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We previously showed that newborns congenitally infected with Trypanosoma cruzi ( M+B+ ) display a strong type 1 parasite-specific T cell immune response , whereas uninfected newborns from T . cruzi-infected mothers ( M+B− ) are prone to produce higher levels of proinflammatory cytokines than control neonates ( M−B− ) ...	Vaccines are of crucial importance to prevent morbidity and mortality due to infectious diseases in childhood . A modulation of the fetal/neonatal immune system ( considered immature ) toward Th1 or Th2 dominance could modify responses to vaccines administered in early life . T . cruzi is the agent of Chagas' disease ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections", "immunology/immunomodulation", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "public", "health", "and", "epidemiology/preventive", "medicine", "public", "health", "and", "epidemiology/infe...	2009	Maternal Infection with Trypanosoma cruzi and Congenital Chagas Disease Induce a Trend to a Type 1 Polarization of Infant Immune Responses to Vaccines
Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division . Despite the wide application , microarray time course experiments have several limitations in identifying cell cycle genes . We thus propose a computational model to predict human ...	Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division . Microarray time course experiments have been successfully used to identify cell cycle regulated genes but with several limitations , e . g . less effective in identifying genes wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "biology", "computational", "biology" ]	2013	Transcription Factor Binding Profiles Reveal Cyclic Expression of Human Protein-coding Genes and Non-coding RNAs
As Bangladesh , India and Nepal progress towards visceral leishmaniasis ( VL ) elimination , it is important to understand the role of asymptomatic Leishmania infection ( ALI ) , VL treatment relapse and post kala-azar dermal leishmaniasis ( PKDL ) in transmission . We reviewed evidence systematically on ALI , relapse ...	The role of asymptomatic Leishmania infection ( ALI ) , PKDL and VL relapse in transmission is unclear as VL elimination is achieved in the Indian subcontinent . ALI , PKDL and relapse studies lacked a reference standard and appropriate biomarker . ALI was 4–17-fold more prevalent than VL . The risk of ALI was higher i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "vector-borne", "diseases", "india", "sand", "flies", "geographical", "locations", "parasitic", "diseases", "pharmaceutics", "neglected", "tropical", "diseases", "infectious", "disease", "control", "insect",...	2016	Transmission Dynamics of Visceral Leishmaniasis in the Indian Subcontinent – A Systematic Literature Review
Single nucleotide polymorphisms ( SNPs ) are among the most common types of genetic variation in complex genetic disorders . A growing number of studies link the functional role of SNPs with the networks and pathways mediated by the disease-associated genes . For example , many non-synonymous missense SNPs ( nsSNPs ) h...	Many genetic diseases in humans and animals are caused by combinations of single-letter mutations , or SNPs . When these mutations occur in a protein-coding region of a genome , they can have a profound effect on the protein's function and ultimately on a health-related phenotype . Recently , a growing number of eviden...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computer", "applications", "algorithms", "systems", "biology", "mutation", "computer", "and", "information", "sciences", "computer", "modeling", "mathematics", "genetics", "applied", "mathematics", "biology", "and", "life", "sciences", "computing", "methods", "physical",...	2014	Determining Effects of Non-synonymous SNPs on Protein-Protein Interactions using Supervised and Semi-supervised Learning
Mutations in BBS6 cause two clinically distinct syndromes , Bardet-Biedl syndrome ( BBS ) , a syndrome caused by defects in cilia transport and function , as well as McKusick-Kaufman syndrome , a genetic disorder characterized by congenital heart defects . Congenital heart defects are rare in BBS , and McKusick-Kaufman...	To understand how mutations in one gene can cause two distinct human syndromes ( McKusick-Kaufman syndrome and Bardet-Bield syndrome ) , we investigated the cellular functions of the implicated gene BBS6 . We found that BBS6 is actively transported between the cytoplasm and nucleus , and this interaction is disrupted i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "293t", "cells", "biological", "cultures", "vertebrates", "animals", "animal", "models", "osteichthyes", "organisms", "developmental", "biology", "cytoplasmic", "staining", "model", "organisms", "experi...	2017	Nuclear/cytoplasmic transport defects in BBS6 underlie congenital heart disease through perturbation of a chromatin remodeling protein
By the age of 40 , one in five adults without symptoms of cardiovascular disease are at risk for developing congestive heart failure . Within this population , dilated cardiomyopathy ( DCM ) remains one of the leading causes of disease and death , with nearly half of cases genetically determined . Though genetic and hi...	A molecular understanding of cardiomyocyte development is an essential goal for improving clinical approaches to CHD . While TBX20 is an essential transcription factor for heart development and its disease relevance is well established , many fundamental questions remain about the mechanism of TBX20 function . Principl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "physiology", "cardiovascular", "anatomy", "gene", "regulation", "regulatory", "proteins", "protein", "interaction", "networks", "dna-binding", "proteins", "animal", "models", "physiological", "processes", "model", ...	2017	Formation of a TBX20-CASZ1 protein complex is protective against dilated cardiomyopathy and critical for cardiac homeostasis
The Arp2/3 complex is essential for actin assembly and motility in many cell processes , and a large number of proteins have been found to bind and regulate it in vitro . A critical challenge is to understand the actions of these proteins in cells , especially in settings where multiple regulators are present . In a sy...	A branched network of growing actin filaments , pushing against a membrane , provides the force for certain cellular movements . The Arp2/3 complex plays a central role in this process by generating new filaments and branch points . A number of proteins bind to and , in some cases , regulate Arp2/3 . It is important to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology" ]	2008	Distinct Roles for Arp2/3 Regulators in Actin Assembly and Endocytosis
Binocular vision requires an exquisite matching of projections from each eye to form a cohesive representation of the visual world . Eye-specific inputs are anatomically segregated , but in register in the visual thalamus , and overlap within the binocular region of primary visual cortex . Here , we show that the trans...	The visual world is represented within the brain as a series of maps of visual space . In species with binocular vision , the inputs from the two eyes are aligned to form a cohesive map; little is known about how this organisation is achieved during development . We show that a transmembrane protein , Ten_m3 , plays an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "mus", "(mouse)", "neuroscience" ]	2007	Ten_m3 Regulates Eye-Specific Patterning in the Mammalian Visual Pathway and Is Required for Binocular Vision
Aquaporins are transmembrane proteins that facilitate the flow of water through cellular membranes . An unusual characteristic of yeast aquaporins is that they frequently contain an extended N terminus of unknown function . Here we present the X-ray structure of the yeast aquaporin Aqy1 from Pichia pastoris at 1 . 15 Å...	All living organisms must regulate precisely the flow of water into and out of cells in order to maintain cell shape and integrity . Proteins of one family , the aquaporins , are found in virtually every living organism and play a major role in maintaining water homeostasis by acting as regulated water channels . Here ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "biophysics/macromolecular", "assemblies", "and", "machines", "cell", "biology/cellular", "death", "and", "stress", "responses", "biophysics/theory", "and", "simulation", "biochemistry/macromolecular", "chemistry", "molecular", "biology/bioinformatics", "biochemis...	2009	Crystal Structure of a Yeast Aquaporin at 1.15 Å Reveals a Novel Gating Mechanism
Megacystis-microcolon-intestinal hypoperistalsis syndrome ( MMIHS ) is a rare disorder of enteric smooth muscle function affecting the intestine and bladder . Patients with this severe phenotype are dependent on total parenteral nutrition and urinary catheterization . The cause of this syndrome has remained a mystery s...	In 1976 , a radiologist , Walter Berdon described a group of patients with a rare intestinal and bladder disorder in which the smooth muscle of those organs failed to contract . These patients are unable to digest food , require multiple abdominal surgeries and are diagnosed with megacystis-microcolon-intestinal hypope...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pediatric", "gastroenterology", "gastrointestinal", "motility", "disorders", "gastroenterology", "and", "hepatology", "genetics", "biology", "and", "life", "sciences", "genomics", "clinical", "genetics" ]	2014	Heterozygous De Novo and Inherited Mutations in the Smooth Muscle Actin (ACTG2) Gene Underlie Megacystis-Microcolon-Intestinal Hypoperistalsis Syndrome
Armigeres subalbatus is a natural vector of the filarial worm Brugia pahangi , but it kills Brugia malayi microfilariae by melanotic encapsulation . Because B . malayi and B . pahangi are morphologically and biologically similar , comparing Ar . subalbatus-B . pahangi susceptibility and Ar . subalbatus-B . malayi refra...	In general , organisms can use two different strategies when confronted with pathogens , tolerance and/or resistance . Resistance reduces the fitness of the invading pathogen , whereas tolerance reduces the damage caused by the pathogen to the host . Mosquitoes that transmit the parasites that cause human lymphatic fil...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/functional", "genomics", "pathology/histopathology", "immunology/innate", "immunity", "molecular", "biology/bioinformatics", "cell", "biology/gene", "expression" ]	2010	Mosquito Transcriptome Profiles and Filarial Worm Susceptibility in Armigeres subalbatus
The metabolic capabilities and regulatory networks of bacteria have been optimized by evolution in response to selective pressures present in each species' native ecological niche . In a new environment , however , the same bacteria may grow poorly due to regulatory constraints or biochemical deficiencies . Adaptation ...	When bacteria encounter a new challenge in their environment , such as treatment with an antibiotic or a poor nutrient source , their population faces tremendous selective pressure to evolve in order to grow better under the new conditions . We typically think of bacterial evolution in terms of what is gained: a bacter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "escherichia", "coli", "systems", "biology", "prokaryotic", "models", "genomics", "model", "organisms", "genetics", "synthetic", "biology", "biology", "computational", "biology", "evolutionary", "biology", "microbiology" ]	2013	Bacterial Adaptation through Loss of Function
