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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Viroids are self replicating non-coding RNAs capable of infecting a wide range of plant hosts . They do not encode any proteins , thus the mechanism by which they escape plant defenses remains unclear . RNAi silencing is a major defense mechanism against virus infections , with the four DCL proteins being principal com...	Viroids consist of a peculiar type of highly structured small circular RNAs , capable of infecting crop plants and ornamentals . They do not encode any protein , yet they manage to replicate , move through the plant and often cause severe symptoms . In order to achieve this , viroids hijack plant cellular machinery . I...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "rna", "interference", "molecular", "probe", "techniques", "gene", "regulation", "rna", "extraction", "viruses", "northern", "blot", "plant", "science", "plant", "pathology", "epigenetics", "molecular", "biology", "techniques", "plants", "gel", "el...	2016	Combined Activity of DCL2 and DCL3 Is Crucial in the Defense against Potato Spindle Tuber Viroid
A number of incurable retinal diseases causing vision impairments derive from alterations in visual phototransduction . Unraveling the structural determinants of even monogenic retinal diseases would require network-centered approaches combined with atomistic simulations . The transducin G38D mutant associated with the...	Incurable retinal diseases causing vision impairments may be due to spontaneous mutations in one component of the visual phototransduction signaling network . Such alterations include the transducin single point mutation G38D associated with the Nougaret Congenital Night Blindness ( NCNB ) . We combined a systems biolo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Network and Atomistic Simulations Unveil the Structural Determinants of Mutations Linked to Retinal Diseases
Chronic Chagas disease cardiomyopathy ( CCC ) is an inflammatory dilated cardiomyopathy with a worse prognosis than other cardiomyopathies . CCC occurs in 30 % of individuals infected with Trypanosoma cruzi , endemic in Latin America . Heart failure is associated with impaired energy metabolism , which may be correlate...	Chronic Chagas disease cardiomyopathy ( CCC ) affects millions in endemic areas and is presenting in growing numbers in the USA and European countries due to migration currents . Clinical progression , length of survival and overall prognosis are significantly worse in CCC patients when compared to patients with dilate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "cardiomyopathies", "immunology", "cardiovascular", "neglected", "tropical", "diseases", "bioenergetics", "infectious", "diseases", "inflammation", "metabolic", "pathways", "biology", "energy-producing", "processes", "heart", "failure", "biochemistry", "chagas", "...	2011	Selective Decrease of Components of the Creatine Kinase System and ATP Synthase Complex in Chronic Chagas Disease Cardiomyopathy
For most organisms , chromosome segregation during meiosis relies on deliberate induction of DNA double-strand breaks ( DSBs ) and repair of a subset of these DSBs as inter-homolog crossovers ( COs ) . However , timing and levels of DSB formation must be tightly controlled to avoid jeopardizing genome integrity . Here ...	Formation of haploid gametes during meiosis relies on deliberate induction of DNA double-strand breaks ( DSBs ) , followed by repair of a subset of DSBs as crossovers between homologous chromosomes . Crossovers form the basis of connections that enable homologs to segregate toward opposite spindle poles at meiosis I , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	The C. elegans DSB-2 Protein Reveals a Regulatory Network that Controls Competence for Meiotic DSB Formation and Promotes Crossover Assurance
Massangam health district ( HD ) , in the West Region of Cameroon , has received ivermectin mass drug administration ( MDA ) for 20 years , however there is evidence of continued high transmission of Onchocerca volvulus . In order to better understand the transmission dynamics in the HD and inform intervention strategi...	The global goal is to eliminate onchocerciasis by 2025 . However , not all areas are on track to do so , as is the case for Massangam health district ( HD ) in the West Region of Cameroon . A new strategy is required in order to accelerate efforts to reach elimination targets . This study aimed to better understand the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "onchocerca", "volvulus", "rivers", "helminths", "tropical", "diseases", "black", "flies", "parasitic", "diseases", "animals", "onchocerca", "parasitology", "diptera",...	2018	On-going transmission of human onchocerciasis in the Massangam health district in the West Region of Cameroon: Better understanding transmission dynamics to inform changes in programmatic interventions
Wolbachia are common endosymbionts of terrestrial arthropods , and are also found in nematodes: the animal-parasitic filaria , and the plant-parasite Radopholus similis . Lateral transfer of Wolbachia DNA to the host genome is common . We generated a draft genome sequence for the strongyloidean nematode parasite Dictyo...	Bovine lungworms are economically important nematode parasites of cattle . We have sequenced the genome of the bovine lungworm to provide information for drug and vaccine discovery . Within the lungworm genome we found extensive evidence of an ancient association between the lungworm and a bacterium called Wolbachia . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "genome", "sequencing", "genomics", "genome", "evolution", "genetics", "biology", "and", "life", "sciences", "comparative", "genomics", "molecular", "biology", "techniques", "computational", "biology", "evolutionary", "biology", "zoology", "mol...	2014	Palaeosymbiosis Revealed by Genomic Fossils of Wolbachia in a Strongyloidean Nematode
The HLA-C gene appears to have evolved in higher primates to serve as a dominant source of ligands for the KIR2D family of inhibitory MHC class I receptors . The expression of NK cell-intrinsic MHC class I has been shown to regulate the murine Ly49 family of MHC class I receptors due to the interaction of these recepto...	It has been proposed that the human HLA-C gene evolved in higher primates to serve as a ligand for the KIR family of inhibitory receptors for MHC class I that are expressed by natural killer ( NK ) cells and regulate their activity . NK cell potential is determined by the level of MHC class I on surrounding cells and o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "mhc", "class", "i", "genes", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "messenger", "rna", "cloning", "alleles", "cell", "differentiation", "developmental", "biology", "clinical", "...	2018	Identification of an elaborate NK-specific system regulating HLA-C expression
Endosomal sorting complex required for transport ( ESCRT ) machinery supports the efficient budding of Marburg virus ( MARV ) and many other enveloped viruses . Interaction between components of the ESCRT machinery and viral proteins is predominantly mediated by short tetrapeptide motifs , known as late domains . MARV ...	Marburg virus ( MARV ) is endemic in central Africa and causes hemorrhagic fever in humans and non-human primates , with high lethality . Presumably , the disease severity primarily depends on the response of host-cell factors interacting with viral proteins . We generated a recombinant MARV encoding an NP with a mutat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "emerging", "infectious", "diseases", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "virology", "biology", "and", "life", "sciences", "microbiology", "pathogenesis" ]	2014	Interaction with Tsg101 Is Necessary for the Efficient Transport and Release of Nucleocapsids in Marburg Virus-Infected Cells
Mutation bias in prokaryotes varies from extreme adenine and thymine ( AT ) in obligatory endosymbiotic or parasitic bacteria to extreme guanine and cytosine ( GC ) , for instance in actinobacteria . GC mutation bias deeply influences the folding stability of proteins , making proteins on the average less hydrophobic a...	The Guanine plus Cytosine ( GC ) content of bacterial genomes varies from 20% to 80% . This variation is attributed to the mutation bias produced by replication and repair machinaries . However , the evolutionary forces that act on these very different machinaries have remained elusive . It is known that the GC content...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "molecular", "biology/molecular", "evolution", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "biophysics/protein", "folding" ]	2010	Mutation Bias Favors Protein Folding Stability in the Evolution of Small Populations
Eumycetoma is a morbid chronic granulomatous subcutaneous fungal disease . Despite high environmental exposure to this fungus in certain regions of the world , only few develop eumycetoma for yet unknown reasons . Animal studies suggest that co-infections skewing the immune system to a Th2-type response enhance eumycet...	Eumycetoma is a mutilating fungal disease of mainly the foot and is found in ( sub ) tropical regions such as Sudan . At the moment it is not understood why some people develop eumycetoma and others not . In the regions were eumycetoma is prevalent many other infections are also found . These infections could alter the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "schistosomiasis", "mycetoma", "neglected", "tropical", "diseases", "fungal", "diseases", "toxoplasmosis" ]	2013	Association of Eumycetoma and Schistosomiasis
Schistosomes , parasitic flatworms that cause the neglected tropical disease schistosomiasis , have been considered to have an entirely carbohydrate based metabolism , with glycolysis playing a dominant role in the adult parasites . However , we have discovered a close link between mitochondrial oxygen consumption by f...	Schistosomes are parasitic worms that are the cause of the Neglected Tropical Disease schistosomiasis . Female schistosomes mated with males produce eggs , which either pass out of the host's body for transmission of the infection , or become trapped in host tissues , where they induce inflammation that contributes to ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "host-pathogen", "interaction", "parasitology" ]	2012	Fatty Acid Oxidation Is Essential for Egg Production by the Parasitic Flatworm Schistosoma mansoni
Outbreaks of cutaneous leishmaniasis are relatively common among soldiers involved in nocturnal activities in tropical forests . We investigated the population dynamics of sand flies in a military training camp located in a remnant of Atlantic rainforest in northeastern Brazil , where outbreaks of cutaneous leishmanias...	Outbreaks of cutaneous leishmaniasis are relatively common among soldiers involved in nocturnal activities in tropical forests . However , there is limited information on the relationship between sand fly population dynamics and cases of cutaneous leishmaniasis in Atlantic forest remnants . In this study , we investiga...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Concluding", "remarks" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "tropical", "diseases", "geographical", "locations", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "leishmania", "neglected", "tropical", "diseases...	2017	Sand fly population dynamics and cutaneous leishmaniasis among soldiers in an Atlantic forest remnant in northeastern Brazil
