introns is particularly affected in RES complex knock-out background . Those introns display th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "neuronal", "differentiation", "vertebrates", "animals", "cell", "differentiation", "animal", "models", "osteichthyes", "developmental", "biology", "mutation", "model", "organisms", "experimental", "organism", "systems", "molecular", "biology", "techniques", "embryo...	2018	RES complex is associated with intron definition and required for zebrafish early embryogenesis
In bacterial cells , gene expression , metabolism , and growth are highly interdependent and tightly coordinated . As a result , stochastic fluctuations in expression levels and instantaneous growth rate show intricate cross-correlations . These correlations are shaped by feedback loops , trade-offs and constraints act...	Small as they are , bacterial cells are influenced by random fluctuations in their macromolecular copy numbers . Single-cell experiments have shown a complex interplay between this compositional “noise” and fluctuations in the cellular growth rate . While it is clear that this interplay originates from the tight interd...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "protein", "metabolism", "engineering", "and", "technology", "signal", "processing", "enzymology", "operons", "cell", "metabolism", "noise", "reduction", "protein", "synthesis", "enzyme", "metabolism", "dna", "enzyme", "chemistry", "chemical", "syn...	2018	Noise propagation in an integrated model of bacterial gene expression and growth
In the developing mammalian visual system , spontaneous retinal ganglion cell ( RGC ) activity contributes to and drives several aspects of visual system organization . This spontaneous activity takes the form of spreading patches of synchronized bursting that slowly advance across portions of the retina . These patche...	Neurons from the immature retina extend axons that make connections in the visual centers of the brain . Chemical markers provide guidance for these axons , but patterned neural activity is necessary to refine their connections . Much of this activity occurs in a distinctive pattern of waves before the retina is respon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "retina", "ophthalmology", "ferret", "computational", "biology", "neuroscience" ]	2007	Retinal Wave Behavior through Activity-Dependent Refractory Periods
Apparent occupancy levels of proteins bound to DNA in vivo can now be routinely measured on a genomic scale . A challenge in relating these occupancy levels to assembly mechanisms that are defined with biochemically isolated components lies in the veracity of assumptions made regarding the in vivo system . Assumptions ...	For proper cell function , cells need to precisely coordinate the expression of their genes on their DNA at precise times . In order to better understand how the cell works , it is important to understand how , when , and why a cell needs to turn on or off certain genes at certain times . In order to assist the cell to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/functional", "genomics" ]	2010	Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data
Neutrophils form the first line of host defense against bacterial pathogens . They are rapidly mobilized to sites of infection where they help marshal host defenses and remove bacteria by phagocytosis . While splenic neutrophils promote marginal zone B cell antibody production in response to administered T cell indepen...	Highly antibiotic resistant Staphylococcus aureus ( S . aureus ) are an important human pathogen and major cause of hospital acquired infections . An early host defense mechanism against bacterial infection is neutrophil recruitment , which helps eliminate the bacteria at the site of invasion . However , unless quickly...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Neutrophil Recruitment to Lymph Nodes Limits Local Humoral Response to Staphylococcus aureus
Quantitative viral outgrowth assays ( QVOA ) use limiting dilutions of CD4+ T cells to measure the size of the latent HIV-1 reservoir , a major obstacle to curing HIV-1 . Efforts to reduce the reservoir require assays that can reliably quantify its size in blood and tissues . Although QVOA is regarded as a “gold standa...	The latent reservoir of resting CD4+ T cells is a major , if not the primary , obstacle to curing HIV . Quantitative viral outgrowth assays ( QVOAs ) are used to measure the latent reservoir in ART-suppressed HIV-infected people . Using QVOA is difficult , however , as the fraction of cells constituting the latent rese...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[]	2019	Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size