The function of neuronal networks relies on selective assembly of synaptic connections during development . We examined how synaptic specificity emerges in the pontocerebellar projection . Analysis of axon-target interactions with correlated light-electron microscopy revealed that developing pontine mossy fibers elabor...	Brain functions rely on highly selective neuronal networks which are assembled during development . Network assembly involves targeted neuronal growth followed by recognition of the appropriate target cells and selective synapse formation . How neuronal processes select their appropriate target cells from an array of i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "cellular", "neuroscience", "neuronal", "morphology", "neuroanatomy", "neural", "networks", "signaling", "pathways", "biology", "neuroscience" ]	2011	Development of Axon-Target Specificity of Ponto-Cerebellar Afferents
Burkholderia pseudomallei causes the tropical infection melioidosis . Pneumonia is a common manifestation of melioidosis and is associated with high mortality . Understanding the key elements of host defense is essential to developing new therapeutics for melioidosis . As a flagellated bacterium encoding type III secre...	Melioidosis is an infection caused by Burkholderia pseudomallei , a bacterium that is found in tropical soil and water . Melioidosis can present in a variety of ways , but lung involvement is common and usually severe . The host response to infection governs outcome . In this study , we examined the role of two host se...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacterial", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "genetics", "of", "the", "immune", "system", "clinical", "immunology", "melioidosis", "biology", "and", "life", "sciences", "immunology", "bacterial", "pneumonia", "immune", "r...	2014	NLRC4 and TLR5 Each Contribute to Host Defense in Respiratory Melioidosis
We discovered a novel interaction between phage P22 and its host Salmonella Typhimurium LT2 that is characterized by a phage mediated and targeted derepression of the host dgo operon . Upon further investigation , this interaction was found to be instigated by an ORFan gene ( designated pid for phage P22 encoded instig...	Viruses of bacteria , also referred to as ( bacterio ) phages , are the most abundant biological entity on earth and have a tremendous impact on the ecology of their hosts . It has traditionally been recognized that upon infection by a temperate phage the host cell is forced either to produce and release new virions du...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "metabolism", "gene", "regulation", "microbiology", "gene", "function", "molecular", "genetics", "bacterial", "pathogens", "microbial", "physiology", "gene", "expression", "microbial", "pathogens", "biology", "salmonella", "microbial", "ecology"...	2013	Expression of a Novel P22 ORFan Gene Reveals the Phage Carrier State in Salmonella Typhimurium
A lack of access to sanitation is an important risk factor child health , facilitating fecal-oral transmission of pathogens including soil-transmitted helminthes and various causes of diarrheal disease . We conducted a meta-analysis of cross-sectional surveys to determine the impact that community-level sanitation acce...	A lack of access to a sanitation facility , i . e . a toilet and/or latrine , leads to numerous health challenges such as parasitic worms and environmental enteropathy . Parasitic worms are transmitted through human feces and cause multiple health complications in children including anemia and child growth stunting . E...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "anemia", "pediatrics", "health", "care", "diarrhea", "age", "groups", "research", "design", "child", "growth", "mathematics", "signs", "and", "symptoms", "statistics", ...	2017	An individual-level meta-analysis assessing the impact of community-level sanitation access on child stunting, anemia, and diarrhea: Evidence from DHS and MICS surveys
The hydrolytic deamination of adenosine to inosine ( A-to-I editing ) in precursor mRNA induces variable gene products at the post-transcription level . How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution , and very little is known about the selective constrai...	One prevalent form of RNA editing is the deamination of adenosines ( A-to-I editing ) in the precursor mRNA molecules , pertaining to most organisms in the metazoan lineage . While examples of A-to-I editing on critical genes have been known for years , it has not been fully characterized how A-to-I editing shapes the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "computational", "biology", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "genome", "analysis", "drosophila", "research", "and", "analysis", "methods", "biological", "databases", "molecular", ...	2016	The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection
Japanese encephalitis ( JE ) is a major cause of mortality and morbidity for which there is no treatment . In addition to direct viral cytopathology , the inflammatory response is postulated to contribute to the pathogenesis . Our goal was to determine the contribution of bystander effects and inflammatory mediators to...	Japanese encephalitis ( JE ) is one of the most important causes of viral encephalitis worldwide , with no specific antiviral treatment available . Despite some recent successes with widespread vaccination , JE will likely remain an important public health problem; because the virus is mosquito-borne and has natural an...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "pathology", "histology", "infectious", "diseases", "medicine", "and", "health", "sciences", "anatomy", "veterinary", "microbiology", "biology", "and", "life", "sciences", "immunology", "microbiology", "neuroscience", "veterinary", "science" ]	2014	Neuropathogenesis of Japanese Encephalitis in a Primate Model
RNA viruses exhibit substantial structural , ecological and genomic diversity . However , genome size in RNA viruses is likely limited by a high mutation rate , resulting in the evolution of various mechanisms to increase complexity while minimising genome expansion . Here we conduct a large-scale analysis of the genom...	Understanding the patterns and mechanisms of genome evolution is one of the most important , yet least understood , aspects of RNA virus biology . The evolutionary challenge faced by RNA viruses is to maximize functional diversity within severe constraints on genome size . Here we show that rhabdoviruses , a family of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolution of Genome Size and Complexity in the Rhabdoviridae
Evolution maintains organismal fitness by preserving genomic information . This is widely assumed to involve conservation of specific genomic loci among species . Many genomic encodings are now recognized to integrate small contributions from multiple genomic positions into quantitative dispersed codes , but the evolut...	Purifying selection is a major force in conserving genomic features . It pushes deleterious mutations to extinction while conserving the specific DNA sequence . Here we show that a large proportion of the yeast genome evolves under compensatory dynamics that conserve genomic properties while modifying the genomic seque...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/evolutionary", "modeling", "computational", "biology/genomics", "evolutionary", "biology", "genetics", "and", "genomics/bioinformatics" ]	2010	Widespread Compensatory Evolution Conserves DNA-Encoded Nucleosome Organization in Yeast
Genome-wide association studies ( GWAS ) have been successful in identifying single nucleotide polymorphisms ( SNPs ) associated with many traits and diseases . However , at existing sample sizes , these variants explain only part of the estimated heritability . Leverage of GWAS results from related phenotypes may impr...	Many diseases have a significant hereditary component , only part of which has been explained by analysis of genome-wide association studies ( GWAS ) . Shared aetiology , treatment protocols , and overlapping results from existing GWAS suggest similarities in genetic susceptibility between related diseases , which may ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Pleiotropy-Informed Bayesian False Discovery Rate Adapted to a Shared Control Design Finds New Disease Associations From GWAS Summary Statistics
An increasing number of genes required for mitochondrial biogenesis , dynamics , or function have been found to be mutated in metabolic disorders and neurological diseases such as Leigh Syndrome . In a forward genetic screen to identify genes required for neuronal function and survival in Drosophila photoreceptor neuro...	Neurodegenerative diseases , as a group , are relatively common and often devastating to those who suffer from them . Key insights are emerging from the study of homologues of identified human disease-causing genes in model organisms such as fruit flies , worms , and mice . In this study , we used the fruit fly to iden...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "model", "organisms", "genetic", "mutation", "neurological", "disorders", "neurology", "genetics", "molecular", "genetics", "biology", "human", "genetics", "neuroscience", "genetics", "and", "genomics", "clinical", "genetics" ]	2012	Mutations in the Mitochondrial Methionyl-tRNA Synthetase Cause a Neurodegenerative Phenotype in Flies and a Recessive Ataxia (ARSAL) in Humans
The causative agent of cholera , Vibrio cholerae , regulates its diverse virulence factors to thrive in the human small intestine and environmental reservoirs . Among this pathogen’s arsenal of virulence factors is the tightly regulated type VI secretion system ( T6SS ) . This system acts as an inverted bacteriophage t...	The type six-secretion system ( T6SS ) is a molecular syringe that many Gram-negative pathogens use to kill other bacteria , including commensal bacteria of the human gut . We investigated how the environment of the intestine , specifically commensal bacteria , the mucus lining , and bile affect the T6SS of the bacteri...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Bile Salts Modulate the Mucin-Activated Type VI Secretion System of Pandemic Vibrio cholerae
Yersinia pestis appears to be maintained in multiple , geographically separate , and phylogenetically distinct subpopulations within the highlands of Madagascar . However , the dynamics of these locally differentiated subpopulations through time are mostly unknown . To address that gap and further inform our understand...	Plague exists in several geographically separate phylogenetic groups within Madagascar , but little is known about the dynamics of these groups through time . We subtyped 773 Malagasy plague samples and identified 18 phylogenetic groups that showed persistence in the same locations over a period of almost two decades ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "taxonomy", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "plagues", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "dynamics", "population", "genetics", "geographical", "locations", "micr...	2017	Temporal phylogeography of Yersinia pestis in Madagascar: Insights into the long-term maintenance of plague
