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Genetic studies have identified substantial non-African admixture in the Horn of Africa ( HOA ) . In the most recent genomic studies , this non-African ancestry has been attributed to admixture with Middle Eastern populations during the last few thousand years . However , mitochondrial and Y chromosome data are suggest...	The Horn of Africa ( HOA ) occupies a central place in our understanding of modern human origins . This region is the location of the earliest known modern human fossils , a possible source for the out-of-Africa migration , and one of the most genetically and linguistically diverse regions of the world . Numerous genet...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "physical", "anthropology", "human", "evolution", "biology", "and", "life", "sciences", "population", "genetics", "gene", "flow", "social", "sciences", "evolutionary", "biology", "anthropology" ]	2014	Early Back-to-Africa Migration into the Horn of Africa
A new generation of vaccines for the neglected tropical diseases ( NTDs ) have now advanced into clinical development , with the Na-GST-1/Alhydrogel Hookworm Vaccine already being tested in Phase 1 studies in healthy adults . The current manuscript focuses on the often overlooked critical aspects of NTD vaccine product...	As vaccines targeting NTDs advance into clinical trials , product development and vaccine maintenance become critical activities for the success of these vaccines . A key activity during this phase of vaccine development is the “relative potency” of a vaccine or the quality of the immune response that the vaccine elici...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "helminths", "immunology", "tropical", "diseases", "hookworms", "sorption", "animals", "vaccines", "preventive", "medicine", "desorption", "neglected", "tropical", "disease...	2017	Advances in neglected tropical disease vaccines: Developing relative potency and functional assays for the Na-GST-1/Alhydrogel hookworm vaccine
The Tetrahymena thermophila DNA replication machinery faces unique demands due to the compartmentalization of two functionally distinct nuclei within a single cytoplasm , and complex developmental program . Here we present evidence for programmed changes in ORC and MCM abundance that are not consistent with conventiona...	The Origin Recognition Complex is required for site-specific replication initiation in eukaryotic chromosomes . Null mutations are lethal in yeast and metazoa , and hypomorphs induce genome instability , a hallmark of cancer . We exploited the unique biology of Tetrahymena to explore ORC's role in conventional and alte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "biology", "biology", "and", "life", "sciences", "molecular", "biology" ]	2015	Developmental Regulation of the Tetrahymena thermophila Origin Recognition Complex
The availability of metagenomic sequencing data , generated by sequencing DNA pooled from multiple microbes living jointly , has increased sharply in the last few years with developments in sequencing technology . Characterizing the contents of metagenomic samples is a challenging task , which has been extensively atte...	Microorganisms are extremely abundant and diverse , and occupy almost every habitat on earth . Most of these habitats contain a complex mixture of many different microorganisms , and the characterization of these metagenomic mixtures , in terms of both taxonomy and function , is of great interest to science and medicin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genomics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Joint Analysis of Multiple Metagenomic Samples
Staphylococcus aureus is a leading cause of community-associated and nosocomial infections . Imperative to the success of S . aureus is the ability to adapt and utilize nutrients that are readily available . Genomic sequencing suggests that S . aureus has the genes required for synthesis of all twenty amino acids . How...	Although Staphylococcus aureus encodes the highly conserved arginine biosynthesis pathway via glutamate , arginine is an essential amino acid . We found that a mutation in ccpA , a gene encoding a protein facilitating carbon catabolite repression , mediates arginine biosynthesis under in vitro growth conditions . Howev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "chemical", "biology", "chemistry", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	CcpA Regulates Arginine Biosynthesis in Staphylococcus aureus through Repression of Proline Catabolism
Genetically controlled resistance of Anopheles gambiae mosquitoes to Plasmodium falciparum is a common trait in the natural population , and a cluster of natural resistance loci were mapped to the Plasmodium-Resistance Island ( PRI ) of the A . gambiae genome . The APL1 family of leucine-rich repeat ( LRR ) proteins wa...	The African malaria vector mosquito Anopheles gambiae possesses immune mechanisms that can protect it against infection with malaria parasites , which kill more than one million people per year . Much work studying mosquito response to malaria has used model rodent malaria parasites that do not infect people , but are ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system" ]	2009	Fine Pathogen Discrimination within the APL1 Gene Family Protects Anopheles gambiae against Human and Rodent Malaria Species
Live-cell imaging has opened an exciting window into the role cellular heterogeneity plays in dynamic , living systems . A major critical challenge for this class of experiments is the problem of image segmentation , or determining which parts of a microscope image correspond to which individual cells . Current approac...	Dynamic live-cell imaging experiments are a powerful tool to interrogate biological systems with single cell resolution . The key barrier to analyzing data generated by these measurements is image segmentation—identifying which parts of an image belong to which individual cells . Here we show that deep learning is a na...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "diagnostic", "radiology", "neural", "networks", "light", "microscopy", "neuroscience", "in", "vivo", "imaging", "microscopy", "cellular", "structures", "and", "organelles", "bacteria", "research", "and...	2016	Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
Co-resistance against the first-line antibiotics ampicillin , chloramphenicol and trimethoprim/sulphamethoxazole or multidrug resistance ( MDR ) is common in non typhoid Salmonella ( NTS ) . Use of alternative antibiotics , such as fluoroquinolones or third generation cephalosporins is threatened by increasing resistan...	Invasive non typhoid Salmonella spp . ( NTS ) are an important cause of bloodstream infection in sub-Saharan Africa and associated with a high mortality . Levels of multidrug resistance have become alarmingly high . Treatment therefore increasingly relies on the oral fluoroquinolones such as ciprofloxacin , with third ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "neglected", "tropical", "diseases", "salmonellosis", "salmonella" ]	2013	Antimicrobial Resistance in Invasive Non-typhoid Salmonella from the Democratic Republic of the Congo: Emergence of Decreased Fluoroquinolone Susceptibility and Extended-spectrum Beta Lactamases
Developmental patterning requires juxtacrine signaling in order to tightly coordinate the fates of neighboring cells . Recent work has shown that Notch and Delta , the canonical metazoan juxtacrine signaling receptor and ligand , mutually inactivate each other in the same cell . This cis-interaction generates mutually ...	Multicellular development requires tightly regulated spatial pattern formation , frequently including the generation of sharp differences over short length scales . Classic examples include boundary formation in the Drosophila wing veins and lateral inhibition patterning in the differentiation of sensory cells . These ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "biology", "computational", "biology", "signaling", "networks", "pattern", "formation", "genetics", "and", "genomics" ]	2011	Mutual Inactivation of Notch Receptors and Ligands Facilitates Developmental Patterning
While a relationship between environmental forcing and influenza transmission has been established in inter-pandemic seasons , the drivers of pandemic influenza remain debated . In particular , school effects may predominate in pandemic seasons marked by an atypical concentration of cases among children . For the 2009 ...	An influenza pandemic virus emerged in North America in 2009 . Although the virus spread worldwide within months of its emergence , the timing of peak pandemic activity varied by nearly a year across global populations . In fact , the most intense period of pandemic activity occurred earlier in temperate countries of t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Impact of School Cycles and Environmental Forcing on the Timing of Pandemic Influenza Activity in Mexican States, May-December 2009
Myelination of the central nervous system ( CNS ) is critical to vertebrate nervous systems for efficient neural signaling . CNS myelination occurs as oligodendrocytes terminally differentiate , a process regulated in part by the myelin regulatory factor , MYRF . Using bioinformatics and extensive biochemical and funct...	Membrane-bound transcription factors are synthesized as integral membrane proteins , but are proteolytically cleaved in response to relevant cues , untethering their transcription factor domains from the membrane to control gene expression in the nucleus . Here , we find that the myelin regulatory factor MYRF , a major...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroglial", "development", "biochemistry", "developmental", "neuroscience", "transmembrane", "proteins", "proteins", "regulatory", "proteins", "biology", "dna-binding", "proteins", "neuroscience" ]	2013	A Bacteriophage Tailspike Domain Promotes Self-Cleavage of a Human Membrane-Bound Transcription Factor, the Myelin Regulatory Factor MYRF
Most of the current knowledge on the genetic basis of adaptive evolution is based on the analysis of single nucleotide polymorphisms ( SNPs ) . Despite increasing evidence for their causal role , the contribution of structural variants to adaptive evolution remains largely unexplored . In this work , we analyzed the po...	Transposable elements are fragments of genomic DNA that have the ability to move around the genome by creating new copies of themselves . Although there is evidence suggesting that transposable elements play important roles in genome function and genome evolution , our current understanding is based on the analysis of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "chemical", "compounds", "statistics", "animals", "invertebrate", "genomics", "organic", "compounds", "animal", "models", "chi", "square", "tests", "drosophila", "melanogaster", "model", "organisms", "mathematics", "experimental", "organism", "systems", "...	2019	Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila
The phytohormone auxin plays critical roles in regulating myriads of plant growth and developmental processes . Microbe infection can disturb auxin signaling resulting in defects in these processes , but the underlying mechanisms are poorly understood . Auxin signaling begins with perception of auxin by a transient co-...	Auxin regulates plant growth and development through auxin signaling , which begins with the interaction of an F-box transport inhibitor response 1/auxin signaling F-box ( TIR1/AFB ) protein and an auxin/indole-3-acetic acid ( Aux/IAA ) protein co-receptor . Auxin binding to the co-receptor complex triggers ubiquitinat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "anatomy", "protein", "interactions", "hormones", "cereal", "crops", "plant", "science", "rice", "model", "organisms", "plant", "hormones", "genetically", "modified", "plants", "crops", "seedlings", "plants", "genetic", "engineering", "research...	2016	Rice Dwarf Virus P2 Protein Hijacks Auxin Signaling by Directly Targeting the Rice OsIAA10 Protein, Enhancing Viral Infection and Disease Development
Interactions of influenza A virus ( IAV ) with sialic acid ( SIA ) receptors determine viral fitness and host tropism . Binding to mucus decoy receptors and receptors on epithelial host cells is determined by a receptor-binding hemagglutinin ( HA ) , a receptor-destroying neuraminidase ( NA ) and a complex in vivo rece...	Influenza A virus ( IAV ) tropism is largely determined by the interaction of virus particles with the sialic acid receptor repertoire of the host . IAVs encounter a diverse range of sialic acid receptors that can function as decoys ( e . g . in the mucus that covers epithelial cells ) or as entry receptors . We studie...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "social", "sciences", "viral", "structure", "signaling", "networks", "orthomyxoviruses", "neuroscience", "...	2018	Kinetic analysis of the influenza A virus HA/NA balance reveals contribution of NA to virus-receptor binding and NA-dependent rolling on receptor-containing surfaces
Planar morphogenesis , a distinct feature of multicellular organisms , is crucial for the development of ovule , progenitor of seeds . Both receptor-like kinases ( RLKs ) such as STRUBBELIG ( SUB ) and auxin gradient mediated by PIN-FORMED1 ( PIN1 ) play instructive roles in this process . Fine-tuned intercellular comm...	Ovules , being the progenitors of seeds , hold an important role in crop production . Ovule is a complex organ connecting two generations , i . e . diploid sporophytic cells and haploid female gametophytes ( FG ) . Fertilization of female gametes leads to the development of embryo and endosperm while the sporophytic ce...	[ "Abstract", "Introduction", "Results", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "vesicles", "plant", "growth", "and", "development", "plant", "embryo", "anatomy", "ovules", "light", "microscopy", "hormones", "pollen", "developmental", "biology", "plant", "science", "confocal", "laser", "microscopy", "microscopy", "plant", "hor...	2016	HAPLESS13-Mediated Trafficking of STRUBBELIG Is Critical for Ovule Development in Arabidopsis
Mutations that decrease insulin-like growth factor ( IGF ) and growth hormone signaling limit body size and prolong lifespan in mice . In vertebrates , these somatotropic hormones are controlled by the neuroendocrine brain . Hormone-like regulations discovered in nematodes and flies suggest that IGF signals in the nerv...	Using a mouse model relevant for humans , we showed that lifespan can be significantly extended by reducing the signaling selectively of a protein called IGF-I in the central nervous system . This effect occurred through changes in specific neuroendocrine pathways . Dissecting the pathophysiological mechanism , we disc...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "physiology", "diabetes", "and", "endocrinology", "genetics", "and", "genomics" ]	2008	Brain IGF-1 Receptors Control Mammalian Growth and Lifespan through a Neuroendocrine Mechanism
Acquisition of partially protective immunity is a dominant feature of the epidemiology of malaria among exposed individuals . The processes that determine the acquisition of immunity to clinical disease and to asymptomatic carriage of malaria parasites are poorly understood , in part because of a lack of validated immu...	Whilst it is clear that natural immunity to malaria infection develops in those living in malaria-endemic regions of the world , the precise way in which it is acquired and the duration of immune memory are less-well-understood . We used a mathematical model that mimics malaria transmission between humans and mosquitoe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematical", "models", "public", "health", "and", "epidemiology", "malaria", "epidemiology" ]	2007	Determination of the Processes Driving the Acquisition of Immunity to Malaria Using a Mathematical Transmission Model
Motor training with the upper limb affected by stroke partially reverses the loss of cortical representation after lesion and has been proposed to increase spontaneous arm use . Moreover , repeated attempts to use the affected hand in daily activities create a form of practice that can potentially lead to further impro...	Stroke often leaves patients with predominantly unilateral functional limitations of the arm and hand . Although recovery of function after stroke is often achieved by compensatory use of the less affected limb , improving use of the more affected limb has been associated with increased quality of life . Here , we deve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/motor", "systems", "neuroscience/neurobiology", "of", "disease", "and", "regeneration", "neurological", "disorders/movement", "disorders", "neuroscience/theoretical", "neuroscience" ]	2008	Stroke Rehabilitation Reaches a Threshold
In the malaria parasite P . falciparum , drug resistance generally evolves first in low-transmission settings , such as Southeast Asia and South America . Resistance takes noticeably longer to appear in the high-transmission settings of sub-Saharan Africa , although it may spread rapidly thereafter . Here , we test the...	The malaria parasite Plasmodium falciparum has evolved resistance to most antimalarial drugs , greatly complicating treatment and control of the disease . Curiously , although sub-Saharan Africa accounts for the majority of the global burden of malaria , the evolution of drug resistance in Africa has been markedly dela...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "evolution", "drugs", "immunology", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "antimalarials", "protozoans", "pharmacology", "cross", "reactivity", "antimi...	2018	Within-host competition can delay evolution of drug resistance in malaria
Entry of enveloped viruses requires fusion of viral and cellular membranes , driven by conformational changes of viral glycoproteins . Crystal structures provide static pictures of pre- and post-fusion conformations of these proteins but the transition pathway remains elusive . Here , using several biophysical techniqu...	Vesicular stomatitis virus ( VSV ) enters cells via endocytosis . At low pH , its unique glycoprotein G catalyzes fusion between viral and endosomal membranes by going from a pre-fusion trimeric conformation to a post-fusion trimeric conformation . There is a lack of information about G structural intermediates during ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "virology", "biology", "microbiology", "biophysics" ]	2012	Characterization of Monomeric Intermediates during VSV Glycoprotein Structural Transition
Dynamic correlations are pervasive in high-throughput data . Large numbers of gene pairs can change their correlation patterns in response to observed/unobserved changes in physiological states . Finding changes in correlation patterns can reveal important regulatory mechanisms . Currently there is no method that can e...	Dynamic correlation is an important area in expression data . However it hasn’t received much attention because of the lack of effective methods that can unravel the complex relationship . Here we describe a new method that represents a substantial improvement over existing approaches . It achieves the goal of efficien...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "simulation", "and", "modeling", "multivariate", "analysis", "probability", "distribution", "mathematics", "statistics", "(mathematics)", "algebra", "polynomials", ...	2018	A new dynamic correlation algorithm reveals novel functional aspects in single cell and bulk RNA-seq data
The sand fly Phlebotomus argentipes is arguably the most important vector of leishmaniasis worldwide . As there is no vaccine against the parasites that cause leishmaniasis , disease prevention focuses on control of the insect vector . Understanding reproductive behaviour will be essential to controlling populations of...	The sand fly Phlebotomus argentipes transmits Leishmania parasites through female blood-feeding . These parasites cause leishmaniasis , a potentially fatal disease for which there is no vaccine . Understanding how insect vectors behave can aid in developing strategies to reduce disease transmission . Here , we investig...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "parasitic", "diseases", "parasitology", "zoology", "veterinary", "science", "veterinary", "diseases", "zoonoses", "insect", "pheromones", "protozoan", "infections", "beha...	2014	Multi-modal Analysis of Courtship Behaviour in the Old World Leishmaniasis Vector Phlebotomus argentipes
The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization . The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link actin to intercellular adhesions . Over time , evolutionar...	The establishment of intercellular adhesions facilitated the genesis of multicellular organisms . The adherens junction , which links the actin cytoskeletons of neighboring cells , arose early in the evolution of multicellularity and selective pressures have shaped its function and molecular composition over time . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "invertebrates", "cell", "motility", "medicine", "and", "health", "sciences", "rna", "interference", "gene", "regulation", "animals", "epithelial", "cells", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "parietal", "...	2019	Evolutionary rate covariation analysis of E-cadherin identifies Raskol as a regulator of cell adhesion and actin dynamics in Drosophila