Heterochromatin and associated gene silencing processes play roles in development , genome defense , and chromosome function . In many species , constitutive heterochromatin is decorated with histone H3 tri-methylated at lysine 9 ( H3K9me3 ) and cytosine methylation . In Neurospora crassa , a five-protein complex , DCD...	The epigenetic information contained in chromatin is essential for development of higher organisms , and if misregulated , can lead to the unregulated growth associated with human cancers . Chromatin is typically classified into two basic types: gene-rich 'euchromatin' , and gene-poor heterochromatin , which is also ri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Neurospora Importin α Is Required for Normal Heterochromatic Formation and DNA Methylation
West Nile Fever is a zoonotic disease caused by a mosquito-borne flavivirus , WNV . By its clinical sensitivity to the disease , the horse is a useful sentinel of infection . Because of the virus’ low-level , short-term viraemia in horses , the primary tools used to diagnose WNV are serological tests . Inter-laboratory...	The European network of National Reference Laboratories ( NRLs ) for equine diseases guarantees West Nile virus ( WNV ) surveillance and warning of the emergence of the disease . The WNV NRL network has gathered together most of the European countries facing WNV outbreaks . In this context , two inter-laboratory profic...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "viruses", "rna", "...	2017	Improved reliability of serological tools for the diagnosis of West Nile fever in horses within Europe
ATM and ATR are two redundant checkpoint kinases essential for the stable maintenance of telomeres in eukaryotes . Previous studies have established that MRN ( Mre11-Rad50-Nbs1 ) and ATRIP ( ATR Interacting Protein ) interact with ATM and ATR , respectively , and recruit their partner kinases to sites of DNA damage . H...	ATM and ATR kinases are two evolutionarily conserved sensors of DNA damage , responsible for maintaining stable genomes in all eukaryotic cells . These two kinases safeguard eukaryotic genomes against undesired double-stranded DNA breaks ( DSBs ) and errors during duplication of genomic DNA . Furthermore , ATM and ATR ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/chromosome", "biology" ]	2010	A Kinase-Independent Role for the Rad3ATR-Rad26ATRIP Complex in Recruitment of Tel1ATM to Telomeres in Fission Yeast
How learned experiences persist as memory for a long time is an important question . In Drosophila the persistence of memory is dependent upon amyloid-like oligomers of the Orb2 protein . However , it is not clear how the conversion of Orb2 to the amyloid-like oligomeric state is regulated . The Orb2 has two protein is...	The formation of stable long-term memories involves the synthesis of new protein , however the biochemical basis of this process is unclear . A family of RNA binding proteins , Cytoplasmic Polyadenylation Element Binding ( CPEB ) proteins , are known to regulate synaptic activity and stabilization of memory . The Droso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "learning", "and", "memory", "molecular", "neuroscience", "biology" ]	2014	Contribution of Orb2A Stability in Regulated Amyloid-Like Oligomerization of Drosophila Orb2
Trypanosoma vivax is the main species involved in trypanosomosis , but very little is known about the immunobiology of the infective process caused by this parasite . Recently we undertook to further characterize the main parasitological , haematological and pathological characteristics of mouse models of T . vivax inf...	Trypanosoma vivax is responsible for animal trypanosomosis , or Nagana , in cattle and small ruminants . Under experimental conditions , the outbred mouse model infected with a well studied West African T . vivax isolate reproduces the main characteristics of the infection and pathology observed in livestock . Anemia a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/leukocyte", "development", "immunology/immune", "response" ]	2010	Trypanosoma vivax Infections: Pushing Ahead with Mouse Models for the Study of Nagana. II. Immunobiological Dysfunctions
A key observation about the human immune response to repeated exposure to influenza A is that the first strain infecting an individual apparently produces the strongest adaptive immune response . Although antibody titers measure that response , the interpretation of titers to multiple strains – from the same sera – in ...	The human immune response to an influenza infection is not the same for every infection . It has often been observed that we tend to have the highest antibody titer ( and presumably our strongest immune response ) against strains of influenza that we were exposed to early in life . In this study , we obtained blood sam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "disease", "dynamics", "population", "dynamics", "biology", "population", "biology" ]	2012	Evidence for Antigenic Seniority in Influenza A (H3N2) Antibody Responses in Southern China