The physiochemical determinants of drug-target interactions in the microenvironment of the cell are complex and generally not defined by simple diffusion and intrinsic chemical reactivity . Non-specific interactions of drugs and macromolecules in cells are rarely considered formally in assessing pharmacodynamics . Here...	Small-molecule drug design assumes target binding of high affinity . Most small molecules can interact with other macromolecules in the cell ‘nonspecifically , ’ i . e . , with significantly lower affinity . The extent to which these nonspecific interactions influence the availability and action of the drug for its spe...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "biological", "cultures", "pigments", "dna", "damage", "materials", "science", "cell", "cultures", "pharmacology", "dna", "dyes", "cellular", "structures", "and", "organelles", "chemical...	2018	Determinants of drug-target interactions at the single cell level
Worldwide hundreds of millions of schistosomiasis patients rely on treatment with a single drug , praziquantel . Therapeutic limitations and the threat of praziquantel resistance underline the need to discover and develop next generation drugs . We studied the antischistosomal properties of the Medicines for Malaria Ve...	To date , praziquantel is the only available drug for the treatment of the tropical neglected disease schistosomiasis and is widely used in morbidity control programs . To discover new chemical scaffolds for the treatment of schistosomiasis , we investigated the Medicines for Malaria Venture malaria box containing 200 ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "neglected", "tropical", "diseases", "infectious", "diseases", "parasitic", "diseases" ]	2014	Orally Active Antischistosomal Early Leads Identified from the Open Access Malaria Box
In the United States , roughly 10% of the population is exposed daily to hazardous levels of noise in the workplace . Twin studies estimate heritability for noise-induced hearing loss ( NIHL ) of approximately 36% , and strain specific variation in sensitivity has been demonstrated in mice . Based upon the difficulties...	Noise-induced hearing loss ( NIHL ) is the most common work-related disease in the world and the second cause of hearing loss . Although several candidate gene association studies for NIHL in humans have been conducted , each are underpowered , un-replicated , and account for only a fraction of the genetic risk . Buoye...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Genome-Wide Association Study Identifies Nox3 as a Critical Gene for Susceptibility to Noise-Induced Hearing Loss
During CNS development , the nuclear protein SATB2 is expressed in superficial cortical layers and determines projection neuron identity . In the adult CNS , SATB2 is expressed in pyramidal neurons of all cortical layers and is a regulator of synaptic plasticity and long-term memory . Common variation in SATB2 locus co...	SATB2 is a homeodomain protein that recruits transcriptional and epigenetic regulators to its DNA binding sites . We have recently shown that deletion of Satb2 from the forebrain of adult mice leads to impaired long-term memory . Human patients with SATB2 haploinsufficiency suffer from severe neurological symptoms incl...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "genome-wide", "association", "studies", "interaction", "networks", "dna-binding", "proteins", "neuroscience", "age", "groups", "adults", "cognition", "genome", "analysis", "epigenetics", "chromatin", "genomics", "chromosome", "biology", "proteins", "gene", "expression", ...	2019	Genes encoding SATB2-interacting proteins in adult cerebral cortex contribute to human cognitive ability
Reported urban malaria cases are increasing in Latin America , however , evidence of such trend remains insufficient . Here , we propose an integrated approach that allows characterizing malaria transmission at the rural-to-urban interface by combining epidemiological , entomological , and parasite genotyping methods ....	Malaria is a disease of rural areas in developing countries . Although a rise in urban malaria cases has been noted during the last decade , this trend could be an artifact due to lack of solid data . In order to better understand “urban” and “peri-urban” malaria , we developed a rigorous and systematic methodology tha...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "neighborhoods", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "parasitology", "developmental", "biology", "apicomplexa", "molecular", "biology"...	2017	Characterizing the malaria rural-to-urban transmission interface: The importance of reactive case detection
Primaquine is the only licensed antimalarial for the radical cure of Plasmodium vivax infections . Many countries , however , do not administer primaquine due to fear of hemolysis in those with glucose-6-phosphate dehydrogenase ( G6PD ) deficiency . In other settings , primaquine is given without G6PD testing , putting...	A single infection with Plasmodium vivax can cause multiple episodes of illness due to dormant liver parasites called hypnozoites . Primaquine is the only drug currently available to treat hypnozoites but is under-used because it can cause life-threatening red blood cell damage in people who have an inherited condition...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "clinical", "laboratory", "sciences", "cost-effectiveness", "analysis", "maternal", "health", "plasmodium", "obstetrics", "and", "gynecology", "economic", "analysis", "drugs", "tropical", "diseases", "social",...	2017	Using G6PD tests to enable the safe treatment of Plasmodium vivax infections with primaquine on the Thailand-Myanmar border: A cost-effectiveness analysis
Proteins of the nuclear envelope ( NE ) are associated with a range of inherited disorders , most commonly involving muscular dystrophy and cardiomyopathy , as exemplified by Emery-Dreifuss muscular dystrophy ( EDMD ) . EDMD is both genetically and phenotypically variable , and some evidence of modifier genes has been ...	Emery-Dreifuss muscular dystrophy ( EDMD ) is an inherited disorder involving muscle wasting and weakness , accompanied by cardiac defects . The disease is variable in its severity and also in its genetic cause . So far , 6 genes have been linked to EDMD , most encoding proteins that form a structural network that supp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Muscular Dystrophy-Associated SUN1 and SUN2 Variants Disrupt Nuclear-Cytoskeletal Connections and Myonuclear Organization
Leishmania infantum is the causative agent of visceral and cutaneous leishmaniasis in the Mediterranean region , South America , and China . MON-1 L . infantum is the predominating zymodeme in all endemic regions , both in humans and dogs , the reservoir host . In order to answer important epidemiological questions it ...	Visceral leishmaniasis is caused by protozoan parasites of the genus Leishmania . This disease is a public health problem in countries bordering the Mediterranean , in China , and South America . Until now , isoenzyme analysis , a method with several advantages but also some limitations , is the gold standard for typin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "molecular", "biology/molecular", "evolution", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "diseases", "microbiology/parasitology", "infectious", "disease...	2008	Differentiation and Gene Flow among European Populations of Leishmania infantum MON-1
Large-scale conformational changes in proteins involve barrier-crossing transitions on the complex free energy surfaces of high-dimensional space . Such rare events cannot be efficiently captured by conventional molecular dynamics simulations . Here we show that , by combining the on-the-fly string method and the multi...	Conformational transitions of proteins have been postulated to play a central role in various protein functions such as catalysis , allosteric regulation , and signal transduction . Among these , the relation between enzymatic catalysis and dynamics has been particularly well-studied . The target molecule in this study...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "chemistry", "molecular", "dynamics", "biophysic", "al", "simulations", "chemistry", "biology", "computational", "biology" ]	2012	Minimum Free Energy Path of Ligand-Induced Transition in Adenylate Kinase
The insula , particularly its posterior portion , is often regarded as a primary cortex for pain . However , this interpretation is largely based on reverse inference , and a specific involvement of the insula in pain has never been demonstrated . Taking advantage of the high spatiotemporal resolution of direct intrace...	A widely accepted notion is that the insula , especially its posterior portion , plays a specific role in the perception of pain . This has led a number of researchers to consider activity recorded from this so-called “ouch zone” as an objective correlate of pain perception . We provide compelling evidence to the contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Nociceptive Local Field Potentials Recorded from the Human Insula Are Not Specific for Nociception
Cytoplasmic flows are an ubiquitous feature of biological systems , in particular in large cells , such as oocytes and eggs in early animal development . Here we show that cytoplasmic flows in starfish oocytes , which can be imaged well with transmission light microscopy , are fully determined by the cortical dynamics ...	As already noted by Aristotle , life is motion . On the molecular scale , thermal motion leads to diffusive transport . On cellular scales , however , diffusion starts to become inefficient , due to the general property of random walks that their spatial excursions grow less than linear with time . Therefore more direc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "classical", "mechanics", "fluid", "mechanics", "geometry", "animals", "cell", "polarity", "germ", "cells", "oocytes", "mathematics", "echinoderms", "starfish", "cellular", "structures", "an...	2018	Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions
We evaluated the sensitivity of the dengue surveillance system in detecting hospitalized cases in ten capital cities in Brazil from 2008 to 2013 using a probabilistic record linkage of two independent information systems hospitalization ( SIH-SUS ) adopted as the gold standard and surveillance ( SINAN ) . Sensitivity w...	This manuscript address essential issues regarding the current and future challenges of a dengue surveillance system . Dengue fever is one of the major public health threats in a large area of the world , including Brazil which represents around 70% of the cases in the Americas . The dengue surveillance system in Brazi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "clinical", "laboratory", "sciences", "geographical", "locations", "tropical", "diseases", "health", "care", "age", "groups", "inpatients", "neglected", "tropical", "diseases", "infectious", "disease", "control", "patients", "pub...	2016	Sensitivity of the Dengue Surveillance System in Brazil for Detecting Hospitalized Cases
Apoptosis is a form of programmed cell death critical for development and homeostasis in multicellular organisms . Apoptosis-like cell death ( ALCD ) has been described in several fungi , including the opportunistic human pathogen Cryptococcus neoformans . In addition , capsular polysaccharides of C . neoformans are kn...	Fungal pathogens can cause life-threatening diseases , and the infections that they cause are notoriously difficult to treat . Despite the availability of antifungal drugs , most inhibit fungal growth but do not consistently or efficiently eliminate the pathogen . In addition , fungal cells are very similar to human ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "drugs", "and", "devices", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2011	Deletion of Cryptococcus neoformans AIF Ortholog Promotes Chromosome Aneuploidy and Fluconazole-Resistance in a Metacaspase-Independent Manner