Autophagy plays a key role during Salmonella infection , by eliminating these pathogens following escape into the cytosol . In this process , selective autophagy receptors , including the myosin VI adaptor proteins optineurin and NDP52 , have been shown to recognize cytosolic pathogens . Here , we demonstrate that myos...	One of the most common causes of food poisoning is the pathogen Salmonella enterica serovar Typhimurium . This pathogen enters the cells of the body through the intestine and after invasion of these cells it survives and multiplies due to its own ability to evade the immune system , thus causing infection . Understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Autophagy Receptor TAX1BP1 and the Molecular Motor Myosin VI Are Required for Clearance of Salmonella Typhimurium by Autophagy
Plants are highly sensitive to environmental changes and even small variations in ambient temperature have severe consequences on their growth and development . Temperature affects multiple aspects of plant development , but the processes and mechanisms underlying thermo-sensitive growth responses are mostly unknown . ...	The increase in average temperatures across the globe has been predicted to have negative impacts on agricultural productivity . Therefore , there is a need to understand the molecular mechanisms that underlie plant growth responses to varying temperature regimes . At present , very little is known about the genes and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Natural Variation Identifies ICARUS1, a Universal Gene Required for Cell Proliferation and Growth at High Temperatures in Arabidopsis thaliana
When mosquitoes infected with DENV are feeding , the proboscis must traverse the epidermis several times ( “probing” ) before reaching a blood vessel in the dermis . During this process , the salivary glands release the virus , which is likely to interact first with cells of the various epidermal and dermal layers , ce...	In this work , we demonstrate that that both human whole skin and freshly isolated skin fibroblasts are productively infected with Dengue virus ( DENV ) . In addition , primary skin fibroblast cultures were established and subsequently infected with DENV-2; we showed in these cells the presence of the viral antigen NS3...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "virology", "biology", "microbiology", "viral", "diseases" ]	2011	Activation of the Innate Immune Response against DENV in Normal Non-Transformed Human Fibroblasts
The proper display of transmembrane receptors on the leading edge of migrating cells and cell extensions is essential for their response to guidance cues . We previously discovered that MADD-4 , which is an ADAMTSL secreted by motor neurons in Caenorhabditis elegans , interacts with an UNC-40/EVA-1 co-receptor complex ...	In most animals , the physical meeting of the pre- and post-synaptic membranes of the neuromuscular junction occurs via axonal extension towards the muscle . In nematodes , however , motor axons do not extend towards the muscle and instead form a dorsal and ventral cord with relatively few branches . To make the physic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "lysosomes", "caenorhabditis", "animals", "animal", "models", "muscle", "components", "muscle", "proteins", "caenorhabditis", "elegans", "model", "organisms", "muscle", "functions", "cellular", "structures", "and",...	2016	The MADD-3 LAMMER Kinase Interacts with a p38 MAP Kinase Pathway to Regulate the Display of the EVA-1 Guidance Receptor in Caenorhabditis elegans
The tapeworm Taenia solium is the parasite responsible for neurocysticercosis , a neglected tropical disease of public health importance , thought to cause approximately 1/3 of epilepsy cases across endemic regions . The consumption of undercooked infected pork perpetuates the parasite’s life-cycle through the establis...	Taenia solium is a serious zoonotic helminth which is thought to be responsible for approximately 1/3rd of epilepsy cases in the developing world . The work presented in this paper aimed to understand what the risk is of acquiring T . solium taeniosis from pork slaughtered and consumed in western Kenya . In order to do...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "diet", "vertebrates", "parasitic", "diseases", "animals", "mammals", "animal", "products", "probability", "distribution", "nutrition", "mathematics", "meat", "neglected", "tropi...	2017	Modelling the risk of Taenia solium exposure from pork produced in western Kenya
The transcription factor Interferon Regulatory Factor 5 ( IRF-5 ) has been shown to be involved in the induction of proinflammatory cytokines in response to viral infections and TLR activation and to play an essential role in the innate inflammatory response . In this study , we used the experimental model of visceral ...	Leishmania donovani is a parasite that currently infects 12 million people around the world . In order to better understand why this parasite causes incurable disease we chose to investigate how the immune system sees L . donovani . The immune system sees infecting organisms by the recognition of molecules that are spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "immunology/innate", "immunity", "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2011	Critical Role of IRF-5 in the Development of T helper 1 responses to Leishmania donovani infection
The use of synthetic insecticides is one of the most common strategies for controlling disease vectors such as mosquitos . However , their overuse can result in serious risks to human health , to the environment , as well as to the selection of insecticidal resistant insect strains . The development of efficient and ec...	Numerous outbreaks of infectious diseases such as dengue , zika , and chikungunya in tropical countries have occurred where the mosquito Aedes aegypti is the transmitting vector . In Brazil , these infections are responsible for deaths and severe sequelae . Thus , many efforts have been made by governmental and researc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "fish", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "vertebrates", "animals", "toxicology", "animal", "models", "osteichthyes", "developmental", "biology", "toxicity", "model", "organisms", "...	2019	Prolonged mosquitocidal activity of Siparuna guianensis essential oil encapsulated in chitosan nanoparticles
Deficiency of autophagy protein beclin 1 is implicated in tumorigenesis and neurodegenerative diseases , but the molecular mechanism remains elusive . Previous studies showed that Beclin 1 coordinates the assembly of multiple VPS34 complexes whose distinct phosphatidylinositol 3-kinase III ( PI3K-III ) lipid kinase act...	Beclin 1 was not only the first-described mammalian autophagy protein , but is one of the most widely-characterized players in autophagy regulation . It is implicated in multiple human disease conditions . As a core component of the essential lipid kinase complex ( PI3K-III ) , beclin 1 has largely been characterized t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "cell", "biology", "biology", "and", "life", "sciences", "neuroscience", "molecular", "biology" ]	2014	Beclin 1 Is Required for Neuron Viability and Regulates Endosome Pathways via the UVRAG-VPS34 Complex
Dysfunction of CFTR in cystic fibrosis ( CF ) airway epithelium perturbs the normal regulation of ion transport , leading to a reduced volume of airway surface liquid ( ASL ) , mucus dehydration , decreased mucus transport , and mucus plugging of the airways . CFTR is normally expressed in ciliated epithelial cells of ...	The ciliated epithelium that lines the conducting airways of the lung normally functions to transport hydrated mucus secretions out of the airways to maintain respiratory sterility . Cystic fibrosis ( CF ) lung disease results from reduced airway surface hydration leading to decreased mucus clearance that precipitates ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "physiology/respiratory", "physiology", "genetics", "and", "genomics/gene", "therapy", "microbiology/applied", "microbiology", "respiratory", "medicine/respiratory", "pediatrics", "cell", "biology/gene", "expression" ]	2009	CFTR Delivery to 25% of Surface Epithelial Cells Restores Normal Rates of Mucus Transport to Human Cystic Fibrosis Airway Epithelium
In both vertebrates and invertebrates , photoreceptors’ output is regulated by feedback signals from interneurons that contribute to several important visual functions . Although synaptic feedback regulation of photoreceptors is known to occur in Drosophila , many questions about the underlying molecular mechanisms and...	Feedback regulation is a common feature of neural circuits during the process of acquiring information . Therefore , it is important to understand how this phenomenon occurs . Using the primary visual system of the fruit fly Drosophila melanogaster as a model , we systematically investigated the molecular mechanisms an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ih Channels Control Feedback Regulation from Amacrine Cells to Photoreceptors
Bacterial chromosomes are organised as two replichores of opposite polarity that coincide with the replication arms from the ori to the ter region . Here , we investigated the effects of asymmetry in replichore organisation in Escherichia coli . We show that large chromosome inversions from the terminal junction of the...	In most bacteria , chromosomes consist of a single replication unit . Replication initiates at a single ori and terminates in the diametrically opposite zone , ter , defining two replication arms . These are also called replichores to account for base composition and sequence motif polarity biases from ori to ter . Thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "genetics", "and", "genomics", "microbiology" ]	2008	Asymmetry of Chromosome Replichores Renders the DNA Translocase Activity of FtsK Essential for Cell Division and Cell Shape Maintenance in Escherichia coli