Recombination rate and linkage disequilibrium , the latter a function of population genomic processes , are the critical parameters for mapping by linkage and association , and their patterns in Caenorhabditis elegans are poorly understood . We performed high-density SNP genotyping on a large panel of recombinant inbre...	C . elegans is a model system for diverse fields of biology , but its ability to serve as a model for quantitative trait gene mapping depends on its recombination rate in the laboratory and in nature . The latter is a function of how worms mate and migrate in the wild . We examined the patterns of recombination in a po...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/population", "genetics", "evolutionary", "biology/animal", "genetics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/chromosome", "biology", "evol...	2009	Recombinational Landscape and Population Genomics of Caenorhabditis elegans
Homeostatic temperature regulation is fundamental to mammalian physiology and is controlled by acute and chronic responses of local , endocrine and nervous regulators . Here , we report that loss of the heparan sulfate proteoglycan , syndecan-1 , causes a profoundly depleted intradermal fat layer , which provides cruci...	All mammals strive to maintain a fixed body temperature , and do so using a remarkable array of different strategies , which vary depending upon the degree of cold challenge . Physiologists many decades ago observed that a fat layer right underneath the epidermis ( and above the dermal muscle layer ) thickens in respon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "cryobiology", "genetics", "biology", "and", "life", "sciences", "molecular", "cell", "biology" ]	2014	Syndecan-1 Is Required to Maintain Intradermal Fat and Prevent Cold Stress
Live attenuated vaccines ( LAVs ) , if sufficiently safe , provide the most potent and durable anti-pathogen responses in vaccinees with single immunizations commonly yielding lifelong immunity . Historically , viral LAVs were derived by blind passage of virulent strains in cultured cells resulting in adaptation to cul...	Live-attenuated vaccines ( LAVs ) mimic a natural virus infection and elicit high levels of neutralizing antibodies that can persist for long times . Historically , LAVs have been created by blind passaging of the virus leading to attenuating mutations in the viral genome with no known mechanism of action . We have use...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "viral", "vaccines", "microbial", "mutation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "eastern", "equine", "encephalitis", "virus", "pathogens", "immunology", "microbiology", "alphaviruses", "viruses", "bone", ...	2019	Rational design of a live-attenuated eastern equine encephalitis virus vaccine through informed mutation of virulence determinants
Axonal transport is responsible for the movement of signals and cargo between nerve termini and cell bodies . Pathogens also exploit this pathway to enter and exit the central nervous system . In this study , we characterised the binding , endocytosis and axonal transport of an adenovirus ( CAV-2 ) that preferentially ...	Adenoviruses commonly cause subclinical morbidity in the ocular , respiratory , and gastrointestinal tracts , and less frequently , adenovirus-induced disease can be fatal for newborns and immunocompromised hosts . In addition , adenoviruses can reach the central nervous system ( CNS ) and cause associated encephalitis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "neurological", "disorders/infectious", "diseases", "of", "the", "nervous", "system", "cell", "biology/membranes", "and", "sorting", "virology/host", "invasion", "and", "cell", "entry", "microbiology/cellular"...	2009	CAR-Associated Vesicular Transport of an Adenovirus in Motor Neuron Axons
A novel form of copy number control ( CNC ) helps maintain a low number of Ty1 retrovirus-like transposons in the Saccharomyces genome . Ty1 produces an alternative transcript that encodes p22 , a trans-dominant negative inhibitor of Ty1 retrotransposition whose sequence is identical to the C-terminal half of Gag . The...	The presence of transposable elements in the eukaryotic genome threatens genomic stability and normal gene function , thus various defense mechanisms exist to silence element expression and target integration to benign locations in the genome . Even though the budding yeast Saccharomyces lacks many of the defense syste...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Ty1 Retrotransposon Restriction Factor p22 Targets Gag
Functional residues in proteins tend to be highly conserved over evolutionary time . However , to what extent functional sites impose evolutionary constraints on nearby or even more distant residues is not known . Here , we report pervasive conservation gradients toward catalytic residues in a dataset of 524 distinct e...	The basic biochemical functions of life are carried out by large molecules called enzymes . Enzymes consist of long chains of amino acids folded into a three-dimensional structure . Within that structure , a specific cluster of amino acids , known as the active site , performs the biochemical function . Substituting on...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "enzymes", "enzymology", "protein", "structure", "prediction", "protein", "structure", "protein", "structure", "databases", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "evolutionary", ...	2016	Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes
Many Gram-negative pathogens use a type IV secretion system ( T4SS ) to deliver effector proteins into eukaryotic host cells . The fidelity of protein translocation depends on the efficient recognition of effector proteins by the T4SS . Legionella pneumophila delivers a large number of effector proteins into eukaryotic...	Intracellular pathogens often manipulate the activities of the eukaryotic host cell in which they reside by using a specialized transport apparatus known as a type IV secretion system to deliver proteins that directly manipulate host cell processes . How proteins to be delivered into eukaryotic cells are recognized by ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "in", "vitro", "eukaryotes", "microbiology", "eubacteria" ]	2007	The Legionella pneumophila IcmSW Complex Interacts with Multiple Dot/Icm Effectors to Facilitate Type IV Translocation
For epidemiological work with soil transmitted helminths the recommended diagnostic approaches are to examine fecal samples for microscopic evidence of the parasite . In addition to several logistical and processing issues , traditional diagnostic approaches have been shown to lack the sensitivity required to reliably ...	As international bodies focus efforts on control of the world’s neglected tropical diseases , the critical importance of accurate and sensitive diagnosis becomes a key factor . The problem arises when the infection load in a community is reduced to a level where the standard diagnostic methodologies are insufficiently ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "parasitic", "diseases", "animals", "urine", "molecular", "biology", "techniques", "strongyloides", "stercoralis", "research", "and", "analysis", "m...	2018	Transrenal DNA-based diagnosis of Strongyloides stercoralis (Grassi, 1879) infection: Bayesian latent class modeling of test accuracy
Cholesterol availability is rate-limiting for myelination , and prior studies have established the importance of cholesterol synthesis by oligodendrocytes for normal CNS myelination . However , the contribution of cholesterol uptake through the endocytic pathway has not been fully explored . To address this question , ...	The myelin sheath in the central nervous system is a specialized extension of the oligodendrocyte plasma membrane that serves as an electrical insulator to ensure proper nerve conduction . To accomplish this , myelin is enriched in lipids , particularly unesterified cholesterol , which is an essential and limiting comp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "neurobiology", "of", "disease", "and", "regeneration", "model", "organisms", "niemann-pick", "disease", "biology", "mouse", "neuroscience", "metabolic", "disorders" ]	2013	Npc1 Acting in Neurons and Glia Is Essential for the Formation and Maintenance of CNS Myelin
Cys-loop receptors constitute a superfamily of pentameric ligand-gated ion channels ( pLGICs ) , including receptors for acetylcholine , serotonin , glycine and γ-aminobutyric acid . Several bacterial homologues have been identified that are excellent models for understanding allosteric binding of alcohols and anesthet...	Communication from one nerve cell to the next is an essential process for brain and muscle function . Nerve impulses result in release of transmitter molecules from one cell that bind to receptors on the next cell . Transmitter binding opens a pore in each receptor and ions flow across the membrane , leading to either ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "membrane", "proteins", "biochemistry", "cell", "membrane", "ion", "channels", "cytochemistry", "molecular", "dynamics", "proteins", "chemistry", "biology", "computational", "chemistry" ]	2012	Molecular Mechanism for the Dual Alcohol Modulation of Cys-loop Receptors
Quantification of the effect of spatial tumour sampling on the patterns of mutations detected in next-generation sequencing data is largely lacking . Here we use a spatial stochastic cellular automaton model of tumour growth that accounts for somatic mutations , selection , drift and spatial constraints , to simulate m...	Sequencing the DNA of cancer cells from human tumours has become one of the main tools to study cancer biology . However , sequencing data are complex and often difficult to interpret . In particular , the way in which the tissue is sampled and the data are collected impact the interpretation of the results significant...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "cell", "death", "medicine", "and", "health", "sciences", "biopsy", "cell", "cycle", "and", "cell", "division", "cell", "processes", "alleles", "surgical", "and", "invasive", "medical", "procedures", "simulation", "and", "modeling", "oncology", "mutation...	2019	Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data
To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history , we generated high-quality genome sequences from three gray wolves , one from each of the three putative centers of dog domestication , two basal dog lineages ( Basenji and Dingo ) and a golden jackal as an outgro...	The process of dog domestication is still poorly understood , largely because no studies thus far have leveraged deeply sequenced whole genomes from wolves and dogs to simultaneously evaluate support for the proposed source regions: East Asia , the Middle East , and Europe . To investigate dog origins , we sequence thr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "genetics", "population", "genetics", "comparative", "genomics", "biology", "genomics" ]	2014	Genome Sequencing Highlights the Dynamic Early History of Dogs
Members of the mammalian tick-borne flavivirus group , including tick-borne encephalitis virus , are responsible for at least 10 , 000 clinical cases of tick-borne encephalitis each year . To attempt to explain the long-term maintenance of members of this group , we followed Ornithodoros parkeri , O . sonrai , and O . ...	Members of the mammalian tick-borne flavivirus group , including tick-borne encephalitis virus , remain a significant cause of human disease and are responsible for at least 10 , 000 clinical cases of tick-borne encephalitis each year . One of the principal questions in their epidemiology is how they persist from year ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Experimental Transmission of Karshi (Mammalian Tick-Borne Flavivirus Group) Virus by Ornithodoros Ticks >2,900 Days after Initial Virus Exposure Supports the Role of Soft Ticks as a Long-Term Maintenance Mechanism for Certain Flaviviruses