CTP synthase is an essential enzyme that plays a key role in energy metabolism . Several independent studies have demonstrated that CTP synthase can form an evolutionarily conserved subcellular structure termed cytoophidium . In budding yeast , there are two isoforms of CTP synthase and both isoforms localize in cytoop...	DNA and RNA are made up from basic building blocks called nucleotides . Those nucleotides also play essential roles in many other biological processes . To separate biological processes within a cell is an important feature of all cell types . For example , mitochondria are specialized structures that contain ATP synth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "cellular", "structures", "drosophila", "melanogaster", "model", "organisms", "molecular", "cell", "biology", "cell", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2013	Only One Isoform of Drosophila melanogaster CTP Synthase Forms the Cytoophidium
Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the infectious cause of several AIDS-related cancers , including the endothelial cell ( EC ) neoplasm Kaposi's sarcoma ( KS ) . KSHV-infected ECs secrete abundant host-derived pro-inflammatory molecules and angiogenic factors that contribute to tumorigenesis . The pre...	We have only scratched the surface in understanding how viruses control host gene expression . Several viruses disrupt important sites of post-transcriptional control of gene expression known as processing bodies ( PBs ) , but underlying regulatory mechanisms and biological relevance remain poorly understood in most ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "medical", "microbiology", "viral", "pathogens", "microbial", "pathogens", "pathogens", "biology", "and", "life", "sciences", "microbiology", "kaposi's", "sarcoma-associated"...	2015	Viral Activation of MK2-hsp27-p115RhoGEF-RhoA Signaling Axis Causes Cytoskeletal Rearrangements, P-body Disruption and ARE-mRNA Stabilization
The finding that regular spatial patterns can emerge in nature from local interactions between organisms has prompted a search for the ecological importance of these patterns . Theoretical models have predicted that patterning may have positive emergent effects on fundamental ecosystem functions , such as productivity ...	Local interactions between organisms in nature can scale up to produce strikingly regular patterns across entire landscapes . With improvements in satellite imagery , such patterns are increasingly reported in the ecological literature . It remains unclear , however , whether the existence of such patterns actually mat...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/evolutionary", "ecology", "ecology/conservation", "and", "restoration", "ecology", "ecology", "evolutionary", "biology/animal", "behavior", "plant", "biology/plant-environment", "interactions", "ecology/community", "ecology", "and", "biodiversity", "ecolo...	2010	Spatial Pattern Enhances Ecosystem Functioning in an African Savanna
Microbe- or host damage-derived patterns mediate activation of pattern-triggered immunity ( PTI ) in plants . Microbial virulence factor ( effector ) -triggered immunity ( ETI ) constitutes a second layer of plant protection against microbial attack . Various necrosis and ethylene-inducing peptide 1 ( Nep1 ) -like prot...	Eukaryotic host immunity to microbial infection requires recognition systems sensing the presence of potential invaders . Microbial surface structures ( patterns ) or host breakdown products generated during microbial attack serve as ligands for host immune receptors ( pattern recognition receptors ) mediating activati...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "biology", "and", "life", "sciences", "immunology", "microbiology", "species", "interactions", "agriculture" ]	2014	A Conserved Peptide Pattern from a Widespread Microbial Virulence Factor Triggers Pattern-Induced Immunity in Arabidopsis
Mapping expression quantitative trait loci ( eQTLs ) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level . In this paper , we present an integrative analysis approach that leverages eQTL data collected from multiple population groups . In particular , our app...	Expression quantitative trait loci ( eQTLs ) are genetic variants associated with gene expression phenotypes . Mapping eQTLs enables us to study the genetic basis of gene expression variation across individuals . In this study , we introduce a statistical framework for analyzing genotype-expression data collected from ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Cross-Population Joint Analysis of eQTLs: Fine Mapping and Functional Annotation
Vascularisation is a key feature of cancer growth , invasion and metastasis . To better understand the governing biophysical processes and their relative importance , it is instructive to develop physiologically representative mathematical models with which to compare to experimental data . Previous studies have succes...	Angiogenesis is a hallmark of tumour growth and a key feature for invasion and metastasis . Thus , to elucidate the governing biological processes of cancer development , it is instructive to develop physiologically representative mathematical and computational ( in-silico ) models with which to compare to experimental...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "classical", "mechanics", "cardiovascular", "physiology", "cardiovascular", "anatomy", "oxygen", "basic", "cancer", "research", "capillaries", "angiogenesis", "oncology", "developmental", "biology", "tumor", "phys...	2017	A Validated Multiscale In-Silico Model for Mechano-sensitive Tumour Angiogenesis and Growth
Nodamura Virus ( NoV ) is a nodavirus originally isolated from insects that can replicate in a wide variety of hosts , including mammals . Because of their simplicity and ability to replicate in many diverse hosts , NoV , and the Nodaviridae in general , provide a unique window into the evolution of viruses and host-vi...	Proteins often contain regions with defined structures that enable their function . While important for maintaining the overall architecture of the protein , structural conservation adds constraints on the ability of the protein to mutate , and thus evolve . Viruses of eukaryotes , however , often encode for proteins w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biology", "and", "life", "sciences", "species", "interactions", "microbiology", "evolutionary", "biology" ]	2014	Rapid Evolution of Virus Sequences in Intrinsically Disordered Protein Regions
The pentatricopeptide repeat ( PPR ) is a helical repeat motif found in an exceptionally large family of RNA–binding proteins that functions in mitochondrial and chloroplast gene expression . PPR proteins harbor between 2 and 30 repeats and typically bind single-stranded RNA in a sequence-specific fashion . However , t...	RNA binding proteins dictate RNA fate and function by modulating RNA processing , localization , translation , and stability . The consequences of RNA/protein interactions are determined , in part , by the position at which the protein binds the RNA . However , it is impossible to predict the target sites of most RNA b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "plant", "science", "molecular", "cell", "biology", "plant", "biology", "genetics", "biology", "evolutionary", "biology", "agricultural", "biotechnology", "genetics", "and", "genomics", "agriculture" ]	2012	A Combinatorial Amino Acid Code for RNA Recognition by Pentatricopeptide Repeat Proteins
BLyS/BAFF is recognized for its role in B-cell ontogenesis , as well as cell fate decision towards the first-line/innate marginal zone ( MZ ) B-cell pool . Excess BLyS/BAFF is associated with hyperglobulinemia and increased frequencies of activated precursor-like MZ B-cells . Herein , we show that HIV highly-exposed se...	Worldwide , most human immunodeficiency virus ( HIV ) infections affect women through heterosexual intercourse . We and others have identified African female commercial sex workers ( CSWs ) , who remain seronegative despite high exposition to HIV ( HESNs ) . Innate marginal zone ( MZ ) B-cells recirculate in humans and...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodefici...	2019	Natural Immunity to HIV is associated with Low BLyS/BAFF levels and low frequencies of innate marginal zone like CD1c+ B-cells in the genital tract
Adhesion and detachment are coordinated critical steps during cell migration . Conceptually , efficient migration requires both effective stabilization of membrane protrusions at the leading edge via nascent adhesions and their successful persistence during retraction of the trailing side via disruption of focal adhesi...	Cell migration is an essential process in both single-cell and multicellular organisms . In higher animals , cell migration is important for many biological processes , including embryonic development , the immune response , and wound healing . Cancer cell invasion into healthy tissues occurs as a result of inappropria...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "cell", "biology/cell", "adhesion", "cell", "biology/cytoskeleton" ]	2009	Nudel and FAK as Antagonizing Strength Modulators of Nascent Adhesions through Paxillin
One of the most influential observations in molecular evolution has been a strong association between local recombination rate and nucleotide polymorphisms across the genome . This is interpreted as evidence for ubiquitous natural selection . The alternative explanation , that recombination is mutagenic , has been reje...	Individuals within a species differ in the DNA sequences of their genes . This sequence variation affects how well individuals survive or reproduce and is transmitted to their offspring . Genes near each other on individual chromosomes tend to be passed to offspring together—neighboring genes are unlikely to be separat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "neutral", "theory", "population", "genetics", "genome", "sequencing", "mutation", "genome", "databases", "genome", "complexity", "genetic", "polymorphism", "biology", "genetic", "drift", "sequence", "databases", "natural", "selection", "genetics", ...	2012	Recombination Modulates How Selection Affects Linked Sites in Drosophila
Chelt , a cholera-like toxin from Vibrio cholerae , and Certhrax , an anthrax-like toxin from Bacillus cereus , are among six new bacterial protein toxins we identified and characterized using in silico and cell-based techniques . We also uncovered medically relevant toxins from Mycobacterium avium and Enterococcus fae...	Computer tools helped us uncover and understand potent protein toxins that empower bacterial pathogens against plants , animals and man . These toxins are potential drug targets and researchers can use them to make vaccines . New toxin knowledge aids the long-term goal of finding alternatives to antibiotics , to which ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "computational", "biology/protein", "homology", "detection", "computational", "biology/protein", "structure", "prediction", "computational", "biology/macromolecular", "sequence", "analysis", "biochemistry/biomacromolecule-liga...	2010	Cholera- and Anthrax-Like Toxins Are among Several New ADP-Ribosyltransferases