Coordinated intra- and inter-organ growth during animal development is essential to ensure a correctly proportioned individual . The Drosophila wing has been a valuable model system to reveal the existence of a stress response mechanism involved in the coordination of growth between adjacent cell populations and to ide...	The coordination of growth between the parts of a given developing organ is an absolute requirement for the generation of functionally integrated structures during animal development . Although this question has fascinated biologists for centuries , the molecular mechanisms responsible have remained elusive to date . I...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "medicine", "and", "health", "sciences", "redox", "signaling", "cell", "processes", "animals", "animal", "models", "c-jun", "n-terminal", "kinase", "signaling", "cascade", "developmental", "biology", "drosophila", "melanogaster", "model...	2019	Eiger/TNFα-mediated Dilp8 and ROS production coordinate intra-organ growth in Drosophila
Gene fusions created by somatic genomic rearrangements are known to play an important role in the onset and development of some cancers , such as lymphomas and sarcomas . RNA-Seq ( whole transcriptome shotgun sequencing ) is proving to be a useful tool for the discovery of novel gene fusions in cancer transcriptomes . ...	Genome rearrangements and associated gene fusions are known to be important oncogenic events in some cancers . We have developed a novel computational method called deFuse for detecting gene fusions in RNA-Seq data and have applied it to the discovery of novel gene fusions in sarcoma and ovarian tumors . We assessed th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "oncology/genitourinary", "cancers", "computer", "science/applications", "oncology/sarcomas", "computational", "biology/genomics" ]	2011	deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
Gammaherpesvirus ( GHV ) pathogenesis is a complex process that involves productive viral replication , dissemination to tissues that harbor lifelong latent infection , and reactivation from latency back into a productive replication cycle . Traditional loss-of-function mutagenesis approaches in mice using murine gamma...	Gammaherpesviruses ( GHVs ) , including the human pathogens Epstein-Barr virus and Kaposi sarcoma-associated herpesvirus , establish lifelong infections that can lead to cancer . Defining the functions of viral gene products in acute replication and chronic infection is important for understanding how these viruses cau...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "microbiology", "viral", "genome", "mammalian", "genomics", "molecular", "biology", "techniques", "microbial", "genetics", "microbial", "genomic...	2018	Conditional mutagenesis in vivo reveals cell type- and infection stage-specific requirements for LANA in chronic MHV68 infection
In response to stress and injury a coordinated activation of conserved signalling modules , such as JNK and JAK/STAT , is critical to trigger regenerative tissue restoration . While these pathways rebuild homeostasis and promote faithful organ recovery , it is intriguing that they also become activated in various tumou...	Signalling pathways modulate cellular responses in developmental and regenerative processes but can also be misused by cancer cells to promote tissue invasion and growth . How signalling outputs are integrated to direct a variety of responses ranging from organ repair to tumour onset remains elusive . Loss of the epige...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "nuclear", "staining", "cloning", "notch", "signaling", "oncology", "c-jun", "n-terminal", "kinase", "signaling", "cascade", "developmental", "signaling", "molecular", "biology", "techniques", "eyes", "research", "and", "analysis...	2018	Signalling crosstalk during early tumorigenesis in the absence of Polycomb silencing
Epidemics of respiratory syncytial virus ( RSV ) are known to occur in wintertime in temperate countries including the United States , but there is a limited understanding of the importance of climatic drivers in determining the seasonality of RSV . In the United States , RSV activity is highly spatially structured , w...	Respiratory syncytial virus ( RSV ) causes annual outbreaks of respiratory disease every winter in temperate climates , which can be severe particularly among infants . In the United States , RSV activity begins each autumn in Florida and appears to spread from the southeast to the northwest . Using data on hospitaliza...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "plant", "science", "medicine", "and", "health", "sciences", "disease", "ecology", "population", "modeling", "infectious", "disease", "epidemiology", "epidemiology", "plant", "pathology", "biology", "a...	2015	Environmental Drivers of the Spatiotemporal Dynamics of Respiratory Syncytial Virus in the United States
Retroviral vectors are widely used in gene therapy to introduce therapeutic genes into patients' cells , since , once delivered to the nucleus , the genes of interest are stably inserted ( integrated ) into the target cell genome . There is now compelling evidence that integration of retroviral vectors follows non-rand...	Understanding how retroviral vectors ( such as Moloney Leukemia Virus–based vectors ) integrate in the human genome became a major safety issue in the field of gene therapy , since a concrete risk of developing tumors associated with the integration process was assessed in the clinical setting . Moloney Leukemia Virus–...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "therapy", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics" ]	2008	Retroviral Integration Process in the Human Genome: Is It Really Non-Random? A New Statistical Approach
The expression of specific transcription factors determines the differentiated features of postmitotic neurons . However , the mechanism by which specific molecules determine neuronal cell fate and the extent to which the functions of transcription factors are conserved in evolution are not fully understood . In C . el...	The correct generation and maintenance of the nervous system is critical for the animal’s life . Dysregulation of these processes leads to multiple neurodevelopmental disorders . It has been a daunting challenge not only to identify the developmental mechanisms that determine neuronal cell fate , but also to understand...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Evolutionarily Conserved LIM Homeodomain Protein LIM-4/LHX6 Specifies the Terminal Identity of a Cholinergic and Peptidergic C. elegans Sensory/Inter/Motor Neuron-Type
Genome-scale metabolic modeling has become widespread for analyzing microbial metabolism . Extending this established paradigm to more complex microbial communities is emerging as a promising way to unravel the interactions and biochemical repertoire of these omnipresent systems . While several modeling techniques have...	The microbes residing in the human gut , collectively known as the gut microbiota , have an intimate and complicated relationship with human health . In this study , we aim to enhance the understanding of the relationship between the gut microbiota composition , the metabolite production , the diet , and the metabolic ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "gut", "bacteria", "microbiome", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "clostridium", "pathogens", "microbiology", "diet", "carbohydrates", "organic", "compounds", "nutrition", "metabolites", "enter...	2017	SteadyCom: Predicting microbial abundances while ensuring community stability
The Notch signaling pathway is thought to regulate multiple stages of inner ear development . Mutations in the Notch signaling pathway cause disruptions in the number and arrangement of hair cells and supporting cells in sensory regions of the ear . In this study we identify an insertional mutation in the mouse Sfswap ...	The organ of Corti is a sensory structure in the cochlea that mediates our sense of hearing . It consists of one row of inner hair cells and three rows of outer hair cells , together with an array of neighboring supporting cells . The precise arrangement of these different cell types is regulated very tightly by a numb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "auditory", "system", "developmental", "biology", "growth", "control", "cell", "fate", "determination", "organism", "development", "organogenesis", "sensory", "systems", "biology", "morphogenesis", "neuroscience", "pattern", "formation", "cell", "differentiation" ]	2014	The Candidate Splicing Factor Sfswap Regulates Growth and Patterning of Inner Ear Sensory Organs
Neurons collect their inputs from other neurons by sending out arborized dendritic structures . However , the relationship between the shape of dendrites and the precise organization of synaptic inputs in the neural tissue remains unclear . Inputs could be distributed in tight clusters , entirely randomly or else in a ...	Dendritic tree structures of nerve cells are built to optimally collect inputs from other cells in the circuit . By looking at how regularly the branch and termination points of dendrites are distributed , we find characteristic differences between cell types that correlate little with other traditional branching stati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "dendritic", "structure", "nervous", "system", "statistics", "electrophysiology", "neuroscience", "mathematics", "ganglion", "cells", "brain", "mapping", "neuronal", "dendrites", "research", "and", "analysis", "methods", "statistic...	2018	A regularity index for dendrites - local statistics of a neuron's input space
Leptospirosis is a global zoonosis affecting millions of people annually . Transcriptional changes in response to temperature were previously investigated using microarrays to identify genes potentially expressed upon host entry . Past studies found that various leptospiral outer membrane proteins are differentially ex...	Leptospirosis , caused by Leptospira spp . , is a disease of worldwide significance affecting millions of people annually . Bacteria of this species are spread by various carrier animals , including rodents and domestic livestock , which shed the leptospires via their urine into the environment . Humans become infected...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "microbiology/medical", "microbiology" ]	2009	Comparative Transcriptional and Translational Analysis of Leptospiral Outer Membrane Protein Expression in Response to Temperature