Faithful meiotic chromosome segregation and fertility require meiotic recombination between homologous chromosomes rather than the equally available sister chromatid , a bias that in Saccharomyces cerevisiae depends on the meiotic kinase , Mek1 . Mek1 is thought to mediate repair template bias by specifically suppressi...	Chromosome segregation errors during meiosis may cause infertility , fetal loss , or birth defects . To avoid meiotic chromosome segregation errors , recombination-mediated linkages are established between previously unattached homologous chromosomes . Such recombination events initiate with breaks in the DNA , but how...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "meiosis", "homologous", "chromosomes", "chromosome", "structure", "and", "function", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "immunologic", "techniques", "research", "and", "analysis", "methods", "synapsis", "chromosom...	2016	Chromosome Synapsis Alleviates Mek1-Dependent Suppression of Meiotic DNA Repair
Through an analysis of polymorphism within and divergence between species , we can hope to learn about the distribution of selective effects of mutations in the genome , changes in the fitness landscape that occur over time , and the location of sites involved in key adaptations that distinguish modern-day species . We...	Species differ genetically , and the way in which they vary is informative about the workings of natural selection: the proportion of the genome subject to selection , the degree to which selection has conserved function versus favoring novel forms , and the location of genes responsible for evolutionarily important ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "evolution", "population", "genetics", "evolutionary", "selection", "animal", "models", "mutation", "phylogenetics", "drosophila", "melanogaster", "model", "organisms", "effective", "population", "size", "biology", "evolutionary", "systematics", "evolutionary", "g...	2011	A Population Genetics-Phylogenetics Approach to Inferring Natural Selection in Coding Sequences
Malaria is initiated when the mosquito introduces sporozoites into the skin of a mammalian host . To successfully continue the infection , sporozoites must invade blood vessels in the dermis and be transported to the liver . A significant number of sporozoites , however , may enter lymphatic vessels in the skin or rema...	Malaria is initiated by a mosquito injecting malaria sporozoites into the skin . To successfully continue the infection , sporozoites must then invade blood vessels in skin for transportation to the liver . However , the majority of these injected sporozoites are unable to reach the blood . The numbers of sporozoites t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "dermatology", "immunology/immunity", "to", "infections" ]	2009	Kinetics of Mosquito-Injected Plasmodium Sporozoites in Mice: Fewer Sporozoites Are Injected into Sporozoite-Immunized Mice
Killer cell immunoglobulin-like receptors ( KIRs ) influence both innate and adaptive immunity . But while the role of KIRs in NK-mediated innate immunity is well-documented , the impact of KIRs on the T cell response in human disease is not known . Here we test the hypothesis that an individual's KIR genotype affects ...	Hepatitis C virus ( HCV ) and human T-cell leukemia virus ( HTLV-I ) infect millions of people worldwide . Some HCV-infected individuals spontaneously clear the virus and many HTLV-1-infected people remain asymptomatic; however , in both cases the infection can lead to serious illness such as cancer . The factors which...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "major", "histocompatibility", "complex", "genetics", "of", "the", "immune", "system", "theoretical", "biology", "immunology", "biology", "immune", "response" ]	2011	KIR2DL2 Enhances Protective and Detrimental HLA Class I-Mediated Immunity in Chronic Viral Infection
The connection between chromatin nuclear organization and gene activity is vividly illustrated by the observation that transcriptional coregulation of certain genes appears to be directly influenced by their spatial proximity . This fact poses the more general question of whether it is at all feasible that the numerous...	Recent high-throughput experiments have shown that chromosome regions ( loci ) which accommodate specific sets of coregulated genes can be in close spatial proximity despite their possibly large sequence separation . The findings pose the question of whether gene coregulation and gene colocalization are related in gene...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology", "biophysics" ]	2013	Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19
The emerging pathogen Cryptococcus gattii causes life-threatening disease in immunocompetent and immunocompromised hosts . Of the four major molecular types ( VGI-VGIV ) , the molecular type VGIII has recently emerged as cause of disease in otherwise healthy individuals , prompting a need to investigate its population ...	Cryptococcus gattii , which is classically divided into four major molecular types ( VGI-VGIV ) , and two serotypes B and C , is the second most important cause of cryptococcosis . The rising incidence of human and animal cryptococcosis cases caused by molecular type VGIII highlights the need for increased vigilance . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "cryptococcus", "gattii", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "population", "genetics", "geographical", "locations", "microbiology", "antifungals", "north", "america",...	2016	MLST and Whole-Genome-Based Population Analysis of Cryptococcus gattii VGIII Links Clinical, Veterinary and Environmental Strains, and Reveals Divergent Serotype Specific Sub-populations and Distant Ancestors
Drug-target interaction ( DTI ) is the basis of drug discovery and design . It is time consuming and costly to determine DTI experimentally . Hence , it is necessary to develop computational methods for the prediction of potential DTI . Based on complex network theory , three supervised inference methods were developed...	Study of drug-target interaction is an important topic toward elucidation of protein functions and understanding of molecular mechanisms inside cells . Traditional methods to predict new targets for known drugs were based on small molecules , protein targets or phenotype features . Here , we proposed a network-based in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "medicine", "clinical", "pharmacology", "medicinal", "chemistry", "drugs", "and", "devices", "chemical", "biology", "toxicology", "mathematical", "computing", "mathematics", "pharmacology", "pharmacoeconomics", "biophysics", "theory", ...	2012	Prediction of Drug-Target Interactions and Drug Repositioning via Network-Based Inference
The peptidoglycan ( PG ) cell wall is a peptide cross-linked glycan polymer essential for bacterial division and maintenance of cell shape and hydrostatic pressure . Bacteria in the Chlamydiales were long thought to lack PG until recent advances in PG labeling technologies revealed the presence of this critical cell wa...	Pathogenic Chlamydia do not assemble their peptidoglycan ( PG ) cell wall in a classical , mesh-like sacculus , but instead apparently confine it to the mid-cell in the actively dividing , non-infectious form . We characterize the assembly and aging of this PG-ring and link its synthesis to MreB , an actin-like protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "chlamydia", "trachomatis", "pathogens", "cell", "processes", "cell", "cycle", "and", "cell", "division", "microbiology", "sexually", "transmitted", "dis...	2016	Pathogenic Chlamydia Lack a Classical Sacculus but Synthesize a Narrow, Mid-cell Peptidoglycan Ring, Regulated by MreB, for Cell Division
Transglutaminase ( TG ) catalyzes protein-protein crosslinking , which has important and diverse roles in vertebrates and invertebrates . Here we demonstrate that Drosophila TG crosslinks drosocrystallin , a peritrophic matrix protein , to form a stable fiber structure on the gut peritrophic matrix . RNA interference (...	Intestinal homeostasis is ensured by a subtle balance between bacteria and host immunity . Gut epithelial barriers , such as the mucus layer in mammals and the peritrophic matrix in invertebrates , have a protective function for the host , as they are impermeable to invading intestinal microbes . Here we found that , i...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Crosslinking of a Peritrophic Matrix Protein Protects Gut Epithelia from Bacterial Exotoxins
Salicylic acid ( SA ) is a key phytohormone that mediates a broad spectrum of resistance against a diverse range of viruses; however , the downstream pathway of SA governed antiviral immune response remains largely to be explored . Here , we identified an orchid protein containing A20 and AN1 zinc finger domains , desi...	The Salicylic acid ( SA ) -mediated plant immunity plays a major role against diverse pathogens including viruses . However , the underlying SA-mediated virus resistance pathway is not fully understood . Here , we identified the A20 and AN1 zinc finger domain containing protein , Pha13 , in Phalaenopsis aphrodite . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "enzymes", "immunology", "brassica", "enzymology", "cloning", "vector", "cloning", "plant", "science", "model", "organisms", "immunoprecipitation", "genetically", "modified", "plants", "experimental", "organism", "...	2018	Plant A20/AN1 protein serves as the important hub to mediate antiviral immunity
Globally , trachoma is the leading cause of infectious blindness . In Ethiopia , the overall Trachomatous Trichiasis ( TT ) surgical coverage is 41% . Identifying determinants for not utilizing TT surgery among TT patients is important to design and monitor effective intervention programs . Therefore , this study aimed...	Trachoma is the common ophthalmic infection and cause of blindness worldwide . It is caused by ocular infections with causative agent of Chlamydia trachomatis that might effect in chronic inflammation of the eyelids , which produces scarring of the conjunctiva that can consequently cause entropion trichiasis , resultin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "medical", "personnel", "tropical", "diseases", "geographical", "locations", "ocular", "anatomy", "surgical", "and", "invasive", "medical", "procedures", "health", "care", "bacterial", "disease...	2018	Determinants for not utilizing trachomatous trichiasis surgery among trachomatous trichiasis patients in Mehalsayint District, North-East Ethiopia
Trypanosoma cruzi ribosomal P proteins , P2β and P0 , induce high levels of antibodies in patients with chronic Chagas' disease Cardiomyopathy ( CCC ) . It is well known that these antibodies alter the beating rate of cardiomyocytes and provoke apoptosis by their interaction with β1-adrenergic and M2-muscarinic cardiac...	Chronic Chagas' disease Cardiomyopathy ( CCC ) is the most frequent and severe consequence of the chronic infection by protozoan parasite T . cruzi . Patients with CCC develop high levels of antibodies against ribosomal P proteins of T . cruzi , called P2β and P0 . These antibodies can cross-react with , and stimulate ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "clinical", "immunology", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "immunology", "tropical", "diseases", "molecular", "cell", "biology...	2014	Cytokine Production but Lack of Proliferation in Peripheral Blood Mononuclear Cells from Chronic Chagas' Disease Cardiomyopathy Patients in Response to T. cruzi Ribosomal P Proteins