A general paradigm to understand protein function is to look at properties of isolated well conserved domains , such as SH3 or PDZ domains . While common features of domain families are well understood , the role of subtle differences among members of these families is less clear . Here , molecular dynamics simulations...	Protein interactions play crucial roles in all biological processes . A common way of studying them is to focus on sub-parts of proteins , called domains , that mediate specific types of interactions . For instance , it is known that most PDZ domains mediate protein interactions by binding to the C-terminus of other pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "biology", "computational", "biology", "biophysics" ]	2012	Beyond the Binding Site: The Role of the β2 – β3 Loop and Extra-Domain Structures in PDZ Domains
CD163 , receptor for the haptoglobin–hemoglobin complex , is expressed on monocytes/macrophages and neutrophils . A soluble form of CD163 ( sCD163 ) has been associated with the M2 macrophage phenotype , and M2 macrophages have been shown to down-modulate inflammatory responses . In particular , previous studies have s...	Visceral leishmaniasis ( VL ) is a systemic , and most severe form of leishmaniasis . Soluble CD163 ( sCD163 ) levels can serve as biomarker for disease severity in several inflammatory disorders . However , no linkage has been reported for its relationship with Leishmania infections . We now demonstrate , for the firs...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "bacterial", ...	2017	sCD163 levels as a biomarker of disease severity in leprosy and visceral leishmaniasis
The heterosexual risk group has become the largest HIV infected group in the United Kingdom during the last 10 years , but little is known of the network structure and dynamics of viral transmission in this group . The overwhelming majority of UK heterosexual infections are of non-B HIV subtypes , indicating viruses or...	Since 1995 , HIV among heterosexuals in the UK increased to the point where the total number of heterosexuals infected with HIV , predominantly of non-B subtypes , exceeds the number of HIV-positive homosexual men . To understand the dynamics of this epidemic , we have applied the novel technique of phylodynamics to th...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases" ]	2009	Molecular Phylodynamics of the Heterosexual HIV Epidemic in the United Kingdom
Robustness is a property built into biological systems to ensure stereotypical outcomes despite fluctuating inputs from gene dosage , biochemical noise , and the environment . During development , robustness safeguards embryos against structural and functional defects . Yet , our understanding of how robustness is achi...	Every embryo develops under its own unique set of circumstances , with variable inputs coming from mother , father , and the environment . To then ensure a reliable outcome , mechanisms are built into development to buffer against challenges like genetic deficiency , maternal fever , alcohol exposure , etc . This buffe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Maternal-to-Zygotic Transition Targets Actin to Promote Robustness during Morphogenesis
The host's immune system plays a key role in modulating growth of pathogens and the intestinal microbiota in the gut . In particular , inflammatory bowel disorders and pathogen infections induce shifts of the resident commensal microbiota which can result in overgrowth of Enterobacteriaceae ( “inflammation-inflicted bl...	Colicins are bacterial protein toxins which show potent activity against sensitive strains in vitro . Ecological models suggest that colicins play a major role in modulating dynamics of bacterial populations in the gut . However , previous studies could not readily confirm these predictions by respective in vivo experi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	Inflammation Fuels Colicin Ib-Dependent Competition of Salmonella Serovar Typhimurium and E. coli in Enterobacterial Blooms
Quantitative modeling is useful for predicting behaviors of a system and for rationally constructing or modifying the system . The predictive power of a model relies on accurate quantification of model parameters . Here , we illustrate challenges in parameter quantification and offer means to overcome these challenges ...	A crown jewel of any scientific investigation is to make accurate and quantitative predictions based on mechanistic understanding of a system . Although quantitative prediction has been the norm and the expectation in physical sciences , living systems are notoriously difficult to predict quantitatively . One of the ma...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "death", "rates", "flow", "cytometry", "cell", "physiology", "cell", "death", "chemical", "compounds", "cell", "processes", "cloning", "nucleotides", "organic", "compounds", "cell", "metabolism", "metabolites", "basic", "amino", "acids", "amino", "acids", "molecular",...	2019	Uncovering and resolving challenges of quantitative modeling in a simplified community of interacting cells
Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations . Nevertheless , little is known about the role of epigenetics in evolution . This is due in part to scant data on epigenetic variation among natural populations . In plants , small interfering R...	Phenotypic variation has been mainly attributed to their differences in genetic materials , i . e . , the DNA sequence . The advances in Epigenetics in past decades has revealed it as a fundamental mechanism that could inheritably influence gene function without change in DNA sequence , but by modulating chemical modif...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "plant", "biology/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/plant", "genomes", "and", "evolution" ]	2008	Small RNA-Directed Epigenetic Natural Variation in Arabidopsis thaliana
The family Polydnaviridae is of interest because it provides the best example of viruses that have evolved a mutualistic association with their animal hosts . Polydnaviruses in the genus Bracovirus are strictly associated with parasitoid wasps in the family Braconidae , and evolved ∼100 million years ago from a nudivir...	Microorganisms form obligate associations with multicellular organisms that range from antagonistic ( parasitic ) to beneficial ( mutualists ) . Although numerous examples of obligate , mutualistic bacteria , fungi , and protozoans exist , viruses are thought to usually form parasitic associations . An exception is the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "species", "interactions", "biology", "and", "life", "sciences", "microbiology" ]	2014	Widespread Genome Reorganization of an Obligate Virus Mutualist
Terpenoid synthases create diverse carbon skeletons by catalyzing complex carbocation rearrangements , making them particularly challenging for enzyme function prediction . To begin to address this challenge , we have developed a computational approach for the systematic enumeration of terpenoid carbocations . Applicat...	Terpenoids , as one of the largest classes of natural products , provide complex carbocycle structures for many drugs ( e . g . taxol ) and prodrugs . The diverse carbocycle structures arise from complex carbocation rearrangements catalyzed by terpenoid synthases . Many putative terpene synthase enzymes identified in g...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "terpenes", "stereoisomers", "chemical", "compounds", "enzymology", "reactants", "alkanes", "organic", "compounds", "isomerism", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "hydrocarbons", "sequence", "analysis...	2016	Defining the Product Chemical Space of Monoterpenoid Synthases
Togo has conducted annual , integrated , community-based mass drug administration ( MDA ) for soil-transmitted helminths ( STH ) and schistosomiasis since 2010 . Treatment frequency and target populations are determined by disease prevalence , as measured by baseline surveys in 2007 and 2009 , and WHO guidelines . Repo...	Mass drug administration ( MDA ) is a key component of programs aimed at controlling soil-transmitted helminths ( STH ) and schistosomiasis , diseases that disproportionately impact individuals in developing countries and adversely affect physical and cognitive development . The World Health Organization recommends eva...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "education", "helminths", "sociology", "tropical", "diseases", "hookworms", "social", "sciences", "parasitic", "diseases", "animals", "urine", "neglected",...	2018	Impact of community-based integrated mass drug administration on schistosomiasis and soil-transmitted helminth prevalence in Togo
An important paradigm in evolutionary genetics is that of a delicate balance between genetic variants that favorably boost host control of infection but which may unfavorably increase susceptibility to autoimmune disease . Here , we investigated whether patients with psoriasis , a common immune-mediated disease of the ...	Individuals with autoimmune disease generally demonstrate excessive immune system activation , leading to inflammation and damage of specific target organs . However , in some cases the detrimental effects of an overactive immune system might be counterbalanced by a beneficial effect in protecting against certain infec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "dermatology", "infectious", "diseases", "public", "health", "and", "epidemiology", "sexually", "transmitted", "diseases", "epidemiology" ]	2012	Psoriasis Patients Are Enriched for Genetic Variants That Protect against HIV-1 Disease
Understanding mosquito host choice is important for assessing vector competence or identifying disease reservoirs . Unfortunately , the availability of an unbiased method for comprehensively evaluating the composition of insect blood meals is very limited , as most current molecular assays only test for the presence of...	Female mosquitoes require a blood meal to acquire the nutrients necessary for egg production . While feeding on host species , mosquitoes can transmit pathogens that cause several diseases including malaria , lymphatic filariasis and dengue . Understanding the mosquito host choice is important to better implement contr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "animals", "molecular", "biology", "techniques", "insect", "vectors", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "sequen...	2016	Unbiased Characterization of Anopheles Mosquito Blood Meals by Targeted High-Throughput Sequencing
The present pilot study investigating the minimum dose for short-course single and double-dose treatment of kala-azar with an apparently new liposomal formulation of amphotericin B , Fungisome , led to identification of immunological components for early detection of success and/or failure to cure . Patients were treat...	Visceral leishmaniasis ( VL ) is a potentially fatal disease without treatment , characterized by prolonged fever , enlargement of spleen and liver , anaemia and weight loss . Treatment for VL is difficult , as it requires prolonged and painful application of toxic drugs with adverse side effects . It is therefore impo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "microbiology/immunity", "to", "infections", "immunology/immunomodulation", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "microbiology/innate", "immunity", "immunology/innate", "immunity", "immunology", "infe...	2010	A Curative Immune Profile One Week after Treatment of Indian Kala-Azar Patients Predicts Success with a Short-Course Liposomal Amphotericin B Therapy