Despite evidence of the clustering of metabolic syndrome components , current approaches for identifying unifying genetic mechanisms typically evaluate clinical categories that do not provide adequate etiological information . Here , we used data from 19 , 486 European American and 6 , 287 African American Candidate Ge...	The metabolic syndrome represents a clustering of metabolic phenotypes ( e . g . elevated blood pressure , cholesterol levels , and plasma glucose , as well as abdominal obesity ) and is associated with an increased risk of atherosclerosis and type 2 diabetes . Although multiple genes influencing the specific metabolic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "cardiovascular", "disease", "epidemiology", "epidemiology", "biology", "population", "biology", "genetic", "epidemiology" ]	2011	A Phenomics-Based Strategy Identifies Loci on APOC1, BRAP, and PLCG1 Associated with Metabolic Syndrome Phenotype Domains
Investigating spatial patterns of loci under selection can give insight into how populations evolved in response to selective pressures and can provide monitoring tools for detecting the impact of environmental changes on populations . Drosophila is a particularly good model to study adaptation to environmental heterog...	The potential of geographic studies of genetic variation for the understanding of adaptation has been recognized for some time . In Drosophila , most of the available studies are based on a priori candidates giving a biased picture of the genes and traits under spatially varying selection . In this work , we performed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics" ]	2010	Genome-Wide Patterns of Adaptation to Temperate Environments Associated with Transposable Elements in Drosophila
Oncolytic adenoviruses , such as ONYX-015 , have been tested in clinical trials for currently untreatable tumors , but have yet to demonstrate adequate therapeutic efficacy . The extent to which viruses infect targeted cells determines the efficacy of this approach but many tumors down-regulate the Coxsackievirus and A...	Novel cancer treatment strategies are urgently needed since currently available non-surgical methods for most solid malignancies have limited impact on survival rates . We used conditionally replicating adenoviruses as cancer-fighting agents since they are designed to target and lyse cells with specific aberrations , l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "virology/viruses", "and", "cancer", "computational", "biology/molecular", "dynamics", "molecular", "biology", "computational", "biology/systems", "biology" ]	2011	A Dynamical Systems Model for Combinatorial Cancer Therapy Enhances Oncolytic Adenovirus Efficacy by MEK-Inhibition
Leishmania species are sand fly-transmitted protozoan parasites that cause leishmaniasis , neglected tropical diseases that affect millions of people . Leishmania amastigotes must overcome a variety of host defenses , including reactive oxygen species ( ROS ) produced by the NADPH oxidase . Leishmania species encode th...	Leishmania protozoan parasites are the causative agents of leishmaniasis , neglected tropical diseases with clinical manifestations ranging from self-limiting cutaneous lesions to invasive disease involving multiple organs . During blood-feeding by an infected sand fly , Leishmania parasites are transmitted to human ho...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "enzymes", "immunology", "microbiology", "enzymology", "dismutases", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cyc...	2018	SODB1 is essential for Leishmania major infection of macrophages and pathogenesis in mice
Genome-wide studies of circadian transcription or mRNA translation have been hindered by the presence of heterogeneous cell populations in complex tissues such as the nervous system . We describe here the use of a Drosophila cell-specific translational profiling approach to document the rhythmic “translatome” of neural...	The circadian clock controls daily rhythms in physiology and behavior via mechanisms that regulate gene expression . While numerous studies have examined the clock regulation of gene transcription and documented rhythms in mRNA abundance , less is known about how circadian changes in protein synthesis contribute to the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Translational Profiling of Clock Cells Reveals Circadianly Synchronized Protein Synthesis