How epigenetic information is propagated during somatic cell divisions is still unclear but is absolutely critical for preserving gene expression patterns and cellular identity . Here we show an unanticipated mechanism for inheritance of DNA methylation patterns where the epigenetic mark not only recruits the catalyzin...	Proper inheritance of DNA methylation patterns is essential for preserving cellular identity and preventing malignant cellular transformation . In mammals , DNMT3A/3B , the de novo methyltransferases , establish the DNA methylation patterns during development and then maintain them in co-operation with the maintenance ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/dna", "methylation" ]	2011	Nucleosomes Containing Methylated DNA Stabilize DNA Methyltransferases 3A/3B and Ensure Faithful Epigenetic Inheritance
Locomotion provides superb examples of cooperation among neuromuscular systems , environmental reaction forces , and sensory feedback . As part of a program to understand the neuromechanics of locomotion , here we construct a model of anguilliform ( eel-like ) swimming in slender fishes . Building on a continuum mechan...	In this article we develop a computationally tractable model for swimming in animals such as eels , lampreys , and aquatic snakes . The model combines motoneuronal activation , muscle dynamics , passive elasticity and damping in the spinal cord and body tissues , and simplified hydrodynamic reaction forces , thus allow...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics/fluids,", "plasmas,", "and", "electric", "discharges", "physiology/muscle", "and", "connective", "tissue", "physiology/motor", "systems" ]	2008	Nonlinear Muscles, Passive Viscoelasticity and Body Taper Conspire To Create Neuromechanical Phase Lags in Anguilliform Swimmers
Environmental or genetic perturbations lead to gene expression changes . While most analyses of these changes emphasize the presence of qualitative differences on just a few genes , we now know that changes are widespread . This large-scale variation has been linked to the exclusive influence of a global transcriptiona...	How can we understand expression changes observed as a result of environmental or genetic perturbations ? This issue has been conventionally answered by examining small groups of genes whose expression becomes qualitatively altered after these perturbations . But this approach is too simplistic , as we now know that ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biochemistry", "regulator", "genes", "transcriptional", "control", "cell", "biology", "chromosome", "biology", "proteins", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "epigenetics", "gene", "types", "dna-binding", "prot...	2019	Complex genetic and epigenetic regulation deviates gene expression from a unifying global transcriptional program
The vertebrate ovary and testis develop from a sexually indifferent gonad . During early development of the organism , primordial germ cells ( the gamete lineage ) and somatic gonad cells coalesce and begin to undergo growth and morphogenesis to form this bipotential gonad . Although this aspect of development is requi...	The genes involved in the early stages of vertebrate gonad development remain largely undefined . The gonad begins to form when primordial germ cells and somatic gonad precursor cells coalesce during early development . However , we know little about the signaling events that lead to the subsequent morphogenesis of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "vertebrates", "animals", "endocrine", "physiology", "germ", "cells", "animal", "models", "osteichthyes", "model", "organisms", "developmental", "signaling", "experimental", "organism", "systems"...	2017	Fibroblast growth factor signaling is required for early somatic gonad development in zebrafish
The human filarial parasite Brugia malayi harbors an endosymbiotic bacterium of the genus Wolbachia . The Wolbachia represent an attractive target for the control of filarial induced disease as elimination of the bacteria affects molting , reproduction and survival of the worms . The molecular basis for the symbiotic r...	The human filarial parasite Brugia malayi harbors a Wolbachia endosymbiotic bacterium that is required for normal reproduction and development . However , the molecular basis of how this essential endosymbiotic relationship is maintained is not understood . As a first step in trying to understand the molecular interact...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "parasitic", "diseases", "filariasis", "neglected", "tropical", "diseases", "biology", "microbiology", "molecular", "cell", "biology", "lymphatic", "filariasis" ]	2013	A Potential Role for the Interaction of Wolbachia Surface Proteins with the Brugia malayi Glycolytic Enzymes and Cytoskeleton in Maintenance of Endosymbiosis
Chagas disease , caused by the parasite Trypanosoma cruzi , can lead to long term cardiac morbidity . Treatment of children with benznidazole is effective , but no pediatric pharmacokinetics data are available and clinical pharmacology information on the drug is scarce . Prospective population pharmacokinetic ( PK ) co...	Chagas disease is a parasitic disease endemic to the Americas . Long term complications include severe cardiac involvement , which can lead to severe disability and death of affected individuals . Treatment options for Chagas disease are limited to 2 drugs ( benznidazole and nifurtimox ) , but knowledge of the pharmaco...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "clinical", "pharmacology", "medicine", "and", "health", "sciences", "clinical", "medicine", "chagas", "disease", "neglected", "tropical", "diseases", "pharmacology", "tropical", "diseases", "protozoan", "infections", "parasitic", "diseases", "ph...	2014	Population Pharmacokinetic Study of Benznidazole in Pediatric Chagas Disease Suggests Efficacy despite Lower Plasma Concentrations than in Adults
Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging hemorrhagic fever caused by a tick-borne bunyavirus ( SFTSV ) in East Asian countries . The role of human leukocyte antigen ( HLA ) in resistance and susceptibility to SFTSV is not known . We investigated the correlation of HLA locus A , B and DRB1 all...	Severe fever with thrombocytopenia syndrome ( SFTS ) is an emerging hemorrhagic fever caused by a tick-borne bunyavirus ( SFTSV ) in East Asian countries . The role of human leukocyte antigen ( HLA ) in resistance and susceptibility to SFTSV is not known . In this study , we investigated the correlation of HLA locus A ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "han", "chinese", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "cells", "pathology", "and", "laboratory", "medicine", "china", "population", "genetics", "geographical", "locations", "immunology", "ethnicities", "signs", "and",...	2016	Correlation Between HLA-A, B and DRB1 Alleles and Severe Fever with Thrombocytopenia Syndrome
The HIV-1 envelope glycoprotein ( Env ) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies ( bNAbs ) . Recombinant native-like soluble Env trimer mimetics , such as SOSIP trimers , have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs . We therefore ...	HIV-1 envelope glycoprotein ( Env ) trimer is the primary antigenic target for neutralizing antibodies . As such , it is the focus of subunit vaccine design efforts that aim to recapitulate the structure and native antigenic profile in a soluble , stable form capable of eliciting neutralizing antibody responses . Here ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Accession", "numbers" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "electron", "cryo-microscopy", "retroviruses", "viruses", "immunodeficiency", "viruses", ...	2019	Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics
Herpesvirus gH/gL envelope glycoprotein complexes are key players in virus entry as ligands for host cell receptors and by promoting fusion of viral envelopes with cellular membranes . Human cytomegalovirus ( HCMV ) has two alternative gH/gL complexes , gH/gL/gO and gH/gL/UL128 , 130 , 131A which both shape the HCMV tr...	The identification of cellular receptors recognized by viral glycoproteins promoting entry is central for understanding virus pathogenesis and transmission for any virus . Although the roles of alternative gH/gL complexes of HCMV in cell tropism and virus spread have been extensively studied in cell culture , transfer ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "hek", "293", "cells", "pathogens", "immunology", "biological", "cultures", "microbiology", "viral", "structure", "fibrob...	2017	Human cytomegalovirus glycoprotein complex gH/gL/gO uses PDGFR-α as a key for entry
We previously mapped a type 2 diabetes ( T2D ) locus on chromosome 16 ( Chr 16 ) in an F2 intercross from the BTBR T ( + ) tf ( BTBR ) Lepob/ob and C57BL/6 ( B6 ) Lepob/ob mouse strains . Introgression of BTBR Chr 16 into B6 mice resulted in a consomic mouse with reduced fasting plasma insulin and elevated glucose leve...	Humans carry many genetic variants that confer small effects on metabolic traits relevant to type 2 diabetes . These effects are amplified by environmental stressors like obesity . We used morbid obesity as a sensitizer to identify genes that contribute to the diabetes susceptibility of the BTBR mouse strain . Using ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "of", "disease", "biochemistry", "genetics", "biology", "metabolism", "genetics", "and", "genomics" ]	2011	Positional Cloning of a Type 2 Diabetes Quantitative Trait Locus; Tomosyn-2, a Negative Regulator of Insulin Secretion
Bst-2/Tetherin inhibits the release of HIV by tethering newly formed virus particles to the plasma membrane of infected cells . Although the mechanisms of Tetherin-mediated restriction are increasingly well understood , the biological relevance of this restriction in the natural target cells of HIV is unclear . Moreove...	Tetherin is a cellular protein that inhibits ( or restricts ) a broad range of enveloped viruses , including HIV , by physically “tethering” nascent particles to the plasma membrane of infected cells . CD4+ T cells and macrophages are the main targets of HIV in vivo , and both cell types express Tetherin . Although the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "immunology", "microbiology", "immunodeficiency", "viruses", "viral", "attachment", "viral", "entry", "viral...	2014	Tetherin Can Restrict Cell-Free and Cell-Cell Transmission of HIV from Primary Macrophages to T Cells
Leptospirosis is an important but neglected bacterial zoonosis that has been largely overlooked in Africa . In this systematic review , we aimed to summarise and compare current knowledge of: ( 1 ) the geographic distribution , prevalence , incidence and diversity of acute human leptospirosis in Africa; and ( 2 ) the g...	Leptospirosis is an important bacterial zoonosis that affects people and animals worldwide . It is common in tropical areas where people and animals live in close contact , but the disease has been widely neglected in Africa . In this study we aimed to demonstrate the extent of leptospirosis in Africa and describe the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Epidemiology of Leptospirosis in Africa: A Systematic Review of a Neglected Zoonosis and a Paradigm for ‘One Health’ in Africa