Predicting the timing of upcoming events enables efficient resource allocation and action preparation . Rhythmic streams , such as music , speech , and biological motion , constitute a pervasive source for temporal predictions . Widely accepted entrainment theories postulate that rhythm-based predictions are mediated b...	Making predictions is a major adaptive brain function . Predicting the timing of upcoming events enables the brain to prepare for them . However , it is unclear how this is achieved . It is believed that in rhythmic environmental context , such as in music and speech , temporal predictions are achieved by synchronizing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "acoustics", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "scalp", "signal", "processing", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "neuroscience", "signal", "filtering", "autocorrelation", "analysis", "of", ...	2017	Neural mechanisms of rhythm-based temporal prediction: Delta phase-locking reflects temporal predictability but not rhythmic entrainment
Arthropod-borne viruses are important emerging pathogens world-wide . Viruses transmitted by mosquitoes , such as dengue , yellow fever , and Japanese encephalitis viruses , infect hundreds of millions of people and animals each year . Global surveillance of these viruses in mosquito vectors using molecular based assay...	Approximately half of the world's population is at risk of viral , mosquito-borne illness such as dengue , yellow fever , Japanese encephalitis , Rift Valley fever , and chikungunya . In the past , these viruses have been regarded as pathogens of the tropics; however , they are emerging as global causes of illness . Ve...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "disease", "epidemiology", "microbiology", "rift", "valley", "fever", "emerging", "infectious", "diseases", "neglected", "tropical", "diseases", "infectious", "disease", "control", "veterinary", "science", "oropouche", "fever", "japanese", "encep...	2013	Multi-Gene Detection and Identification of Mosquito-Borne RNA Viruses Using an Oligonucleotide Microarray
Many viruses depend on host microtubule motors to reach their destined intracellular location . Viral particles of neurotropic alphaherpesviruses such as herpes simplex virus 1 ( HSV1 ) show bidirectional transport towards the cell center as well as the periphery , indicating that they utilize microtubule motors of opp...	Many viruses , particularly neurotropic alphaherpesviruses such as herpes simplex virus ( HSV ) , require an intact microtubule network for efficient replication and pathogenesis . In living cells , host and viral cargo show rapid reversals in transport direction , suggesting that they can recruit motors of opposing di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "virology/virion", "structure,", "assembly,", "and", "egress", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/macromolecular...	2010	Plus- and Minus-End Directed Microtubule Motors Bind Simultaneously to Herpes Simplex Virus Capsids Using Different Inner Tegument Structures
Plague ( Yersinia pestis ) and zoonotic cutaneous leishmaniasis ( Leishmania major ) are two rodent-associated diseases which are vectored by fleas and phlebotomine sand flies , respectively . In Central Asia , the great gerbil ( Rhombomys opimus ) serves as the primary reservoir for both diseases in most natural foci ...	Plague and cutaneous leishmaniasis are two diseases transmissible to humans vectored by fleas and sand flies , respectively . Although the diseases are vectored by two different insect types , the primary reservoir host for both diseases in desert foci in Central Asia is the great gerbil . Therefore , a promising strat...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "plagues", "body", "fluids", "vertebrates", "sand", "flies", "animals", "mammals", "diptera", "bacterial", "diseases", "fleas", "infectious", "disease", "control", "insect", "vectors", "infectious", "diseases", ...	2018	Field evaluation of a 0.005% fipronil bait, orally administered to Rhombomys opimus, for control of fleas (Siphonaptera: Pulicidae) and phlebotomine sand flies (Diptera: Psychodidae) in the Central Asian Republic of Kazakhstan
Alu elements make up the largest family of human mobile elements , numbering 1 . 1 million copies and comprising 11% of the human genome . As a consequence of evolution and genetic drift , Alu elements of various sequence divergence exist throughout the human genome . Alu/Alu recombination has been shown to cause appro...	DNA double-strand breaks ( DSBs ) are a highly mutagenic form of DNA damage that can be repaired through one of several pathways with varied degrees of sequence preservation . Faithful repair of DSBs often occurs through gene conversion in which a sister chromatid is used as a repair template . Unfaithful repair of DSB...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Contribution of Alu Elements to Mutagenic DNA Double-Strand Break Repair
Regulation of capsid disassembly is crucial for efficient HIV-1 cDNA synthesis after entry , yet host factors involved in this process remain largely unknown . Here , we employ genetic screening of human T-cells to identify maternal embryonic leucine zipper kinase ( MELK ) as a host factor required for optimal uncoatin...	Phosphorylation of the HIV-1 capsid has long been known to regulate viral uncoating and cDNA synthesis processes , but the cellular kinases responsible for this have remained unidentified . Here , we report that a host cell kinase MELK dictates optimal capsid disassembly through phosphorylation of Ser-149 in the multim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "viral", "structure", "retroviruses", "viruses", "immunodeficiency", "viru...	2017	Phosphorylation of the HIV-1 capsid by MELK triggers uncoating to promote viral cDNA synthesis
Proper determination of cell fates depends on epigenetic information that is used to preserve memory of decisions made earlier in development . Post-translational modification of histone residues is thought to be a central means by which epigenetic information is propagated . In particular , modifications of histone H3...	During development , naïve precursor cells acquire distinct identities through differential regulation of gene expression . The process of cell fate specification is progressive and depends on memory of prior developmental decisions . Maintaining cell identities over time is not dependent on changes in genome sequence ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "chemical", "compounds", "dna-binding", "proteins", "organic", "compounds", "animals", "alleles", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "basic", "amino", "acids", "amino", "acids", ...	2019	Lysine 27 of replication-independent histone H3.3 is required for Polycomb target gene silencing but not for gene activation
The origin , range , and structure of prions causing the most common human prion disease , sporadic Creutzfeldt-Jakob disease ( sCJD ) , are largely unknown . To investigate the molecular mechanism responsible for the broad phenotypic variability of sCJD , we analyzed the conformational characteristics of protease-sens...	Sporadic Creutzfeldt-Jakob disease ( sCJD ) is the most common human prion disease worldwide . This neurodegenerative disease , which is transmissible and invariably fatal , is characterized by the accumulation of an abnormally folded isoform ( PrPSc ) of a host-encoded protein ( PrPC ) , predominantly in the brain . M...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "chemistry", "biology" ]	2011	Protease-Sensitive Conformers in Broad Spectrum of Distinct PrPSc Structures in Sporadic Creutzfeldt-Jakob Disease Are Indicator of Progression Rate
Membrane fusion is critical to biological processes such as viral infection , endocrine hormone secretion , and neurotransmission , yet the precise mechanistic details of the fusion process remain unknown . Current experimental and computational model systems approximate the complex physiological membrane environment f...	Membrane fusion is the transport process used for neurotransmitter release , insulin secretion , and infection by enveloped viruses . The precise mechanism of fusion is not yet understood , nor is the means by which membrane properties such as composition and curvature affect the fusion process . Here , we use molecula...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics", "in", "vitro", "computational", "biology" ]	2007	Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
Normative models of human cognition often appeal to Bayesian filtering , which provides optimal online estimates of unknown or hidden states of the world , based on previous observations . However , in many cases it is necessary to optimise beliefs about sequences of states rather than just the current state . Importan...	When studying human cognition , it is often assumed that agents form and update beliefs only about the current state of the world , an approach known as Bayesian filtering . However , in many situations there are advantages to making inferences about the most likely sequence of states that have occurred , which involve...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "elderly", "decision", "making", "nervous", "system", "prefrontal", "cortex", "brain", "social", "sciences", "neuroscience", "magnetic", "resonance", "imaging", "age", "groups", "brain", "morphometry", ...	2017	Sequential inference as a mode of cognition and its correlates in fronto-parietal and hippocampal brain regions
Neisseria gonorrhoeae deploys a novel immune evasion strategy wherein the lacto-N-neotetraose ( LNnT ) structure of lipooligosaccharide ( LOS ) is capped by the bacterial sialyltransferase , using host cytidine-5’-monophosphate ( CMP ) -activated forms of the nine-carbon nonulosonate ( NulO ) sugar N-acetyl-neuraminic ...	Neisseria gonorrhoeae , the causative agent of the sexually transmitted infection gonorrhea , has developed widespread resistance to almost every conventional antibiotic currently in clinical use . Novel therapeutics are urgently needed against this pathogen . Gonococci have the capacity to scavenge CMP-N-acetyl-neuram...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Utilizing CMP-Sialic Acid Analogs to Unravel Neisseria gonorrhoeae Lipooligosaccharide-Mediated Complement Resistance and Design Novel Therapeutics
In the post-genomic era , Genome-scale metabolic networks ( GEMs ) have emerged as invaluable tools to understand metabolic capabilities of organisms . Different parts of these metabolic networks are defined as subsystems/pathways , which are sets of functional roles to implement a specific biological process or struct...	Stoichiometric models have been used in the area of metabolic engineering and systems biology for many decades . The early examples of these models include simplified ad hoc built metabolic pathways , and biomass compositions . The development of genome scale models ( GEMs ) brought a standard to metabolic network mode...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "metabolic", "networks", "enzymology", "fungi", "model", "organisms", "metabolites", "network", "analysis", "experimental", "organism", "systems", "enzyme", "metabolism", "enzyme", "chemistry", "saccharomyces", "research", "and", "analysis", "meth...	2017	lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites
Despite intense interest and considerable effort via high-throughput screening , there are few examples of small molecules that directly inhibit protein-protein interactions . This suggests that many protein interaction surfaces may not be intrinsically “druggable” by small molecules , and elevates in importance the fe...	Identifying small-molecule inhibitors of protein interactions has traditionally presented a challenge for modern screening methods , despite interest stemming from the fact that such interactions comprise the underlying mechanisms for cell proliferation , differentiation , and survival . This suggests that many protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicinal", "chemistry", "biophysic", "al", "simulations", "chemical", "biology", "protein", "structure", "chemistry", "biology", "computational", "biology", "macromolecular", "structure", "analysis" ]	2013	Druggable Protein Interaction Sites Are More Predisposed to Surface Pocket Formation than the Rest of the Protein Surface
Behavior is used to assess memory and cognitive deficits in animals like Fmr1-null mice that model Fragile X Syndrome , but behavior is a proxy for unknown neural events that define cognitive variables like recollection . We identified an electrophysiological signature of recollection in mouse dorsal Cornu Ammonis 1 ( ...	Behavior is often used as proxy to study memory and cognitive deficits in animals like Fmr1-KO mice that model Fragile X Syndrome , the most prevalent single-gene cause of intellectual disability and autism . However , it is unclear what neural events define cognitive variables like recollection of memory and cognitive...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cognitive", "neurology", "medicine", "and", "health", "sciences", "brain", "vertebrates", "mice", "neuroscience", "animals", "mammals", "learning", "and", "memory", "animal", "models", "cognitive", "neuroscience", "model", "organisms", "animal", "behavior", "ganglion",...	2018	Control of recollection by slow gamma dominating mid-frequency gamma in hippocampus CA1
Population genetic theory predicts discordance in the true phylogeny of different genomic regions when studying recently diverged species . Despite this expectation , genome-wide discordance in young species groups has rarely been statistically quantified . The house mouse subspecies group provides a model system for e...	The phylogenetic history of individual genes can differ strongly from the species history if taxa are recently derived , making inferences of a species history from only a handful of genes especially difficult in these cases . Genome-scale data sets now allow phylogenetic histories to be reconstructed from a large numb...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "evolutionary", "biology/genomics", "evolutionary", "biology/bioinformatics", "evolutionary", "biology", "genetics", "and", "genomics/population", "genetics" ]	2009	Fine-Scale Phylogenetic Discordance across the House Mouse Genome
The experimental evolution of laboratory populations of microbes provides an opportunity to observe the evolutionary dynamics of adaptation in real time . Until very recently , however , such studies have been limited by our inability to systematically find mutations in evolved organisms . We overcome this limitation b...	Adaptive evolution is a central biological process that underlies diverse phenomena from the acquisition of antibiotic resistance by microbes to the evolution of niche specialization . Two unresolved questions regarding adaptive evolution are what types of genomic variation are associated with adaptation and how repeat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "expression", "microbiology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/g...	2008	The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast
Fundamental to biological decision-making is the ability to generate bimodal expression patterns where 2 alternate expression states simultaneously exist . Here , we use a combination of single-cell analysis and mathematical modeling to examine the sources of bimodality in the transcriptional program controlling HIV’s ...	A central and recurring feature of cell-fate regulating circuits is their ability to generate bimodal expression—2 alternate expression states that exist simultaneously—with each state corresponding to a different cell fate . To understand the mechanisms enabling bimodality in a natural decision-making circuit , we exa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "signal", "processing", "immunology", "microbi...	2017	Nonlatching positive feedback enables robust bimodality by decoupling expression noise from the mean
CD4+CD25+Foxp3+ regulatory T cells ( Tregs ) regulate disease-associated immunity and excessive inflammatory responses , and numbers of CD4+CD25+Foxp3+ Tregs are increased during malaria infection . The mechanisms governing their generation , however , remain to be elucidated . In this study we investigated the role of...	Infection with the malaria parasite Plasmodium falciparum affects 300–600 million people each year . Regulatory T cells ( Tregs ) expressing the transcription factor Foxp3 , which drives genes involved in immunosuppression , are specialized immune cells that can inhibit both protective and harmful inflammatory response...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/immunomodulation", "infectious", "diseases/protozoal", "infections" ]	2009	Plasmodium falciparum–Mediated Induction of Human CD25hiFoxp3hi CD4 T Cells Is Independent of Direct TCR Stimulation and Requires IL-2, IL-10 and TGFβ
Different pediatric physiologically-based pharmacokinetic ( PBPK ) models have been described incorporating developmental changes that influence plasma drug concentrations . Drug disposition into cerebrospinal fluid ( CSF ) is also subject to age-related variation and can be further influenced by brain diseases affecti...	Developmental processes in children affect pharmacokinetics and should ideally be taken into account when establishing drug dosing regimens . One way to incorporate developmental differences is by making use of physiologically-based pharmacokinetic ( PBPK ) models in which kinetic equations are used to describe drug di...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "inflammatory", "diseases", "medicine", "and", "health", "sciences", "body", "fluids", "nervous", "system", "blood-brain", "barrier", "permeability", "pediatrics", "physiological", "parameters", "materials", "science", "cardiovascular", "analysis", "bioassays", "and", "ph...	2019	Development of a physiologically-based pharmacokinetic pediatric brain model for prediction of cerebrospinal fluid drug concentrations and the influence of meningitis
Dengue and chikungunya are viral diseases transmitted to humans by infected Aedes spp . mosquitoes . With an estimated 390 million infected people per year dengue virus ( DENV ) currently causes the most prevalent arboviral disease . During the last decade chikungunya virus ( CHIKV ) has caused large outbreaks and has ...	Dengue virus ( DENV ) currently causes the most important arthropod-borne viral disease in humans . Chikungunya virus ( CHIKV ) re-emerged explosively in 2005–2006 afflicting millions of people in the Indian Ocean area and ever since continues its spread . The increasing co-circulation of these mosquito-borne viruses a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "dengue", "virus", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "immunology", "tropical", "diseases", "mi...	2017	Suppression of chikungunya virus replication and differential innate responses of human peripheral blood mononuclear cells during co-infection with dengue virus
Many studies have proved that oncogenic viruses develop redundant mechanisms to alter the functions of the tumor suppressor p53 . Here we show that Epstein-Barr virus ( EBV ) , via the oncoprotein LMP-1 , induces the expression of ΔNp73α , a strong antagonist of p53 . This phenomenon is mediated by the LMP-1 dependent ...	Approximately 20% of worldwide human cancers have been associated with viral infections . Many oncogenic viruses exert their transforming properties by inactivating the products of tumour suppressor genes . One of the best characterized events induced by ongocenic viruses is the inactivation of the transcriptional fact...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	Epstein - Barr Virus Transforming Protein LMP-1 Alters B Cells Gene Expression by Promoting Accumulation of the Oncoprotein ΔNp73α
Cytoplasmic incompatibility ( CI ) induced by the endosymbiont Wolbachia pipientis causes complex patterns of crossing sterility between populations of the Culex pipiens group of mosquitoes . The molecular basis of the phenotype is yet to be defined . In order to investigate what host changes may underlie CI at the mol...	Wolbachia are maternally inherited bacteria that manipulate invertebrate reproduction . Cytoplasmic incompatibility is embryo death that occurs when males carrying Wolbachia mate with females that do not , or that carry a different Wolbachia variant; its mechanism is poorly understood . In Culex mosquitoes , in the pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Transcriptional Regulation of Culex pipiens Mosquitoes by Wolbachia Influences Cytoplasmic Incompatibility
Although the metabolic networks of the three domains of life consist of different constituents and metabolic pathways , they exhibit the same scale-free organization . This phenomenon has been hypothetically explained by preferential attachment principle that the new-recruited metabolites attach preferentially to those...	The metabolic networks of the three domains of life exhibit the same scale-free organization , which has been hypothetically explained in terms of preferential attachment principle . Here we reveal that the scale-free organization of metabolic networks may have a chemical basis . Through a chemoinformatic analysis on m...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computer", "science", "chemistry", "biology" ]	2011	Chemical Basis of Metabolic Network Organization