Advances in high-throughput , single cell gene expression are allowing interrogation of cell heterogeneity . However , there is concern that the cell cycle phase of a cell might bias characterizations of gene expression at the single-cell level . We assess the effect of cell cycle phase on gene expression in single cel...	Recent technological advances have enabled the measurement of gene expression in individual cells , revealing that there is substantial variability in expression , even within a homogeneous cell population . In this paper , we develop new analytical methods that account for the intrinsic , stochastic nature of single c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics", "cell", "biology", "statistics", "(mathematics)", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "physical", "sciences", "computational", "biology", "molecular", "cell", "biology", "biostatistics", "statisti...	2014	Modeling Bi-modality Improves Characterization of Cell Cycle on Gene Expression in Single Cells
The current article suggests that deterministic chaos self-organized in cortical dynamics could be responsible for the generation of spontaneous action sequences . Recently , various psychological observations have suggested that humans and primates can learn to extract statistical structures hidden in perceptual seque...	Various psychological observations have suggested that the spontaneously generated behaviors of humans reflect statistical structures extracted via perceptual learning of everyday practices and experiences while interacting with the world . Although those studies have further suggested that such acquired statistical st...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "cognitive", "neuroscience", "psychology", "social", "and", "behavioral", "sciences", "mathematics", "cognitive", "psychology", "decision", "making", "biology", "neuroscience", "nonlinear", "dynamics" ]	2011	A Neurodynamic Account of Spontaneous Behaviour
Dihydrodipicolinate synthase ( DHDPS ) is an essential enzyme involved in the lysine biosynthesis pathway . DHDPS from E . coli is a homotetramer consisting of a ‘dimer of dimers’ , with the catalytic residues found at the tight-dimer interface . Crystallographic and biophysical evidence suggest that the dimers associa...	Enzyme function requires the specific placement of residues in the active site so that the correct chemistry is available for efficient catalysis . However , the inherent flexibility of proteins can present challenges in fulfilling these stringent requirements . We have investigated the role of flexibility in the enzym...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biochemistry", "enzyme", "structure", "biochemistry", "simulations", "proteins", "biophysic", "al", "simulations", "enzymes", "enzyme", "regulation", "biology", "computational", "biology" ]	2012	Structural and Dynamic Requirements for Optimal Activity of the Essential Bacterial Enzyme Dihydrodipicolinate Synthase
Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats , including artisanal and industrial dairy products , the oral cavity , intestinal tract or vagina . To gain insights into the genetic complexity and ecological versatility of the species L . rhamnosus , we examin...	Some bacterial species are specialists and adapted to a single niche , while others are generalists and able to grow in various environmental conditions . Lactobacillus rhamnosus is a generalist and its members can often be found in different human cavities but also in various artisanal and industrial dairy products . ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "evolution", "biology", "microbiology" ]	2013	Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG
Among the rare colonizers of heavy-metal rich toxic soils , Arabidopsis halleri is a compelling model extremophile , physiologically distinct from its sister species A . lyrata , and A . thaliana . Naturally selected metal hypertolerance and extraordinarily high leaf metal accumulation in A . halleri both require Heavy...	Existing genetic diversity reflects evolutionary history , but it has rarely been possible to probe for footprints of selection at loci known to functionally govern adaptive traits . Both naturally selected metal hypertolerance and extraordinary leaf metal accumulation of the extremophile Arabidopsis halleri require st...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "ecology", "genetic", "mutation", "mutation", "types", "ecology", "natural", "selection", "genetics", "population", "genetics", "molecular", "genetics", "plant", "ecology", "biology", "evolutionary", "biology", "gene", "duplication", "plant-environment", "...	2013	Hard Selective Sweep and Ectopic Gene Conversion in a Gene Cluster Affording Environmental Adaptation
Plants respond to herbivory with the emission of induced plant volatiles . These volatiles may attract parasitic wasps ( parasitoids ) that attack the herbivores . Although in this sense the emission of volatiles has been hypothesized to be beneficial to the plant , it is still debated whether this is also the case und...	In nature , plants often release volatiles in response to damage by herbivores ( e . g . , by caterpillars ) , and these can indirectly help defend the plants . Indeed , it is well documented that volatiles can recruit the natural enemies of herbivores , such as predators and parasitoid wasps , whose offspring feed on ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "community", "ecology", "chemical", "ecology", "ecology", "entomology", "biology", "plant", "ecology", "zoology", "terrestrial", "ecology", "behavioral", "ecology" ]	2012	Hyperparasitoids Use Herbivore-Induced Plant Volatiles to Locate Their Parasitoid Host