In the present study , the frequency , the activation and the cytokine and chemokine profile of HTLV-1 carriers with or without dermatological lesions were thoroughly described and compared . The results indicated that HTLV-1-infected patients with dermatological lesions have distinct frequency and activation status wh...	In the present study , the immunological profiles of HTLV-1 carriers with or without dermatological lesions were thoroughly described and compared . The results indicated that HTLV-1-infected patients with dermatological lesions have distinct frequency and activation status than asymptomatic carriers . Alterations in c...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology", "biology" ]	2013	Immunological Profile of HTLV-1-Infected Patients Associated with Infectious or Autoimmune Dermatological Disorders
Increasing evidence indicates that microRNAs ( miRNAs ) are contributing factors to neurodegeneration . Alterations in miRNA signatures have been reported in several neurodegenerative dementias , but data in prion diseases are restricted to ex vivo and animal models . The present study identified significant miRNA expr...	miRNAs are small non-coding RNAs that regulate gene expression through complementary binding to their mRNA targets . Specific miRNA signatures have been proposed for several neurodegenerative diseases supporting the idea that miRNA deregulation is a common disease hallmark . Here we present the comprehensive miRNA sign...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "nervous", "system", "gene", "regulation", "neurodegenerative", "diseases", "rna", "extraction", "micrornas", "extraction", "techniques", "alzheimer's", "disease", "research", "and", "analysis", "methods", "infe...	2018	Regional and subtype-dependent miRNA signatures in sporadic Creutzfeldt-Jakob disease are accompanied by alterations in miRNA silencing machinery and biogenesis
Cellular processes are “noisy” . In each cell , concentrations of molecules are subject to random fluctuations due to the small numbers of these molecules and to environmental perturbations . While noise varies with time , it is often measured at steady state , for example by flow cytometry . When interrogating aspects...	Variability from one cell to another is a pronounced and universal trend in living organisms; much of this variability is related to varying concentrations of proteins and other chemical species across the cells . Understanding this variability is necessary if we are to fully understand cellular functions , particularl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "computational", "biology" ]	2011	Computation of Steady-State Probability Distributions in Stochastic Models of Cellular Networks
The Yorkie/Yap transcriptional coactivator is a well-known regulator of cellular proliferation in both invertebrates and mammals . As a coactivator , Yorkie ( Yki ) lacks a DNA binding domain and must partner with sequence-specific DNA binding proteins in the nucleus to regulate gene expression; in Drosophila , the dev...	The Hippo tumor suppressor pathway controls proliferation in a tissue-nonspecific fashion in Drosophila epithelial progenitor tissues via the transcriptional coactivator Yorkie ( Yki ) . However , despite the tissue-nonspecific role that Yki plays in tissue growth , the transcription factors that recruit Yki to DNA , m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Divergent Transcriptional Regulatory Logic at the Intersection of Tissue Growth and Developmental Patterning
The widespread distribution of lentiviruses among African primates , and the lack of severe pathogenesis in many of these natural reservoirs , are taken as evidence for long-term co-evolution between the simian immunodeficiency viruses ( SIVs ) and their primate hosts . Evidence for positive selection acting on antivir...	Old World primates in Africa are reservoir hosts for more than 40 species of simian immunodeficiency viruses ( SIVs ) , including the sources of the human immunodeficiency viruses , HIV-1 and HIV-2 . To investigate the prehistoric origins of these lentiviruses , we looked for patterns of evolution in the antiviral host...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolutionary and Functional Analysis of Old World Primate TRIM5 Reveals the Ancient Emergence of Primate Lentiviruses and Convergent Evolution Targeting a Conserved Capsid Interface
Tungiasis ( sand flea disease ) is a neglected tropical skin disease caused by female sand fleas ( Tunga spp . ) embedded in the skin of the host . The disease is common in sub-Saharan Africa and predominantly affects children living in impoverished rural communities . In these settings tungiasis is associated with imp...	Although tungiasis ( sand flea disease ) is associated with important morbidity and affects millions of people in South America , the Caribbean and sub-Saharan Africa , it has been largely ignored by health care providers up to now . In this study we show that the restriction of life quality due to tungiasis goes far b...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "dermatology", "invertebrates", "children", "medicine", "and", "health", "sciences", "pruritus", "pathology", "and", "laboratory", "medicine", "education", "sociology", "social", "sciences", "parasitic", "diseases", "animals", "neuroscience", "age", "groups", "signs", "...	2018	Tungiasis-related life quality impairment in children living in rural Kenya
Cryptosporidium is a major cause of severe diarrhea , especially in malnourished children . Using a murine model of C . parvum oocyst challenge that recapitulates clinical features of severe cryptosporidiosis during malnutrition , we interrogated the effect of protein malnutrition ( PM ) on primary and secondary respon...	Cryptosporidium attributable morbidities in malnourished children are increasingly recognized . Exactly how malnutrition interferes with host mucosal immunity to diarrheal pathogens and mucosal vaccine responses remains unclear . Dissecting these interactions in an experimental model of cryptosporidiosis can uncover ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immune", "cells", "pathogens", "immunology", "microbiology", "diet", "cryptosporidium", "salmonel...	2016	Cryptosporidium Priming Is More Effective than Vaccine for Protection against Cryptosporidiosis in a Murine Protein Malnutrition Model
Recent research suggests that genetic interactions involving more than two loci may influence a number of complex traits . How these ‘higher-order’ interactions arise at the genetic and molecular levels remains an open question . To provide insights into this problem , we dissected a colony morphology phenotype that se...	Although it is well known that interactions among genetic variants contribute to many complex traits , the forms of these interactions have not been fully characterized . Most work on this problem to date has focused on relatively simple cases involving two or three loci . However , higher-order interactions involving ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "epistasis", "phenotypes", "heredity", "trait", "loci", "genetics", "biology", "and", "life", "sciences", "quantitative", "traits", "genetic", "linkage", "complex", "traits" ]	2014	Genetic Interactions Involving Five or More Genes Contribute to a Complex Trait in Yeast
Neurons typically release both a small-molecule neurotransmitter and one or more neuropeptides , but how these two types of signal from the same neuron might act together remains largely obscure . For example , serotonergic neurons in mammalian brain express the neuropeptide Substance P , but it is unclear how this co-...	Activity of the brain results from neurons communicating with each other using chemical signals . A typical neuron releases two kinds of chemical signals: a small molecule neurotransmitter , such as serotonin , and one or more small proteins , called neuropeptides . For example , neurons in the human brain that release...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "neurochemistry", "muscle", "tissue", "caenorhabditis", "nervous", "system", "neuroscience", "animals", "muscle", "contraction", "hormones", "animal", "models", "serotonin", "caenorhabditis...	2019	Serotonin and neuropeptides are both released by the HSN command neuron to initiate Caenorhabditis elegans egg laying
WNT signaling has been implicated in both embryonic and postnatal bone formation . However , the pertinent WNT ligands and their downstream signaling mechanisms are not well understood . To investigate the osteogenic capacity of WNT7B and WNT5A , both normally expressed in the developing bone , we engineered mouse stra...	The human bone tissue is of considerable regenerative capacity as reflected in bone remodeling and in fracture healing . However , bone tissue regeneration deteriorates with age , and tremendous unmet medical needs exist for safe and effective strategies to stimulate bone formation in older individuals commonly inflict...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "developmental", "biology", "biology" ]	2014	WNT7B Promotes Bone Formation in part through mTORC1
The wing of the fruit fly , Drosophila melanogaster , with its simple , two-dimensional structure , is a model organ well suited for a systems biology approach . The wing arises from an epithelial sac referred to as the wing imaginal disc , which undergoes a phase of massive growth and concomitant patterning during lar...	Scaling , the fitting of pattern to size , manifests itself in numerous examples around us . During development , individual body parts scale up to fit the overall body size . Starved animals form smaller adults with proportionally smaller parts , and amphibian embryos can form normally proportioned adults after extrem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "morphogens", "systems", "biology", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "mathematics", "signaling", "molecular", "development", "statistics", "biology", "pattern", "formation", "genetics", "and", "genomics" ]	2011	Dpp Signaling Activity Requires Pentagone to Scale with Tissue Size in the Growing Drosophila Wing Imaginal Disc
Despite important advances from Genome Wide Association Studies ( GWAS ) , for most complex human traits and diseases , a sizable proportion of genetic variance remains unexplained and prediction accuracy ( PA ) is usually low . Evidence suggests that PA can be improved using Whole-Genome Regression ( WGR ) models wher...	Despite great advances in genotyping technologies , the ability to predict complex traits and diseases remains limited . Increasing evidence suggests that many of these traits may be affected by a large number of small-effect genes that are difficult to detect in single-variant association studies . Whole-Genome Regres...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mathematics", "medicine", "agriculture" ]	2013	Prediction of Complex Human Traits Using the Genomic Best Linear Unbiased Predictor
The Kato-Katz ( KK ) stool smear is the standard test for the diagnosis of Schistosoma mansoni infection , but suffers from low sensitivity when infections intensities are moderate to low . Thus , misdiagnosed individuals remain untreated and contribute to the disease transmission , thereby forestalling public health e...	Detecting parasite eggs in stool by the Kato-Katz ( KK ) stool smear is the standard diagnostic test for infection with the flatworm parasite , Schistosoma mansoni . However , the test can miss those who have low burdens of infection , i . e . , with few eggs in their feces . These misdiagnosed individuals , therefore ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2016	Evaluation of the CCA Immuno-Chromatographic Test to Diagnose Schistosoma mansoni in Minas Gerais State, Brazil