During millions of years of coevolution with their hosts , cytomegaloviruses ( CMVs ) have succeeded in adapting to overcome host-specific immune defenses , including the protein kinase R ( PKR ) pathway . Consequently , these adaptations may also contribute to the inability of CMVs to cross species barriers . Here , w...	Cytomegaloviruses ( CMVs ) are highly species-specific , but the host factors that prevent replication in heterologous species are largely unknown . Based on data indicating that the broadly-acting host antiviral factor protein kinase R ( PKR ) has diversified rapidly during evolution , we hypothesized that PKR may con...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "cytomegalovirus", "infection", "animals", "mammals", "plasmid", "construction", "primates", "viruses", "dna", "vi...	2016	A Single Amino Acid Dictates Protein Kinase R Susceptibility to Unrelated Viral Antagonists
Due to the large number of putative microRNA gene targets predicted by sequence-alignment databases and the relative low accuracy of such predictions which are conducted independently of biological context by design , systematic experimental identification and validation of every functional microRNA target is currently...	MicroRNAs regulate the expression of genes in cells and are important in cancer development and progression . Designing new microRNA-based treatments requires the understanding of their mechanisms of action . Previous biological studies lack in depth since only a few genes are confirmed as microRNA targets . Additional...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/disease", "models", "molecular", "biology/translational", "regulation", "oncology/head", "and", "neck", "cancers", "genetics", "and", "genomics/bioinformatic...	2010	Network Modeling Identifies Molecular Functions Targeted by miR-204 to Suppress Head and Neck Tumor Metastasis
Autophagy is a cellular process required for the removal of aged organelles and cytosolic components through lysosomal degradation . All types of eukaryotic cells from yeasts to mammalian cells have the machinery to activate autophagy as a result of many physiological and pathological situations . The most frequent sti...	In spite of its old discovery , more than one hundred years ago , Trypanosoma cruzi , the causative agent of Chagas’ disease , is still prevalent in the world , infecting more than 6 million people mostly in Latin America , where this illness is endemic . Only two approved drugs , benznidazole and nifurtimox , are curr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "lysosomes", "vesicles", "cell", "processes", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans", "cell", "differentiation", "developm...	2017	The regulation of autophagy differentially affects Trypanosoma cruzi metacyclogenesis
Broadly neutralizing antibodies targeting a highly conserved region in the hemagglutinin ( HA ) stem protect against influenza infection . Here , we investigate the protective efficacy of a protein ( HB36 . 6 ) computationally designed to bind with high affinity to the same region in the HA stem . We show that intranas...	Influenza is a major public health threat , and pandemics , such as the 2009 H1N1 outbreak , are inevitable . Due to low efficacy of seasonal flu vaccines and the increase in drug-resistant strains of influenza viruses , there is a crucial need to develop new antivirals to protect from seasonal and pandemic influenza ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "viruses", "animal", "models", "developmen...	2016	A Computationally Designed Hemagglutinin Stem-Binding Protein Provides In Vivo Protection from Influenza Independent of a Host Immune Response
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes . In particular , Hi-C sequencing is becoming an economical method for generating chromosome-scale scaffolds . Despite its increasing popularity , there are limited ...	Hi-C technology was originally proposed to study the 3D organization of a genome . Recently , it has also been applied to assemble large eukaryotic genomes into chromosome-scale scaffolds . Despite this , there are few open source methods to generate these assemblies . Existing methods are also prone to small inversion...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infographics", "sequencing", "techniques", "sequence", "assembly", "tools", "genome", "sequencing", "chromosome", "mapping", "genome", "analysis", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "genomic", "librarie...	2019	Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Active-sensing systems abound in nature , but little is known about systematic strategies that are used by these systems to scan the environment . Here , we addressed this question by studying echolocating bats , animals that have the ability to point their biosonar beam to a confined region of space . We trained Egypt...	Most sensory systems have an active component , i . e . driven by an animal's behavior , which contributes directly to its perception . For example , eye movements are important for visual perception , sniffs are crucial for olfactory percepts , and finger movements for touch percepts . A classic example of an active-s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "sensory", "perception", "neuroscience" ]	2011	Active Control of Acoustic Field-of-View in a Biosonar System
One of the most conserved features of the invasion process in Apicomplexa parasites is the formation of a moving junction ( MJ ) between the apex of the parasite and the host cell membrane that moves along the parasite and serves as support to propel it inside the host cell . The MJ was , up to a recent period , comple...	A unique feature of apicomplexan parasites is the formation of an intimate contact between the apex of the parasite and the host cell membrane called the moving junction that moves along the parasite during invasion . Proteins originated from two distinct secretory organelles , the microneme for AMA1 and the rhoptry ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/parasitology" ]	2009	Export of a Toxoplasma gondii Rhoptry Neck Protein Complex at the Host Cell Membrane to Form the Moving Junction during Invasion
Mosquito-borne viruses encompass a range of virus families , comprising a number of significant human pathogens ( e . g . , dengue viruses , West Nile virus , Chikungunya virus ) . Virulent strains of these viruses are continually evolving and expanding their geographic range , thus rapid and sensitive screening assays...	This paper describes a simple and cost-effective system for screening biological samples for virus-infection . The authors demonstrate the application of two antibodies to detect double-stranded RNA ( dsRNA ) which is a common molecule produced in infection by a number of different viruses . The use of antibodies which...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Viral RNA Intermediates as Targets for Detection and Discovery of Novel and Emerging Mosquito-Borne Viruses
In plants , specific recognition of pathogen effector proteins by nucleotide-binding leucine-rich repeat ( NLR ) receptors leads to activation of immune responses . RPP1 , an NLR from Arabidopsis thaliana , recognizes the effector ATR1 , from the oomycete pathogen Hyaloperonospora arabidopsidis , by direct association ...	Plants defend themselves against pathogens using specific multi-domain immune receptors , which are able to recognize secreted “effector” proteins from the pathogen , and thus activate an immune response . Variants of the Arabidopsis immune receptor RPP1 recognize different alleles of the oomycete effector ATR1 through...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Recognition and Activation Domains Contribute to Allele-Specific Responses of an Arabidopsis NLR Receptor to an Oomycete Effector Protein
Usually , the occurrence of random cell behavior is appointed to small copy numbers of molecules involved in the stochastic process . Recently , we demonstrated for a variety of cell types that intracellular Ca2+ oscillations are sequences of random spikes despite the involvement of many molecules in spike generation ....	The number of proteins organizing cellular processes is huge . The challenge for systems biology is to connect the properties of all these proteins to cellular behavior . Do individual state changes of molecules matter for cell behavior despite these large numbers ? Recently , we have experimentally shown for four cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics/interdisciplinary", "physics", "cell", "biology/cell", "signaling", "computational", "biology/signaling", "networks", "computational", "biology/molecular", "dynamics", "computational", "biology", "computational", "biology/systems", "biology" ]	2010	Calcium Signals Driven by Single Channel Noise
The definitive method for diagnosis of porcine cysticercosis is the detection of cysticerci at necropsy . Cysts are typically located in the striated muscle and brain . Until recently Taenia solium cysticerci have not been definitively identified in other tissue locations , despite several comprehensive investigations ...	The only currently available method for accurate assessment of the prevalence of porcine cysticercosis is to undertake detailed examination of tissues at necropsy . Most investigations have found that in pigs , Taenia solium encysts in the striated muscles and nervous tissue . Recently an investigation of porcine cysti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "liver", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "muscle", "tissue", "spleen", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "lungs", "organisms", "respiratory...	2019	Accurate diagnosis of lesions suspected of being caused by Taenia solium in body organs of pigs with naturally acquired porcine cysticercosis
A standard view in neuroeconomics is that to make a choice , an agent first assigns subjective values to available options , and then compares them to select the best . In choice tasks , these cardinal values are typically inferred from the preference expressed by subjects between options presented in pairs . Alternati...	In economic decision theory , value is a construct that provides a metric to compare options: agents are likely to select options leading to high-value outcomes . In neuroscience , different behavioral tasks have been used to elicit the subjective values of potential outcomes , notably rating tasks , which demand an ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "economic", "agents", "medicine", "and", "health", "sciences", "decision", "making", "engineering", "and", "technology", "thermometers", "behavioral", "economics", "social", "sciences", "limbs", "(anatomy)", "neuroscience", "neuroeconomics", "cognitive", "psychology", "co...	2017	Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks
Bdellovibrio bacteriovorus is a Delta-proteobacterium that oscillates between free-living growth and predation on Gram-negative bacteria including important pathogens of man , animals and plants . After entering the prey periplasm , killing the prey and replicating inside the prey bdelloplast , several motile B . bacte...	Bdellovibrio bacteriovorus is a tiny bacterium that preys upon other bacteria including pathogenic bacteria that cause infections in humans , animals , or crop plants . Bdellovibrio don't attack human , plant or animal cells and so could in future be used as “living antibiotics” . Here we have discovered , using geneti...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "systems", "biology", "medicine", "infectious", "diseases", "drugs", "and", "devices", "complementary", "and", "alternative", "medicine", "genetics", "biology", "microbiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Discrete Cyclic di-GMP-Dependent Control of Bacterial Predation versus Axenic Growth in Bdellovibrio bacteriovorus