One goal of human genetics is to understand how the information for precise and dynamic gene expression programs is encoded in the genome . The interactions of transcription factors ( TFs ) with DNA regulatory elements clearly play an important role in determining gene expression outputs , yet the regulatory logic unde...	An important question in genomics is to understand how a class of proteins called “transcription factors” controls the expression level of other genes in the genome in a cell-type-specific manner – a process that is essential to human development . One major approach to this problem is to study where these transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "expression", "analysis", "genomics", "functional", "genomics", "rna", "interference", "gene", "expression", "genetics", "gene", "regulation", "molecular", "genetics", "biology", "human", "genetics", "gene", "networks" ]	2014	The Functional Consequences of Variation in Transcription Factor Binding
While many disease-associated single nucleotide polymorphisms ( SNPs ) are associated with gene expression ( expression quantitative trait loci , eQTLs ) , a large proportion of complex disease genome-wide association study ( GWAS ) variants are of unknown function . Some of these SNPs may contribute to disease by regu...	While it is known that chronic obstructive pulmonary disease ( COPD ) is caused in part by genetic factors , few studies have identified specific causative genes . Genetic variants that alter the expression levels of genes have explained part of the genetic component of COPD , however , there are additional genetic var...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "body", "fluids", "gene", "regulation", "pulmonology", "alternative", "splicing", "chronic", "obstructive", "pulmonary", "disease", "genome", "analysis", "gene", "expression", "genetic", "...	2019	Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene
Cytomegalovirus ( CMV ) is frequently transmitted by solid organ transplantation and is associated with graft failure . By forming the boundary between circulation and organ parenchyma , endothelial cells ( EC ) are suited for bidirectional virus spread from and to the transplant . We applied Cre/loxP-mediated green-fl...	More than sixty years ago Frank Fenner proposed that virus dissemination during acute infection originates from organs replicating virus to high titer ( often liver or spleen ) early in infection . Although never formally proven , this model has become commonly accepted and was applied to acute virus infections in gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "oncology", "infectious", "diseases", "model", "organisms", "medical", "microbiology", "virology", "surgery", "biology", "microbiology", "host-pathogen", "interaction" ]	2011	Shedding Light on the Elusive Role of Endothelial Cells in Cytomegalovirus Dissemination
Numerous studies have suggested that hub proteins in the S . cerevisiae physical interaction network are more likely to be essential than other proteins . The proposed reasons underlying this observed relationship between topology and functioning have been subject to some controversy , with recent work suggesting that ...	Network analyses of large-scale interactomes have been a great aid in advancing our understanding of cellular functioning and organization . Here , we examine one of the most basic and intensely-studied structure-to-function relationships observed in cellular networks: that between the number of interactions a protein ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genomics", "functional", "genomics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2013	From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization
As humans age , they experience a progressive loss of thymic function and a corresponding shift in the makeup of the circulating CD8+ T cell population from naïve to memory phenotype . These alterations are believed to result in impaired CD8+ T cell responses in older individuals; however , evidence that these global c...	The prevalence and severity of viral infections increases with advanced age , a phenomenon associated with a defective immune system . The thymic output of naïve T cells declines as we age and it is this lack of naïve T cells that is believed to contribute to the inability of the aged to respond to novel infections and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunology", "biology" ]	2012	The Polyfunctionality of Human Memory CD8+ T Cells Elicited by Acute and Chronic Virus Infections Is Not Influenced by Age
Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins—interpretation of mutation phenotypes is an invaluable source of new knowledge . The results of this research effort are recorded in the scientific literature , but it is difficult for v...	Naturally occurring mutations within the HIV proteome are of therapeutic interest as they can affect the virulence of the virus or result in drug resistance . Furthermore , directed mutagenesis of specific residues is a common method to investigate the function and mechanism of the viral proteins . We have developed no...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "text", "mining", "computer", "and", "information", "sciences", "virology", "biology", "and", "life", "sciences", "microbiology", "information", "technology" ]	2014	The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data
Mycoplasma hominis is an opportunistic human mycoplasma . Two other pathogenic human species , M . genitalium and Ureaplasma parvum , reside within the same natural niche as M . hominis: the urogenital tract . These three species have overlapping , but distinct , pathogenic roles . They have minimal genomes and , thus ...	Mycoplasma hominis , M . genitalium , and Ureaplasma parvum are human pathogenic bacteria that colonize the urogenital tract . They have minimal genomes , and thus have a minimal metabolic capacity . However , they have distinct energy-generating pathways and distinct pathogenic roles . We compared the genomes of these...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "microbiology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/genome", "projects", "microbiology/medical", "microbiology" ]	2009	Life on Arginine for Mycoplasma hominis: Clues from Its Minimal Genome and Comparison with Other Human Urogenital Mycoplasmas
We often learn and recall long sequences in smaller segments , such as a phone number 858 534 22 30 memorized as four segments . Behavioral experiments suggest that humans and some animals employ this strategy of breaking down cognitive or behavioral sequences into chunks in a wide variety of tasks , but the dynamical ...	Because chunking is a hallmark of the brain’s organization , efforts to understand its dynamics can provide valuable insights into the brain and its disorders . For identifying the dynamical principles of chunking learning , we hypothesize that perceptual sequences can be learned and stored as a chain of metastable fix...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Learning of Chunking Sequences in Cognition and Behavior
Understanding the genetic architecture of gene expression traits is key to elucidating the underlying mechanisms of complex traits . Here , for the first time , we perform a systematic survey of the heritability and the distribution of effect sizes across all representative tissues in the human body . We find that loca...	Gene regulation is known to contribute to the underlying mechanisms of complex traits . The GTEx project has generated RNA-Seq data on hundreds of individuals across more than 40 tissues providing a comprehensive atlas of gene expression traits . Here , we systematically examined the local versus distant heritability a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "evolutionary", "biology", "gene", "regulation", "population", "genetics", "mathematics", "forecasting", "statistics", "(mathematics)", "genome", "analysis", "population", "biology", "research", "and", "analysis",...	2016	Survey of the Heritability and Sparse Architecture of Gene Expression Traits across Human Tissues
During the first meiotic division , crossovers ( COs ) between homologous chromosomes ensure their correct segregation . COs are produced by homologous recombination ( HR ) -mediated repair of programmed DNA double strand breaks ( DSBs ) . As more DSBs are induced than COs , mechanisms are required to establish a regul...	During meiosis , faithful separation of chromosomes into gametes is essential for fertility and healthy progeny . During the first meiotic division , crossovers ( CO ) between parental homologs ensure their correct segregation . Programmed DNA double strand breaks ( DSBs ) and resection steps generate single-stranded o...	[ "Abstract", "Introduction", "Results", "Discussion", "Experimental", "Procedures" ]	[ "invertebrates", "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "animal", "models", "germ", "cells", "caenorhabditis", "elegans", "oo...	2016	Separable Roles for a Caenorhabditis elegans RMI1 Homolog in Promoting and Antagonizing Meiotic Crossovers Ensure Faithful Chromosome Inheritance