T cells adopt a polarized morphology in lymphoid organs , where cell-to-cell transmission of HIV-1 is likely frequent . However , despite the importance of understanding virus spread in vivo , little is known about the HIV-1 life cycle , particularly its late phase , in polarized T cells . Polarized T cells form two en...	CD4+ T cells are natural targets of HIV-1 . Efficient spread of HIV-1 from infected T cells to uninfected T cells is thought to occur via cell-cell contact structures . One of these structures is a virological synapse where both viral and cellular proteins have been shown to localize specifically . However , the steps ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/leukocyte", "signaling", "and", "gene", "expression", "virology/virion", "structure,", "assembly,", "and", "egress", "cell", "biology/morphogenesis", "and", "cell", "biology", "virology/immunodeficiency", "viruses", "virology", "cell", "biology/membranes", ...	2010	Nucleocapsid Promotes Localization of HIV-1 Gag to Uropods That Participate in Virological Synapses between T Cells
Triatoma infestans —the principal vector of the infection that causes Chagas disease— defies elimination efforts in the Gran Chaco region . This study identifies the types of human-made or -used structures that are key sources of these bugs in the initial stages of house reinfestation after an insecticide spraying camp...	The major vectors of Chagas disease are species of triatomine bugs adapted to human sleeping quarters and peridomestic annexes where they feed on humans and domestic or synanthropic mammals or birds . Knowledge of the demography and nutritional status of Triatominae in real-life settings is still fragmentary , and this...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences" ]	2014	Key Source Habitats and Potential Dispersal of Triatoma infestans Populations in Northwestern Argentina: Implications for Vector Control
T . cruzi strains have been divided into six discrete typing units ( DTUs ) according to their genetic background . These groups are designated T . cruzi I to VI . In this context , amastigotes from G strain ( T . cruzi I ) are highly infective in vitro and show no parasitemia in vivo . Here we aimed to understand why ...	Trypanosoma cruzi , an obligate intracellular protozoan , is the etiological agent of Chagas disease that represents an important public health burden in Latin America . The infection with this parasite can lead to severe complications in cardiac and gastrointestinal tissue depending on the strain of parasite and host ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "model", "organisms", "immunology", "biology" ]	2012	IFN-γ Plays a Unique Role in Protection against Low Virulent Trypanosoma cruzi Strain
Human schistosomiasis , mainly due to Schistosoma mansoni species , is one of the most prevalent parasitic diseases worldwide . To overcome the drawbacks of classical parasitological and serological methods in detecting S . mansoni infections , especially in acute stage of the disease , development of cost-effective , ...	Schistosomiasis is one of the most widespread of all human parasitic diseases , Schistosoma mansoni being the most important species causing human intestinal schistosomiasis . The diagnosis of the disease is mainly based on parasitological and serological methods , but they are not effective in detecting S . mansoni in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "schistosomiasis", "medicine", "and", "health", "sciences", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "intestinal", "parasites", "parasitic", "diseases", "parasitology" ]	2014	A Loop-Mediated Isothermal Amplification (LAMP) Assay for Early Detection of Schistosoma mansoni in Stool Samples: A Diagnostic Approach in a Murine Model
Variation in synonymous codon usage is abundant across multiple levels of organization: between codons of an amino acid , between genes in a genome , and between genomes of different species . It is now well understood that variation in synonymous codon usage is influenced by mutational bias coupled with both natural s...	Synonymous mutations in genes have no effect on the encoded proteins and were once thought to be evolutionarily neutral . By examining codon usage bias across codons , genes , and genomes of 327 species in the budding yeast subphylum , we show that synonymous codon usage is shaped by both neutral processes and selectio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "taxonomy", "transfer", "rna", "engineering", "and", "technology", "developmental", "biology", "fungi", "phylogenetics", "model", "organisms", "data", "management", "non-coding", "rna", "plant", "science", "experimental", "organism", "systems", "plant", ...	2019	Variation and selection on codon usage bias across an entire subphylum
Neutrophils are the host's first line of defense against infections , and their extracellular traps ( NET ) were recently shown to kill Leishmania parasites . Here we report a NET-destroying molecule ( Lundep ) from the salivary glands of Lutzomyia longipalpis . Previous analysis of the sialotranscriptome of Lu . longi...	Salivary components from disease vectors help the arthropod to acquire blood . Here we show that an arthropod vector salivary enzyme affects the innate immune system of the host—mainly the destruction of neutrophil traps—allowing the Leishmania parasite to evade the host immune response and to cause an infection . This...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "immunology", "biology" ]	2014	Lundep, a Sand Fly Salivary Endonuclease Increases Leishmania Parasite Survival in Neutrophils and Inhibits XIIa Contact Activation in Human Plasma
Candida albicans in the immunocompetent host is a benign member of the human microbiota . Though , when host physiology is disrupted , this commensal-host interaction can degenerate and lead to an opportunistic infection . Relatively little is known regarding the dynamics of C . albicans colonization and pathogenesis ....	Candida albicans has both a benign and pathogenic association with the human host . Previous to this study , little was known in regard to how the host humoral system responds to the commensal colonization of C . albicans , as well as the development of hematogenously disseminated candidiasis . We show using a C . albi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "microbiology/immunity", "to", "infections" ]	2010	Serological Profiling of a Candida albicans Protein Microarray Reveals Permanent Host-Pathogen Interplay and Stage-Specific Responses during Candidemia
Bacillus anthracis , the causative agent of anthrax , secretes lethal toxin that down-regulates immune functions . Translocation of B . anthracis across mucosal epithelia is key for its dissemination and pathogenesis . Group 3 innate lymphocytes ( ILC3s ) are important in mucosal barrier maintenance due to their expres...	Bacillus anthracis , the bacterium that causes the deadly disease anthrax , is commonly known for its use in bioterrorism . We have used B . anthracis to study the effect of MAPK signaling pathways in group 3 innate immune lymphocytes ( ILC3s ) . B . anthracis enters the host through the lungs or gastrointestinal ( GI ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2017	Bacillus anthracis lethal toxin negatively modulates ILC3 function through perturbation of IL-23-mediated MAPK signaling
De novo biosynthesis of lipids is essential for Trypanosoma brucei , a protist responsible for the sleeping sickness . Here , we demonstrate that the ketogenic carbon sources , threonine , acetate and glucose , are precursors for both fatty acid and sterol synthesis , while leucine only contributes to sterol production...	In this study , we have ( i ) determined the carbon sources used by the Trypanosoma brucei procyclic insect form to feed the essential lipid biosynthetic pathways , ( ii ) further characterized the metabolic pathways leading to their degradation into acetyl-CoA ( fatty acid precursor ) and 3-hydroxy-3-methylglutaryl-Co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "carbohydrate", "metabolism", "chemical", "compounds", "aliphatic", "amino", "acids", "carbohydrates", "threonine", "organic", "compounds", "parasitic", "protozoans", "glucose", "glucose", "metabolism", "leucine", "protozoans", "amino", "acids", "lipids", "proteins", "che...	2018	De novo biosynthesis of sterols and fatty acids in the Trypanosoma brucei procyclic form: Carbon source preferences and metabolic flux redistributions
Two recombinant Fasciola hepatica antigens , saposin-like protein-2 ( recSAP2 ) and cathepsin L-1 ( recCL1 ) , were assessed individually and in combination in enzyme-linked immunosorbent assays ( ELISA ) for the specific serodiagnosis of human fasciolosis in areas of low endemicity as encountered in Central Europe . A...	To improve the serodiagnosis of human fasciolosis caused by Fasciola hepatica , we comparatively evaluated the accuracy of two different enzyme-linked immunosorbent assays ( ELISAs ) based on the use of two published recombinant antigens . The best performance was achieved with the recombinant F . hepatica saposin-like...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "helminth", "infections", "medicine", "and", "health", "sciences", "veterinary", "diseases", "zoonoses", "biology", "and", "life", "sciences", "fascioliasis", "parasitic", "diseases", "veterinary", "science" ]	2014	Comparative Assessment of ELISAs Using Recombinant Saposin-Like Protein 2 and recombinant Cathepsin L-1 from Fasciola hepatica for the Serodiagnosis of Human Fasciolosis
Somatosensory thalamocortical ( TC ) neurons from the ventrobasal ( VB ) thalamus are central components in the flow of sensory information between the periphery and the cerebral cortex , and participate in the dynamic regulation of thalamocortical states including wakefulness and sleep . This property is reflected at ...	Thalamocortical neurons are one of the main components of the thalamocortical system , which is implicated in key functions including sensory transmission and the transition between brain states . These functions are reflected at the cellular level by the ability to generate action potentials in two distinct modes , ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "membrane", "potential", "brain", "electrophysiology", "neuroscience", "ion", "channels", "ionic", "current", "bioenergetics", "neuronal", "dendrites", "animal", "cells", "proteins", "thalamus", "biophysics"...	2019	Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons
Male breast cancer accounts for approximately 1% of all breast cancer . To date , risk factors for male breast cancer are poorly defined , but certain risk factors and genetic features appear common to both male and female breast cancer . Genome-wide association studies ( GWAS ) have recently identified common single n...	Breast cancer is the most common female cancer in the United Kingdom but also occurs in men , albeit at a much lower frequency . Relatively little is known regarding risk factors for male breast cancer . Here , we examine the effect of common genetic variants that are known to be associated with female breast cancer to...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "oncology", "medicine", "genetic", "causes", "of", "cancer", "genetic", "association", "studies", "genetics", "cancer", "risk", "factors", "biology", "human", "genetics", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2011	Genetic Variants at Chromosomes 2q35, 5p12, 6q25.1, 10q26.13, and 16q12.1 Influence the Risk of Breast Cancer in Men