Adipose tissue lipolysis occurs during the development of heart failure as a consequence of chronic adrenergic stimulation . However , the impact of enhanced adipose triacylglycerol hydrolysis mediated by adipose triglyceride lipase ( ATGL ) on cardiac function is unclear . To investigate the role of adipose tissue lip...	Chronic heart failure ( CHF ) is still one of the leading causes of morbidity and mortality worldwide , and new therapeutic approaches are required . Here we show that perturbation of adipose tissue lipolysis by tissue-specific deletion of the lypolytic enzyme ATGL ( adipose trigylceride lipase ) protects against heart...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "lipolysis", "cell", "death", "medicine", "and", "health", "sciences", "body", "fluids", "cardiovascular", "anatomy", "cell", "processes", "lipid", "analysis", "cardiology", "lipids", "biological", "tissue", "chemistry", "heart", "failure", "molecular", "biology", "bl...	2018	Adipose tissue ATGL modifies the cardiac lipidome in pressure-overload-induced left ventricular failure
The properties of disordered proteins are thought to depend on intrinsic conformational propensities for polyproline II ( PPII ) structure . While intrinsic PPII propensities have been measured for the common biological amino acids in short peptides , the ability of these experimentally determined propensities to quant...	Molecular models of disordered protein structures are needed to elucidate the functional mechanisms of intrinsically disordered proteins , a class of proteins implicated in many disease pathologies and human health issues . Several studies have measured intrinsic conformational propensities for polyproline II helix , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Hydrodynamic Radii of Intrinsically Disordered Proteins Determined from Experimental Polyproline II Propensities
The World Health Organization has recommended three rounds of mass drug administration ( MDA ) with antibiotics in districts where the prevalence of follicular trachoma ( TF ) is ≥10% in children aged 1–9 years , with treatment coverage of at least 80% . For districts at 5–10% TF prevalence it was recommended that TF b...	Trachoma , which results from infection with a bacterium Chlamydia trachomatis ( Ct ) , is a leading cause of preventable blindness in the world . One of the currently used control methods is mass drug administration ( MDA ) with azithromycin , which is initiated according to rates of follicular trachoma ( TF ) in chil...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "eye", "infections", "medicine", "bacterial", "diseases", "infectious", "diseases", "disease", "ecology", "clinical", "research", "design", "global", "health", "clinical", "trials", "ophthalmology", "neglected", "tropical", "diseases", "infectious", "disease", "control", ...	2013	Mass Treatment with Azithromycin for Trachoma: When Is One Round Enough? Results from the PRET Trial in The Gambia
Females of all blood-feeding arthropod vectors must find and feed on a host in order to produce offspring . For tsetse—vectors of the trypanosomes that cause human and animal African trypanosomiasis—the problem is more extreme , since both sexes feed solely on blood . Host location is thus essential both for survival a...	Tsetse flies are the vectors of human and animal African trypanosomiasis . The flies rely solely on vertebrate blood for food and water and changes in vertebrate host density may therefore influence tsetse survival . We develop models including starvation-dependent mortality to explain changes in numbers of the savanna...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "demography", "population", "dynamics", "geographical", "locations", "animals", "glossina", "developmental", "biology", "mathematics", "pupae", "tsetse", "fly", "population", "biology", "insect", ...	2017	Host-seeking efficiency can explain population dynamics of the tsetse fly Glossina morsitans morsitans in response to host density decline
Zoonoses , diseases affecting both humans and animals , can exert tremendous pressures on human and veterinary health systems , particularly in resource limited countries . Anthrax is one such zoonosis of concern and is a disease requiring greater public health attention in Nigeria . Here we describe the genetic divers...	Anthrax , caused by the soil-borne bacterium Bacillus anthracis , is a disease with important public health and national security implications globally . Understanding the global genetic diversity of the pathogen is important for epidemiological and forensic investigations of anthrax events . Toward this , we describe ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Bacillus anthracis Diversity and Geographic Potential across Nigeria, Cameroon and Chad: Further Support of a Novel West African Lineage
A genome-wide association study was performed to identify genetic factors involved in susceptibility to psoriasis ( PS ) and psoriatic arthritis ( PSA ) , inflammatory diseases of the skin and joints in humans . 223 PS cases ( including 91 with PSA ) were genotyped with 311 , 398 single nucleotide polymorphisms ( SNPs ...	Psoriasis ( PS ) and psoriatic arthritis ( PSA ) are common inflammatory diseases of humans affecting the skin and joints . Approximately 2% of Europeans are affected with PS , and ∼10–30% of patients develop PSA . Genetic variation in the MHC ( multiple histocompatibility locus antigen cluster ) increases risk of deve...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/functional", "genomics", "dermatology/psoriasis", "and", "other", "inflammatory", "diseases", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomic...	2008	A Genome-Wide Association Study of Psoriasis and Psoriatic Arthritis Identifies New Disease Loci
Analysis of the spatial sub-cellular distribution of proteins is of vital importance to fully understand context specific protein function . Some proteins can be found with a single location within a cell , but up to half of proteins may reside in multiple locations , can dynamically re-localise , or reside within an u...	Sub-cellular localisation of proteins provides insights into sub-cellular biological processes . For a protein to carry out its intended function it must be localised to the correct sub-cellular environment , whether that be organelles , vesicles or any sub-cellular niche . Correct sub-cellular localisation ensures the...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "ellipses", "geometry", "membrane", "proteins", "probability", "distribution", "mathematics", "stem", "cells", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "cell", "potency", "animal", "cells", "embryonic", "stem", "cells", ...	2018	A Bayesian mixture modelling approach for spatial proteomics
Aging is characterized by degeneration of unique tissues . However , dissecting the interconnectedness of tissue aging remains a challenge . Here , we employ a muscle-specific DNA damage model in Drosophila to reveal secreted factors that influence systemic aging in distal tissues . Utilizing this model , we uncovered ...	Aging in multicellular organisms is characterized by a progressive decline in the proper function of organs . This deterioration of organ function is a risk factor for many diseases . However , it is unlikely that organs age in isolation , as damage in one organ can presumably impact aging of other organs through eithe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "rna", "interference", "immune", "physiology", "cytokines", "cell", "processes", "immunology", "animals", "animal", "models", "dna", "damage", "physiological", "pr...	2018	A virus-acquired host cytokine controls systemic aging by antagonizing apoptosis
We report on 4 patients ( 1 immunocompetent , 3 immunosuppressed ) in whom visceral leishmaniasis had become unresponsive to ( or had relapsed after ) treatment with appropriate doses of liposomal amphotericin B . Under close follow-up , full courses of pentavalent antimony were administered without life-threatening ad...	Visceral leishmaniasis causes fever , enlargement of internal organs like the liver and the spleen , and leads to death if no treatment is given . It is caused by a microbe called Leishmania and affects children and adults in warm and temperate regions of the world . Antimony in different forms has been used to treat V...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Discussion" ]	[]	2016	Antimony to Cure Visceral Leishmaniasis Unresponsive to Liposomal Amphotericin B
Lassa virus ( LASV ) is endemic in several West African countries and is the etiological agent of Lassa fever . Despite the high annual incidence and significant morbidity and mortality rates , currently there are no approved vaccines to prevent infection or disease in humans . Genetically , LASV demonstrates a high de...	Lassa fever ( LF ) is an acute viral infection which is often associated with hemorrhagic manifestations and multi-organ failure in humans . The etiological agent responsible for LF is Lassa virus ( LASV ) , a rodent-borne Arenavirus which is endemic in several West African countries . Up to 500 , 000 cases of LF are d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Recombinant Vesicular Stomatitis Virus-Based Lassa Fever Vaccine Protects Guinea Pigs and Macaques against Challenge with Geographically and Genetically Distinct Lassa Viruses
Prions are unusual protein assemblies that propagate their conformationally-encoded information in absence of nucleic acids . The first prion identified , the scrapie isoform ( PrPSc ) of the cellular prion protein ( PrPC ) , caused epidemic and epizootic episodes [1] . Most aggregates of other misfolding-prone protein...	Prions are unusual infectious pathogens that do not contain any nucleic acid . They consist of assemblies of misfolded proteins . The scrapie isoform of the mammalian prion protein , PrPSc , is the most notorious prion , and is responsible for deadly neurodegenerative diseases affecting humans , like Creutzfeldt-Jakob ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "bonding", "animal", "diseases", "medicine", "and", "health", "sciences", "molecular", "dynamics", "monomers", "electron", "cryo-microscopy", "simulation", "and", "modeling", "animal", "prion", "diseases", "microscopy", "protein", "structure", "zoology", "hy...	2019	Full atomistic model of prion structure and conversion