Current genome-wide association studies ( GWAS ) have high power to detect intermediate frequency SNPs making modest contributions to complex disease , but they are underpowered to detect rare alleles of large effect ( RALE ) . This has led to speculation that the bulk of variation for most complex diseases is due to R...	Current GWA studies typically only explain a small fraction of heritable variation in complex traits , resulting in speculation that a large fraction of variation in such traits may be due to rare alleles of large effect ( RALE ) . The most parsimonious evolutionary mechanism that results in an inverse relationship bet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetic", "polymorphism", "genetics", "population", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2013	Properties and Modeling of GWAS when Complex Disease Risk Is Due to Non-Complementing, Deleterious Mutations in Genes of Large Effect
Globally re-emerging dengue viruses are transmitted from human-to-human by Aedes mosquitoes . While viral determinants of human pathogenicity have been defined , there is a lack of knowledge of how dengue viruses influence mosquito transmission . Identification of viral determinants of transmission can help identify is...	Dengue is a re-emerging global disease transmitted from human-to-human by mosquitoes . While environmental and host immune factors are important , viral determinants of mosquito transmission also shape the epidemiology of dengue . Understanding how dengue viruses influence transmission will help identify isolates with ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "rna", "extraction", "microbiology", "saliva", "animals", "viruses", "rna", "viruses", "insect", "ve...	2017	Dengue subgenomic flaviviral RNA disrupts immunity in mosquito salivary glands to increase virus transmission
New experimental results on bacterial growth inspire a novel top-down approach to study cell metabolism , combining mass balance and proteomic constraints to extend and complement Flux Balance Analysis . We introduce here Constrained Allocation Flux Balance Analysis , CAFBA , in which the biosynthetic costs associated ...	The intracellular protein levels of exponentially growing bacteria are known to vary strongly with growth conditions , as described by quantitative “growth laws” . This work introduces a computational genome-scale framework ( Constrained Allocation Flux Balance Analysis , CAFBA ) which incorporates growth laws into can...	[ "Abstract", "Introduction", "Model", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "protein", "metabolism", "chemical", "compounds", "enzymes", "enzymology", "carbohydrates", "cell", "metabolism", "organic", "compounds", "glucose", "physiological", "processes", "enzyme", "metabolism", "enzym...	2016	Constrained Allocation Flux Balance Analysis
Aside from malaria , infectious diseases are an important cause of death in sub-Saharan Africa and continue to pose major public health problems in African countries , notably pneumonia . Streptococcus pneumoniae remains the most common bacterial cause of pneumonia in all age groups . The skin is one of the main infect...	Infectious diseases are one of the leading causes of morbidity and mortality in the world . They kill nearly 17 million people worldwide each year , mainly in developing countries . They are transmitted through four main channels: air , oral , parenteral and contact . The prevention of infectious diseases requires an u...	[ "Abstract", "Introduction", "Materials", "and", "method", "Results", "Discussion", "Conclusion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "pathogens", "microbiology", "staphylococcus", "aureus", "age", "groups", "streptococcus", "pyogenes", "skin", "infections", "body", "limbs", "bacteria", ...	2018	Asymptomatic carriage of Streptococcus pneumoniae detected by qPCR on the palm of hands of populations in rural Senegal
The earliest stages of animal development are controlled by maternally deposited mRNA transcripts and proteins . Once the zygote is able to transcribe its own genome , maternal transcripts are degraded , in a tightly regulated process known as the maternal to zygotic transition ( MZT ) . While this process has been wel...	Genetic control of embryonic development in all animals requires precise coordination between mother and zygote . The mother provides gene products to the egg to drive the earliest stages of development , until the zygote is able to transcribe its own genome . Many processes of early development are highly conserved ov...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "invertebrates", "medicine", "and", "health", "sciences", "animals", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "phylogenetics", "drosophila", "melanogaster", "model", "organisms", "data", "management", "experimental", "organism"...	2018	Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo
That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926 . Our knowledge of how these inversions originate is still very limited , although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences . ...	The organization of genes on chromosomes changes over evolutionary time . In some organisms , such as fruit flies and mosquitoes , inversions of chromosome regions are widespread . This has been associated with adaptation to environmental pressures and speciation . However , the mechanisms by which inversions are gener...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "drosophila", "genetics", "and", "genomics" ]	2007	Principles of Genome Evolution in the Drosophila melanogaster Species Group
Varicose veins of lower extremities ( VVs ) are a common multifactorial vascular disease . Genetic factors underlying VVs development remain largely unknown . Here we report the first large-scale study of VVs performed on a freely available genetic data of 408 , 455 European-ancestry individuals . We identified the 12 ...	Varicose veins of lower extremities ( VVs ) affect about 30% of adults in developed countries and cause both cosmetic and health problems . A strong body of evidence indicates that heredity plays an important role in the etiology of this condition . However , genetic basis of VVs remains poorly understood . Here , we p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Varicose veins of lower extremities: Insights from the first large-scale genetic study
The current Ebola outbreak poses a threat to individual and global public health . Although the disease has been of interest to the scientific community since 1976 , an effective vaccination approach is still lacking . This fact questions past global public health strategies , which have not foreseen the possible impac...	For the first time in the history of the disease , the Ebola virus left its local setting and affected people not only in isolated rural areas , but reached larger towns and cities leading to worldwide repercussions . This development prompted a joint global response to this health threat . This encompassed not only im...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Ebola and Its Global Research Architecture—Need for an Improvement
Tropheryma whipplei is a bacterium commonly found in feces of young children in Africa , but with no data from Asia . We estimated the prevalence of T . whipplei carriage in feces of children in Lao PDR ( Laos ) . Using specific quantitative real-time PCR , followed by genotyping for each positive specimen , we estimat...	Tropheryma whipplei is a common bacterium carried in feces of young children . Here , using specific PCR , we estimated the prevalence of T . whipplei in 113 feces from 106 children in Vientiane , the Lao PDR ( Laos ) . T . whipplei was detected in 48% ( 51/106 ) of children . Eight genotypes were detected , including ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	High Prevalence of Tropheryma whipplei in Lao Kindergarten Children
Stochasticity in gene expression affects many cellular processes and is a source of phenotypic diversity between genetically identical individuals . Events in elongation , particularly RNA polymerase pausing , are a source of this noise . Since the rate and duration of pausing are sequence-dependent , this regulatory m...	Investigation on how phenotypic diversity of genetically identical organisms is generated and regulated has focused on noise in gene expression . It is unknown to what extent noise in gene expression and genetic networks is evolvable , and by which mechanisms it evolves . The noise has several sources , e . g . , noise...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/synthetic", "biology", "molecular", "biology/transcription", "initiation", "and", "activation", "computational", "biology/transcriptional", "regulation", "computational", "biology/molecular", "genetics", "molecular", "biology/transcription", "elongation" ]	2010	Effects of Transcriptional Pausing on Gene Expression Dynamics
Protein misfolding is common across many neurodegenerative diseases , with misfolded proteins acting as seeds for "prion-like" conversion of normally folded protein to abnormal conformations . A central hypothesis is that misfolded protein accumulation , spread , and distribution are restricted to specific neuronal pop...	Normal brain function requires tight regulation of protein folding; when this goes wrong , proteins can fold into abnormal conformations , which have severe impacts on brain performance , leading to conditions like dementia . Previous studies show that abnormally folded proteins are found in restricted parts of the bra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "brain", "neuroscience", "microglial", "cells", "cerebellum", "infectious", "diseases", "zoonoses", "animal", "cells", "gene", "expression", "glial", "cells", "thalamus", "brain", "diseases", "brainstem", "cellular", "neuroscienc...	2016	Distribution of Misfolded Prion Protein Seeding Activity Alone Does Not Predict Regions of Neurodegeneration

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