Porphyromonas gingivalis is a major pathogen in severe and chronic manifestations of periodontal disease , which is one of the most common infections of humans . A central feature of P . gingivalis pathogenicity is dysregulation of innate immunity at the gingival epithelial interface , including suppression of IL-8 pro...	Periodontal diseases are one of the most common infections of humans , and are characterized by gingival inflammation and destruction of the hard and soft tissues that support the tooth , eventually causing tooth loss . Porphyromonas gingivalis is a major pathogen in periodontal diseases and a key pathogenic attribute ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "microbiology" ]	2013	The Serine Phosphatase SerB of Porphyromonas gingivalis Suppresses IL-8 Production by Dephosphorylation of NF-κB RelA/p65
Core protein of Flaviviridae is regarded as essential factor for nucleocapsid formation . Yet , core protein is not encoded by all isolates ( GBV- A and GBV- C ) . Pestiviruses are a genus within the family Flaviviridae that affect cloven-hoofed animals , causing economically important diseases like classical swine fev...	Virus particles of members of the Flaviviridae consist of an inner complex of viral RNA genome and core protein that together form the nucleocapsid , and an outer lipid layer containing the viral glycoproteins . Functional analyses of core protein of the classical swine fever virus ( CSFV ) , a pestivirus related to he...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "veterinary", "diseases", "biology", "microbiology", "veterinary", "science" ]	2012	The Core Protein of Classical Swine Fever Virus Is Dispensable for Virus Propagation In Vitro
Tungiasis is a parasitic skin disease caused by penetrating female sand fleas . By nature , tungiasis is a self-limiting infection . However , in endemic settings re-infection is the rule and parasite load gradually accumulates over time . Intensity of infection and degree of morbidity are closely related . This case s...	Tungiasis ( also called sand flea disease ) is a neglected tropical disease ( NTD ) caused by the penetration of female sand fleas in the skin , typically at the toes , the sole or the heel . Once embedded in the upper strata of the skin , the parasite hypertrophies , enlarging its body size by a factor of 2000 within ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "knees", "medicine", "and", "health", "sciences", "legs", "feet", "pathology", "and", "laboratory", "medicine", "parasitic", "diseases", "anemia", "animals", "signs", "and", "symptoms", "fleas", "body", "limbs", "musculoskeletal", "system", "hands", ...	2019	Very severe tungiasis in Amerindians in the Amazon lowland of Colombia: A case series
Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements ( TEs ) . TE silencing requires substantial resources from the plant host , including the production of small interfering RNAs ( siRNAs ) . Thus , the interaction between TEs and siRNAs is a critical aspect of both the function an...	Because transposable elements ( TEs ) constitute most angiosperm nuclear DNA , the interaction between TEs and their host genome is a key component for understanding the function and evolution of plant genomes . The diversity of the host response has been studied a great deal , including the biogenesis of small interfe...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "plant", "science", "model", "organisms", "genetics", "biology", "and", "life", "sciences", "population", "biology", "genomics", "evolutionary", "biology", "research", "and", "analysis", "methods" ]	2014	Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome
The molecular mechanisms underlying transcriptional regulation in apicomplexan parasites remain poorly understood . Recently , the Apicomplexan AP2 ( ApiAP2 ) family of DNA binding proteins was identified as a major class of transcriptional regulators that are found across all Apicomplexa . To gain insight into the reg...	Plasmodium falciparum is the main cause of the devastating human disease malaria . This parasitic organism has a complex lifecycle spanning a variety of different cell types in the mosquito vector and human host . To adapt and survive in these different environments , the parasite precisely regulates the transcription ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/transcription", "initiation", "and", "activation", "microbiology/parasitology", "genetics", "and", "genomics/gene", "expression" ]	2010	Identification and Genome-Wide Prediction of DNA Binding Specificities for the ApiAP2 Family of Regulators from the Malaria Parasite
Hypoxia inducible factor 1α ( HIF1α ) is the mammalian transcriptional factor that controls metabolism , survival , and innate immunity in response to inflammation and low oxygen . Previous work established that generation of hypoxic microenvironments occurs within the lung during infection with the human fungal pathog...	Due to the limited treatment options and severity of invasive fungal infections , a better understanding of fungal-host interactions is needed for the development of new therapies . Recent studies have implicated a role for hypoxia inducible factor 1-alpha ( HIF1α ) in the regulation of inflammation and host defense re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "disease", "immunology", "aspergillus", "fumigatus", "mycology", "immune", "cells", "cell", "biology", "animal", "cells", "clinical", "immunology", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "cellular", "type...	2014	Myeloid Derived Hypoxia Inducible Factor 1-alpha Is Required for Protection against Pulmonary Aspergillus fumigatus Infection
Simple models of therapy for viral diseases such as hepatitis C virus ( HCV ) or human immunodeficiency virus assume that , once therapy is started , the drug has a constant effectiveness . More realistic models have assumed either that the drug effectiveness depends on the drug concentration or that the effectiveness ...	Fitting simple models of therapy for viral diseases , such as hepatitis C virus ( HCV ) or human immunodeficiency virus , to patient data has yielded significant insights into the underlying viral dynamics . In general , these models assume that , once therapy is started , the drug has a constant effectiveness . More r...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "hepatitis", "c", "infectious", "diseases", "medicine", "and", "health", "sciences", "infectious", "hepatitis", "hepatitis", "population", "modeling", "gastroenterology", "and", "hepatology", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", "co...	2014	A Hepatitis C Virus Infection Model with Time-Varying Drug Effectiveness: Solution and Analysis
Understanding the principles by which agents interact with both complex environments and each other is a key goal of decision neuroscience . However , most previous studies have used experimental paradigms in which choices are discrete ( and few ) , play is static , and optimal solutions are known . Yet in natural envi...	Most studies of strategic decision making make use of simple tasks in which agents choose among only a limited number of distinct options . But real-world behavior is complex , requiring ongoing adjustment of strategies . Here , we propose a new model that is capable of reproducing the rich behavior of monkeys playing ...	[ "Abstract", "Introduction", "Methods", "and", "models", "Results", "Discussion" ]	[]	2019	Latent goal models for dynamic strategic interaction
To understand the molecular processes underlying aging , we screened modENCODE ChIP-seq data to identify transcription factors that bind to age-regulated genes in C . elegans . The most significant hit was the GATA transcription factor encoded by elt-2 , which is responsible for inducing expression of intestinal genes ...	A central question in aging is to uncover the molecular drivers of the normal aging process . Using the roundworm C . elegans as a model organism , we found that the ELT-2 GATA transcription factor regulates many gene expression changes that occur during aging . During development , elt-2 functions as a key regulator o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "physiological", "processes", "developmental", "biology", "age", "groups", "adults", "regulator", "genes", "organism", "development",...	2016	Deactivation of the GATA Transcription Factor ELT-2 Is a Major Driver of Normal Aging in C. elegans
Patients with dengue fever and comorbidities seem to be at higher risk of developing complications and/or severe dengue compared to healthier individuals . This study systematically reviews the evidence related to comorbidities and dengue . A systematic literature review was performed in five databases ( EMBASE , PUBME...	Dengue fever is a viral disease , transmitted by Aedes mosquitoes . Although for most cases of dengue fever the illness is self-limiting or asymptomatic , severe dengue can occur . Severe dengue is now classified by 1 ) plasma leakage , and/or 2 ) severe haemorrhage and/or 3 ) organ failure . Complications and deaths o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Relevance of Non-communicable Comorbidities for the Development of the Severe Forms of Dengue: A Systematic Literature Review
As a universal energy generation pathway utilizing carbon metabolism , glycolysis plays an important housekeeping role in all organisms . Pollen tubes expand rapidly via a mechanism of polarized growth , known as tip growth , to deliver sperm for fertilization . Here , we report a novel and surprising role of glycolysi...	Glycolysis , which breaks down glucose to produce energy , has long been considered a “housekeeping” pathway in living cells , i . e . , it helps maintain basic cellular functions . Here , we found that the glycolysis pathway plays an unconventional regulatory role in cell polarity , i . e . , the intrinsic asymmetry i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "plant", "anatomy", "vesicles", "metabolic", "processes", "enzymology", "glycolysis", "cell", "polarity", "pollen", "plant", "science", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "enzyme", "chemistry", "pollen", ...	2018	Glycolysis regulates pollen tube polarity via Rho GTPase signaling
We develop a statistical mechanical model to analyze the competitive behavior of transitions to multiple alternate conformations in a negatively supercoiled DNA molecule of kilobase length and specified base sequence . Since DNA superhelicity topologically couples together the transition behaviors of all base pairs , a...	The stresses imposed on DNA within organisms can drive the molecule from its standard B-form double-helical structure into other conformations at susceptible sites within the sequence . We present a theoretical method to calculate this transition behavior due to stresses induced by supercoiling . We also develop a nume...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "algorithms", "physics", "computer", "science", "mathematics", "statistical", "mechanics", "theoretical", "biology", "applied", "mathematics", "biology", "computational", "biology", "computing", "methods", "biophysics", "numerical", "analysis" ]	2012	Theoretical Analysis of Competing Conformational Transitions in Superhelical DNA
Three major forms of human disease , cutaneous leishmaniasis , visceral leishmaniasis and mucocutaneous leishmaniasis , are caused by several leishmanial species whose geographic distribution frequently overlaps . These Leishmania species have diverse reservoir hosts , sand fly vectors and transmission patterns . In th...	Protozoal parasites of the genus Leishmania are transmitted by sand fly bites to humans and animals . Three major forms of disease are caused by these parasites: cutaneous leishmaniasis , responsible for disfiguring skin wounds; mucocutaneous leishmaniasis , causing non-healing ulceration around the mouth and nose; and...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2010	Detection and Identification of Old World Leishmania by High Resolution Melt Analysis