Evidence of an adverse influence of soil transmitted helminth ( STH ) infections on cognitive function and educational loss is equivocal . Prior meta-analyses have focused on randomized controlled trials only and have not sufficiently explored the potential for disparate influence of STH infection by cognitive domain ....	Previous systematic reviews of the effect of STH infection on cognitive and educational performance were either inconclusive or found little to no evidence of associated benefit . Lack of consensus in prior reviews and their narrow emphasis on randomized controlled trials prompted this comprehensive assessment of wheth...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "children", "cognitive", "neurology", "medicine", "and", "health", "sciences", "education", "sociology", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "neuroscience", "learning", "and", "memory", "pediatrics", "age", "groups", "cogni...	2018	Soil-transmitted helminth infection, loss of education and cognitive impairment in school-aged children: A systematic review and meta-analysis
An important goal in molecular evolution is to understand the genetic and physical mechanisms by which protein functions evolve and , in turn , to characterize how a protein's physical architecture influences its evolution . Here we dissect the mechanisms for an evolutionary shift in function in the mollusk ortholog of...	An important goal in evolutionary genetics is to understand how genetic mutations cause the evolution of new protein functions and how a protein's structure shapes its evolution . Here we address these questions by studying a dramatic lineage-specific shift in function in steroid hormone receptors ( SRs ) , a physiolog...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "biochemistry", "biology", "evolutionary", "biology", "biophysics", "evolutionary", "genetics" ]	2014	Vestigialization of an Allosteric Switch: Genetic and Structural Mechanisms for the Evolution of Constitutive Activity in a Steroid Hormone Receptor
Brucellosis and leptospirosis are among neglected tropical zoonotic diseases particularly in the resource limited countries . Despite being endemic in these countries , there is paucity of information on its magnitude . This study investigated seropositivity of Brucella spp . and Leptospira spp . , and associated facto...	Brucellosis and leptospirosis are among neglected diseases in many low-income countries affecting both animals and human populations . Despite being common , the information on their distribution are scarce . In a view of that , this study investigated the proportion of participants with positive antibody test specific...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "sociology", "tropical", "diseases", "microbiology", "diet", "social", "sciences", "animal", "products", "social", "systems", "regression", "analysis", "bac...	2018	Seropositivity of Brucella spp. and Leptospira spp. antibodies among abattoir workers and meat vendors in the city of Mwanza, Tanzania: A call for one health approach control strategies
The biotrophic basidiomycete fungus Ustilago maydis causes smut disease in maize . Hallmarks of the disease are large tumors that develop on all aerial parts of the host in which dark pigmented teliospores are formed . We have identified a member of the WOPR family of transcription factors , Ros1 , as major regulator o...	The fungus Ustilago maydis is a pathogen of maize which induces tumor formation in the infected tissue . In these tumors huge amounts of fungal spores develop . As a biotrophic pathogen , U . maydis establishes itself in the plant with the help of a large number of secreted effector proteins . Many effector proteins ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fungal", "spores", "ustilago", "maydis", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "cereal", "crops", "fungi", "regulator", "genes", "model", "organisms", "plant", "science", "transcription", "factors", "crops", "gene", "types", "plan...	2016	The WOPR Protein Ros1 Is a Master Regulator of Sporogenesis and Late Effector Gene Expression in the Maize Pathogen Ustilago maydis
Cells employ multiple levels of regulation , including transcriptional and translational regulation , that drive core biological processes and enable cells to respond to genetic and environmental changes . Small-molecule metabolites are one category of critical cellular intermediates that can influence as well as be a ...	It is now possible to score variations in DNA across whole genomes , RNA levels and alternative isoforms , metabolite levels , protein levels and protein state information , protein–protein interactions , and protein–DNA interactions , in a comprehensive fashion in populations of individuals . Interactions among these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "genomics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation
Serological studies are the gold standard method to estimate influenza infection attack rates ( ARs ) in human populations . In a common protocol , blood samples are collected before and after the epidemic in a cohort of individuals; and a rise in haemagglutination-inhibition ( HI ) antibody titers during the epidemic ...	Each year , seasonal influenza is responsible for about three to five million severe illnesses and about 250 , 000 to 500 , 000 deaths worldwide . In order to assess the burden of disease and guide control policies , it is important to quantify the proportion of people infected by an influenza virus each year . Since i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Ethics", "statement" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology" ]	2012	Influenza Infection Rates, Measurement Errors and the Interpretation of Paired Serology
Apoptosis is an important mechanism by which virus-infected cells are eliminated from the host . Accordingly , many viruses have evolved strategies to prevent or delay apoptosis in order to provide a window of opportunity in which virus replication , assembly and egress can take place . Interfering with apoptosis may a...	Among the variety of defense systems employed by mammalian cells to combat virus infection , apoptosis or programmed cell death is the most drastic response . Some large DNA viruses encode proteins whose sole function is to block apoptosis . Conversely , very little is known about whether RNA viruses encode analogous p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "antiviral", "responses", "virology", "virology/viral", "replication", "and", "gene", "regulation", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2011	The Rubella Virus Capsid Is an Anti-Apoptotic Protein that Attenuates the Pore-Forming Ability of Bax
Extensive experimental information supports the formation of ligand-specific conformations of G protein-coupled receptors ( GPCRs ) as a possible molecular basis for their functional selectivity for signaling pathways . Taking advantage of the recently published inactive and active crystal structures of GPCRs , we have...	G protein-coupled receptors ( GPCRs ) constitute one of the most important classes of cellular targets owing to their known response to a host of extracellular stimuli , and consequent involvement in numerous vital biological processes . Compelling evidence herein referred to as ‘functional selectivity’ shows that liga...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "computational", "biology", "biophysics" ]	2011	Ligand-Induced Modulation of the Free-Energy Landscape of G Protein-Coupled Receptors Explored by Adaptive Biasing Techniques
Gene duplication is supposed to be the major source for genetic innovations . However , how a new duplicate gene acquires functions by integrating into a pathway and results in adaptively important phenotypes has remained largely unknown . Here , we investigated the biological roles and the underlying molecular mechani...	Gene duplication has long been appreciated as a major source for new genes and new functions . Nevertheless , it is still a fascinating mystery how new duplicate genes are functionally integrated into the existing gene network and how they contribute to the novel functions of organisms at the pathway level . By studyin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "biology/morphogenesis", "and", "cell", "biology", "evolutionary", "biology/developmental", "evolution" ]	2010	A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes
To date , the contribution of disrupted potentially cis-regulatory conserved non-coding sequences ( CNCs ) to human disease is most likely underestimated , as no systematic screens for putative deleterious variations in CNCs have been conducted . As a model for monogenic disease we studied the involvement of genetic ch...	Long-range genetic control is an inherent feature of genes harbouring a highly complex spatiotemporal expression pattern , requiring a combined action of multiple cis-regulatory elements such as promoters , enhancers , and silencers . Consequently , disruption of the long-range genetic control of a target gene by genom...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/chromatin", "structure", "computational", "biology/comparative", "sequence", "analysis", "genetics", "and", "genomics/genetics", "of", "disease", "developmental", "biology/molecular", "development", "ophthalmology/inherited", "eye", "disorders", "genetics", ...	2009	Disease-Causing 7.4 kb Cis-Regulatory Deletion Disrupting Conserved Non-Coding Sequences and Their Interaction with the FOXL2 Promotor: Implications for Mutation Screening
A correct assessment of the quaternary structure of proteins is a fundamental prerequisite to understanding their function , physico-chemical properties and mode of interaction with other proteins . Currently about 90% of structures in the Protein Data Bank are crystal structures , in which the correct quaternary struc...	X-ray diffraction experiments are the main experimental technique to reveal the detailed atomic 3-dimensional structure of proteins . In these experiments , proteins are packed into crystals , an environment that is far away from their native solution environment . Determining which parts of the structure reflect the p...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "dimers", "(chemical", "physics)", "crystal", "structure", "condensed", "matter", "physics", "crystal", "lattices", "crystals", "materials", "science", "protein", "structure", "crystallography", "materials", "by", "structure", "solid", "state", "physics", "protein", "st...	2018	Automated evaluation of quaternary structures from protein crystals
K-Ras , one of the most common small GTPases of the cell , still presents many riddles , despite the intense efforts to unveil its mysteries . Such is the case of its interaction with Calmodulin , a small acidic protein known for its role as a calcium ion sensor . Although the interaction between these two proteins and...	K-Ras is one of the most mutated oncogenes in human cancer . Although several studies validate K-Ras protein as good candidate for direct therapeutic targeting , pharmacologic targeting has not been successful . During the last years increasing evidences demonstrate that oncogenic K-Ras activity can be modulated in viv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "interactions", "bioelectrochemical", "analysis", "molecular", "dynamics", "biochemical", "analysis", "simulation", "and", "modeling", "membrane", "proteins", "bioassays", "and", "physiological", "analysis", "cellular", "structures", "and", "organelles", "researc...	2018	Modeling and subtleties of K-Ras and Calmodulin interaction