The elimination of autoreactive T cells occurs via thymocyte apoptosis and removal by thymic phagocytes , but the sequence of events in vivo , and the relationship between thymocyte death and phagocytic clearance , are unknown . Here we address these questions by following a synchronized cohort of thymocytes undergoing...	As an important safeguard against autoimmunity , T cells bearing autoreactive T cell antigen receptors are eliminated during their development in the thymus , a process known as negative selection . Although much is known about the molecular events involved in negative selection , surprisingly little is known about the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immune", "cells", "immunity", "t", "cells", "immunology", "immune", "tolerance", "biology" ]	2013	Elimination of Self-Reactive T Cells in the Thymus: A Timeline for Negative Selection
The autoencoder algorithm is a simple but powerful unsupervised method for training neural networks . Autoencoder networks can learn sparse distributed codes similar to those seen in cortical sensory areas such as visual area V1 , but they can also be stacked to learn increasingly abstract representations . Several com...	In the brain areas responsible for sensory processing , neurons learn over time to respond to specific features in the external world . Here , we propose a new , biologically plausible model for how groups of neurons can learn which specific features to respond to . Our work connects theoretical arguments about the opt...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2015	Mirrored STDP Implements Autoencoder Learning in a Network of Spiking Neurons
Rhythmic voltage oscillations resulting from the summed activity of neuronal populations occur in many nervous systems . Contemporary observations suggest that coexistent oscillations interact and , in time , may switch in dominance . We recently reported an example of these interactions recorded from in vitro preparat...	Since the late 19th century , rhythmic electrical activity has been observed in the mammalian brain . Although subject to intense scrutiny , only a handful of these rhythms are understood in terms of the biophysical elements that produce the oscillations . Even less understood are the mechanisms that underlie interacti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2008	Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex
Bistability has important implications in signaling pathways , since it indicates a potential cell decision between alternative outcomes . We present two approaches developed in the framework of the Chemical Reaction Network Theory for easy and efficient search of multiple steady state behavior in signaling networks ( ...	Type I interferons ( IFNs ) regulate a variety of cell functions , exhibiting , amongst others , antiviral , antiproliferative and immunomodulatory activities . Due to their anticancer effects , type I IFNs have a long record of applications in clinical oncology . It is still an open question how type I IFNs generate s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "signaling", "networks", "conservation", "of", "mass", "optimization", "mathematics", "chemical", "equilibrium", "network", "analysis", "physical", "laws", "and", "principles", "physical", "chemistry", "computer", "and", "information", "sciences", "proteins", "chemistry",...	2017	Chemical Reaction Network Theory elucidates sources of multistability in interferon signaling
HIV-1 frequently escapes from CD8 T cell responses via HLA-I restricted adaptation , leading to the accumulation of adapted epitopes ( AE ) . We previously demonstrated that AE compromise CD8 T cell responses during acute infection and are associated with poor clinical outcomes . Here , we examined the impact of AE on ...	HIV-1 infection remains a critical public health threat across the world . Over the past two decades , CD8 T cells have been clearly shown to exert immune pressure on HIV and drive viral adaptation . Previously , our group reported that such HLA-I associated adaptations can predict clinical outcomes and are beneficial ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "t", "helper", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cytotoxicity", "assay", "microbiology", "toxicology", "retrov...	2019	CD8 T cells targeting adapted epitopes in chronic HIV infection promote dendritic cell maturation and CD4 T cell trans-infection
Following the recognition of pathogen-encoded effectors , plant TIR-NB-LRR immune receptors induce defense signaling by a largely unknown mechanism . We identify a novel and conserved role for the SQUAMOSA PROMOTER BINDING PROTEIN ( SBP ) -domain transcription factor SPL6 in enabling the activation of the defense trans...	Pathogen infection causes significant economic loss of crops worldwide . To fend off pathogens , plants use the Nucleotide-Binding domain and Leucine Rich Repeat ( NB-LRR ) class of immune receptors . Although we have some insight into how plant NB-LRRs recognizes pathogens , we know little about NB-LRR spatial distrib...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "model", "organisms", "plant", "and", "algal", "models", "plant", "biology", "plant", "pathogens", "plant", "pathology", "biology", "arabidopsis", "thaliana" ]	2013	Novel Positive Regulatory Role for the SPL6 Transcription Factor in the N TIR-NB-LRR Receptor-Mediated Plant Innate Immunity
The current treatment of eumycetoma utilizing ketoconazole is unsatisfactory because of high recurrence rates , which often leads to complications and unnecessary amputations , and its comparatively high cost in endemic areas . Hence , an effective and affordable drug is required to improve therapeutic outcome . E1224 ...	Madurella mycetomatis is the most common etiologic agent of eumycetoma worldwide . Treatment of this infection is very difficult and associated with high recurrence rates and low cure rates . Currently the treatment consists of a combination of surgery and antifungal therapy . Antifungal therapy is usually given for at...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Madurella mycetomatis Is Highly Susceptible to Ravuconazole
The formation of protein-protein complexes is essential for proteins to perform their physiological functions in the cell . Mutations that prevent the proper formation of the correct complexes can have serious consequences for the associated cellular processes . Since experimental determination of protein-protein bindi...	Few proteins carry out their tasks in isolation . Instead , proteins combine with each other in complicated ways that can be affected by either the natural genetic variation that occurs among people or by disease causing mutations such as those that occur in cancer or in genetic disorders . To understand how these muta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles
The HIV/AIDS pandemic is a major global health threat and understanding the detailed molecular mechanisms of HIV replication is critical for the development of novel therapeutics . To replicate , HIV-1 must access the nucleus of infected cells and integrate into host chromosomes , however little is known about the even...	HIV-1 , the causative agent of AIDS , is a virus that enters the nucleus of infected cells and must integrate its genome into the host cell DNA . Here we show that efficient HIV-1 integration depends on a host cell factor called Transportin 3 . We also show that Transportin 3 can export out of the nucleus the viral cap...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Acknowledgments" ]	[ "medicine", "biochemistry", "rna", "infectious", "diseases", "rna", "transport", "cofactors", "nucleic", "acids", "hiv", "retrovirology", "and", "hiv", "immunopathogenesis", "biology", "viral", "diseases" ]	2011	Transportin 3 Promotes a Nuclear Maturation Step Required for Efficient HIV-1 Integration
Model-based phylodynamic approaches recently employed generalized linear models ( GLMs ) to uncover potential predictors of viral spread . Very recently some of these models have allowed both the predictors and their coefficients to be time-dependent . However , these studies mainly focused on predictors that are assum...	What drives the geographic dispersal and genetic diversity of avian influenza A virus H9N2 in Asia ? We used two model-based approaches , DTA and MASCOT , to reconstruct the phylogeographic dynamics of the virus genetic sequence and predictor data . To do so , we compiled multiple potential predictors to inform migrati...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "livestock", "ecology", "and", "environmental", "sciences", "animal", "genetics", "population", "genetics", "geographical", "locations", "social", "sciences", "vertebrates", "animals", "animal", "behavior", "effective", "population", "size", "bird", "genet...	2019	Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration
Yellow fever virus ( YFV ) is a mosquito-borne flavivirus that is a major public health problem in tropical areas of Africa and South America . There have been detailed studies on YFV ecology in West Africa and South America , but current understanding of YFV circulation on the African continent is incomplete . This in...	Yellow fever virus ( YFV ) is a mosquito-transmitted pathogen of great public health significance , which is endemic to tropical areas of Africa and South America . Despite the availability of an effective vaccine , and programs that exist in many endemic areas to reduce populations of mosquitoes , YFV continues to cir...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "zoonoses", "neglected", "tropical", "diseases", "infectious", "disease", "modeling", "viral", "diseases" ]	2013	Phylogeographic Reconstruction of African Yellow Fever Virus Isolates Indicates Recent Simultaneous Dispersal into East and West Africa
Insufficient or dysregulated energy metabolism may underlie diverse inherited and degenerative diseases , cancer , and even aging itself . ATP is the central energy carrier in cells , but critical pathways for regulating ATP levels are not systematically understood . We combined a pooled clustered regularly interspaced...	There is abundant evidence that insufficient energy , or energy failure , contributes to the pathophysiology of many inherited and degenerative diseases , cancer , and aging . However , we understand little about how cellular energy levels are regulated . To begin to address this gap , we developed a screening approach...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "cell", "physiology", "luciferase", "enzymes", "metabolic", "processes", "enzymology", "cell", "metabolism", "glycolysis", "fluorophotometry", "mitochondria", "molecular", "biology", "techniques", "bioenergetics", "cellular", "structures", "and", "organ...	2018	A high-throughput screen of real-time ATP levels in individual cells reveals mechanisms of energy failure
The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes , including those for the ESX-1 secretion apparatus , a major virulence determinant . Mutations in phoP lead to compromised production of pathogen-specific cell wall comp...	One of the best characterized two-component systems in Mycobacterium tuberculosis is represented by the PhoPR pair , with PhoR being the transmembrane sensor kinase and PhoP playing an essential part in controlling expression of virulence-associated genes , such as those encoding the ESX-1 secretion apparatus . Previou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "and", "life", "sciences", "microbiology", "genomics" ]	2014	The PhoP-Dependent ncRNA Mcr7 Modulates the TAT Secretion System in Mycobacterium tuberculosis

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