In placental mammals , inactivation of one of the X chromosomes in female cells ensures sex chromosome dosage compensation . The 17 kb non-coding Xist RNA is crucial to this process and accumulates on the future inactive X chromosome . The most conserved Xist RNA region , the A region , contains eight or nine repeats s...	In placental mammal females , Xist RNA is crucial for inactivation of one of the two X chromosomes in order to maintain proper X chromosome dosage . It is known that the conserved A region of Xist RNA , which contains eight or nine repeated elements , plays an essential role in this process , however , little is known ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/histone", "modification", "biochemistry/rna", "structure" ]	2010	2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association
Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression . However , the mechanisms underlying cooperation between cis-acting elements are poorly documented , notably in vertebrates . The mouse gene Krox20 encodes...	The formation of multicellular organisms from the egg to the adult stage is largely under genetic control . The activation of specific genes is governed by regulatory DNA sequences present nearby on the chromosome . Most of these sequences promote activation and are called enhancers . In this paper , we study two enhan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "embryology", "developmental", "biology", "genetic", "loci", "enhancer", "elements", "cell", "biology", "chromosome", "biology", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "epigenetics", "embryos", "genomics", "mammalia...	2017	Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
Arboviral infections are a public health concern and an escalating problem worldwide . Estimating the burden of these diseases represents a major challenge that is complicated by the large number of unapparent infections , especially those of dengue fever . Serological surveys are thus required to identify the distribu...	Arthropod-borne viruses ( arboviruses ) are among the most important of the emerging infectious disease public health problems facing the world . The actual impact of arboviruses worldwide remains unknown , and estimating the true burden of these diseases represents a current challenge . Serological surveys are the mos...	[ "Abstract", "Introduction", "Materials", "and", "method", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "alphaviruses", "viruses", "chikungunya...	2018	Current challenges and implications for dengue, chikungunya and Zika seroprevalence studies worldwide: A scoping review
Failure of the human heart to maintain sufficient output of blood for the demands of the body , heart failure , is a common condition with high mortality even with modern therapeutic alternatives . To identify molecular determinants of mortality in patients with new-onset heart failure , we performed a meta-analysis of...	In this study , we applied a genome-wide mapping approach to study molecular determinants of mortality in subjects with heart failure . We identified a genetic variant on chromosome 5q22 that was associated with mortality in this group and observed that this variant conferred increased function of an enhancer region ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "death", "rates", "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "body", "fluids", "demography", "genome", "analysis", "epigenetics", "dna", "population", "biology", "dna", "methylation", "chromatin", "cardiology", "genomics", "chromos...	2016	Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure
Vinculin can interact with F-actin both in recruitment of actin filaments to the growing focal adhesions and also in capping of actin filaments to regulate actin dynamics . Using molecular dynamics , both interactions are simulated using different vinculin conformations . Vinculin is simulated either with only its vinc...	The interface between a cell and its substrate is strengthened by the formation of focal adhesions . In this study molecular dynamics simulations are used to explore the connectivity of one focal adhesion forming protein , vinculin , and the cytoskeletal filament , F-actin . The simulations demonstrate: ( 1 ) that vinc...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "bioengineering", "biological", "systems", "engineering", "biology", "computational", "biology", "engineering" ]	2013	The Interaction of Vinculin with Actin
Chronic chagasic cardiomyopathy ( CCC ) is observed in 30% to 50% of the individuals infected by Trypanosoma cruzi and heart failure is the important cause of death among patients in the chronic phase of Chagas disease . Although some studies have elucidated the role of adaptive immune responses involving T and B lymph...	Chronic chagasic cardiomyopathy ( CCC ) is the main cause of death during Trypanosoma cruzi ( T . cruzi ) infection in patients . Individuals with CCC have high production of inflammatory mediators such as IFN-γ , TNF-α , IL-1β and nitric oxide ( NO ) which are involved with myocarditis , fibrosis , and myocardial hype...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "cardiomyopathies", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "develop...	2018	Innate immune receptors over expression correlate with chronic chagasic cardiomyopathy and digestive damage in patients
A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues . This study focuses on elucidating how gene expression is initiated in the notochord , an axial structure that provides support and patterning signals to embry...	Transcription factors control the spatial and temporal expression of a multitude of genes by binding their cis-regulatory modules ( CRMs ) . In this study , we investigated the architecture and composition of CRMs that direct gene expression in the notochord , a structure necessary for the support and patterning of the...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Brachyury, Foxa2 and the cis-Regulatory Origins of the Notochord
The fecal egg count reduction test ( FECRT ) is recommended to monitor drug efficacy against soil-transmitted helminths ( STHs ) in public health . However , the impact of factors inherent to study design ( sample size and detection limit of the fecal egg count ( FEC ) method ) and host-parasite interactions ( mean bas...	The reduction in number of eggs excreted in stools after drug administration is a primary parameter to monitor the efficacy of drugs against parasitic worms . Guidelines on how to perform such a fecal egg count reduction test ( FECRT ) are provided by the World Health Organization . However , it remains unclear to whic...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "clinical", "research", "design", "drugs", "and", "devices", "global", "health", "public", "health" ]	2011	Novel Insights in the Fecal Egg Count Reduction Test for Monitoring Drug Efficacy against Soil-Transmitted Helminths in Large-Scale Treatment Programs
The mitochondrial ( mt ) genome is present in many copies in human cells , and intra-individual variation in mtDNA sequences is known as heteroplasmy . Recent studies found that heteroplasmies are highly tissue-specific , site-specific , and allele-specific , however the functional implications have not been explored ....	The total number of mitochondrial genomes in a human cell differs between individuals and between the tissues of a single individual; however the factors that influence this variation remain unknown . We estimated mtDNA copy number ( mtCN ) in 12 different tissues of 152 individuals applying three different methods , a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "mitochondrial", "dna", "population", "genetics", "computational", "biology", "cloning", "regression", "analysis", "mathematics", "chromosome", "mapping", "statistics", "(mathematics)", "dna", "replication", "genome", "analysis", "shotgun", "sequ...	2016	Age-Related and Heteroplasmy-Related Variation in Human mtDNA Copy Number
Laboratory-based studies have highlighted that pooling stool and urine samples can reduce costs and diagnostic burden without a negative impact on the ability to estimate the intensity of soil-transmitted helminth ( STH , Ascaris lumbricoides , Trichuris trichiura and hookworms ) and schistosome infections ( Schistosom...	Infections with intestinal ( roundworms , whipworm and hookworms ) and blood-dwelling ( schistosomes ) worms pose a significant public health burden in developing tropical countries . To optimize control programs against these worms , large-scale surveys are required to determine the worm distribution to initiate contr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "salaries", "education", "engineering", "and", "technology", "helminths", "sociology", "tropical", "diseases", "hookworms", "social", "sciences", "parasitic", "diseases", "a...	2018	Comparison of individual and pooled diagnostic examination strategies during the national mapping of soil-transmitted helminths and Schistosoma mansoni in Ethiopia
Viewing of ambiguous stimuli can lead to bistable perception alternating between the possible percepts . During continuous presentation of ambiguous stimuli , percept changes occur as single events , whereas during intermittent presentation of ambiguous stimuli , percept changes occur at more or less regular intervals ...	Patients suffering from schizophrenia show specific cognitive deficits . One way to study these cognitive phenomena works with the presentation of ambiguous stimuli . During viewing of an ambiguous stimulus , perception alters spontaneously between different percepts . Percept changes occur as single events during cont...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "markov", "models", "fluid", "mechanics", "social", "sciences", "electrophysiology", "random", "variables", "neuroscience", "perception", "cognitive", "psychology", "mathematics", "probability", "distributio...	2017	A hierarchical stochastic model for bistable perception
The basis for correctly assessing the burden of parasitic infections and the effects of interventions relies on a somewhat shaky foundation as long as we do not know how reliable the reported laboratory findings are . Thus virtual microscopy , successfully introduced as a histopathology tool , has been adapted for medi...	Here , we describe a novel tool to observe parasites by virtual microscopy on the Internet . Microscopy-based identification of parasites is the basis for both diagnostics and epidemiological assessment of parasite burden globally . Yet , quality assessment of diagnostic parasitology laboratories is difficult , as deli...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "computer", "science/applications", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/helminth", "infections", "evidence-based", "healthcare/methods", "for", "diagnostic", ...	2008	Web-Based Virtual Microscopy for Parasitology: A Novel Tool for Education and Quality Assurance
Genome-wide RNA expression data provide a detailed view of an organism's biological state; hence , a dataset measuring expression variation between genetically diverse individuals ( eQTL data ) may provide important insights into the genetics of complex traits . However , with data from a relatively small number of ind...	Gene expression data of genetically diverse individuals ( eQTL data ) provide a unique perspective on the effect of genetic variation on cellular pathways . However , the burden of multiple hypotheses , combined with the challenges of linkage disequilibrium , makes it difficult to correctly identify causal polymorphism...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/genomics", "computational", "biology" ]	2009	Learning a Prior on Regulatory Potential from eQTL Data

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