A key question in mapping dynamics of protein-ligand interactions is to distinguish changes at binding sites from those associated with long range conformational changes upon binding at distal sites . This assumes a greater challenge when considering the interactions of low affinity ligands ( dissociation constants , K...	Ligand interactions with proteins result in broad changes that are propagated throughout the target proteins , across space and time . These changes can be broadly classified into: orthosteric effects at the ligand binding site and allosteric changes at distal sites . These allosteric changes are difficult to localize ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "allosteric", "regulation", "protein", "interactions", "chemical", "compounds", "crystal", "structure", "particle", "physics", "condensed", "matter", "physics", "enzymology", "deuterium", "amides", "organic", "compounds", "atoms", "crystallography", "composite", "particles"...	2016	Predicting Allosteric Effects from Orthosteric Binding in Hsp90-Ligand Interactions: Implications for Fragment-Based Drug Design
SKN-1 , the Caenorhabditis elegans Nrf1/2/3 ortholog , promotes both oxidative stress resistance and longevity . SKN-1 responds to oxidative stress by upregulating genes that detoxify and defend against free radicals and other reactive molecules , a SKN-1/Nrf function that is both well-known and conserved . Here we sho...	The mechanisms through which organisms defend against environmental stresses are critical during diverse disease processes and are likely to be important for longevity . The nematode C . elegans is advantageous for genetic analysis of how stress defenses function and contribute to survival . The evolutionarily conserve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "cell", "biology", "biology", "molecular", "cell", "biology" ]	2011	Specific SKN-1/Nrf Stress Responses to Perturbations in Translation Elongation and Proteasome Activity
Many eukaryotic genes play essential roles in multiple biological processes in several different tissues . Conditional mutants are needed to analyze genes with such pleiotropic functions . In vertebrates , conditional gene inactivation has only been feasible in the mouse , leaving other model systems to rely on surroga...	Some genes are expressed and function in a single tissue , and the effect of their loss on that tissue can be readily determined . Frequently , however , genes that are necessary for the development or maintenance of one tissue are also important for other tissues or cell types . Genes of the latter type are difficult ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fish", "vertebrates", "nucleotides", "animals", "alleles", "animal", "models", "organisms", "osteichthyes", "developmental", "biology", "model", "organisms", "experimental", "organism", "systems", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "em...	2018	Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish
There is growing evidence that CD8+ cytotoxic T lymphocyte ( CTL ) responses can contribute to long-term remission of many malignancies . The etiological agent of adult T-cell leukemia/lymphoma ( ATL ) , human T lymphotropic virus type-1 ( HTLV-1 ) , contains highly immunogenic CTL epitopes , but ATL patients typically...	Human T lymphotropic virus-1 infects T cells , causing them to multiply . In some people , cellular replication is unchecked , resulting in an aggressive blood cancer called adult T-cell leukemia/lymphoma . The virus proteins are efficiently recognised as ‘foreign’ by the immune system in most infected individuals . Pe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cloning", "retroviruses", "organisms", "viruses", "clinical", "medicine", "rna", ...	2016	T Cell Receptor Vβ Staining Identifies the Malignant Clone in Adult T cell Leukemia and Reveals Killing of Leukemia Cells by Autologous CD8+ T cells
Activation of cannabinoid CB1 receptors ( CB1R ) by delta9-tetrahydrocannabinol ( THC ) produces a variety of negative effects with major consequences in cannabis users that constitute important drawbacks for the use of cannabinoids as therapeutic agents . For this reason , there is a tremendous medical interest in har...	Delta-9-tetrahydrocannabinol ( THC ) , the main psychoactive compound of marijuana , induces numerous undesirable effects , including memory impairments , anxiety , and dependence . Conversely , THC also has potentially therapeutic effects , including analgesia , muscle relaxation , and neuroprotection . However , the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Cognitive Impairment Induced by Delta9-tetrahydrocannabinol Occurs through Heteromers between Cannabinoid CB1 and Serotonin 5-HT2A Receptors
Preterm birth ( PTB ) affects ~12% of pregnancies in the US . Despite its high mortality and morbidity , the molecular etiology underlying PTB has been unclear . Numerous studies have been devoted to identifying genetic factors in maternal and fetal genomes , but so far few genomic loci have been associated with PTB . ...	Preterm birth is a prevalent pregnancy condition and leads to substantial morbidity and mortality . Its genetic association has been well observed , but the underlying etiology remains unclear . Current research has been focused on identifying risk factors in maternal genomes . In this study , we tested an unexplored h...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "brain", "development", "children", "deletion", "mutation", "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "computational", "biology", "preterm", "birth", "age", "groups", "mutation", "developmental", "biology", "women'...	2017	Fetal de novo mutations and preterm birth
The survival characteristics of the mosquito Aedes aegypti affect transmission rates of dengue because transmission requires infected mosquitoes to survive long enough for the virus to infect the salivary glands . Mosquito survival is assumed to be high in tropical , dengue endemic , countries like Vietnam . However , ...	Prolonged survival of adult mosquitoes is critical to dengue transmission cycles , particularly because it takes time for the dengue viruses to infect the mosquito midgut , replicate and infect the salivary glands before transmission can occur . Reducing mosquito lifespan is one avenue to fight dengue , and may be achi...	[ "Abstract", "Introduction", "Methods", "and", "Materials", "Results", "Discussion" ]	[ "aging", "population", "metrics", "infectious", "disease", "epidemiology", "epidemiology", "population", "modeling", "gene", "expression", "death", "rate", "population", "biology", "biology", "population", "ecology", "molecular", "cell", "biology", "dna", "transcription" ...	2014	Adult Survivorship of the Dengue Mosquito Aedes aegypti Varies Seasonally in Central Vietnam
Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations . We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propag...	When organisms are exposed to different environments , the rates and types of mutations that spontaneously arise in each environment can vary due to differing mutagenic pressures imposed by each environment , and these can potentially influence the evolution of the organism . Little is known about the types of mutation...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "insertion", "mutation", "microbiology", "mutation", "substitution", "mutation", "genetic", "elements", "bacterial", "genetics", "dna", "microbial", "genetics", "microbial", "genomics", "bacterial", "genomics", "repeated", "sequences", "biochemistry", "nucle...	2017	Anaerobically Grown Escherichia coli Has an Enhanced Mutation Rate and Distinct Mutational Spectra
Patients with biallelic truncating mutations in PALB2 have a severe form of Fanconi anaemia ( FA-N ) , with a predisposition for developing embryonal-type tumours in infancy . Here we describe two unusual patients from a single family , carrying biallelic PALB2 mutations , one truncating , c . 1676_1677delAAinsG; ( p ....	PALB2 is a protein that creates a molecular bridge that promotes the recruitment of Homologous Recombination Repair ( HRR ) proteins BRCA1 , BRCA2 and Rad51 to sites of DNA damage . Cells with functional loss of PALB2 show a defect in HRR and are characterized by an increased number of spontaneous chromosome breaks and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "medicine", "and", "health", "sciences", "anemia", "fibroblasts", "dna", "damage", "mutation", "immunoprecipitation", "connective", "tissue", "cells", "dna", "research", "and", "analysis", "methods", "animal", "cells", "chromosome", "biology", ...	2016	A Hypomorphic PALB2 Allele Gives Rise to an Unusual Form of FA-N Associated with Lymphoid Tumour Development
Genome duplications are important evolutionary events that impact the rate and spectrum of beneficial mutations and thus the rate of adaptation . Laboratory evolution experiments initiated with haploid Saccharomyces cerevisiae cultures repeatedly experience whole-genome duplication ( WGD ) . We report recurrent genome ...	Whole genome duplications—the simultaneous doubling of each chromosome—can have a profound influence on evolution . Evidence of ancient whole genome duplications can be seen in most modern genomes . Experimental evolution , the long-term propagation of organisms under well-controlled laboratory conditions , yields valu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "genome", "evolution", "population", "genetics", "computational", "biology", "ploidy", "cloning", "mutation", "fungal", "evolution", "nonsense", "mutation", "molecular", "biology", "techniques", "population", "biology", "evolutionary", "adaptation", ...	2018	Adaptive genome duplication affects patterns of molecular evolution in Saccharomyces cerevisiae
Phenylketonuria ( PKU ) , one of the most common inherited diseases of amino acid metabolism , is caused by mutations in the phenylalanine hydroxylase ( PAH ) gene . Recently , PAH exon 11 was identified as a vulnerable exon due to a weak 3’ splice site , with different exonic mutations affecting exon 11 splicing throu...	Splicing defects constitute a major cause of human disease . Mutations affecting conserved splicing sequences at exon-intron junctions are easily recognized as possibly pathogenic , whereas variants in exonic or intronic regions are difficult to classify without functional evidence provided by transcript analysis or in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "rna", "extraction", "nucleotides", "mutation", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "extraction", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "genome", "complexity", "artificial", "gene...	2018	Intronic PAH gene mutations cause a splicing defect by a novel mechanism involving U1snRNP binding downstream of the 5’ splice site
Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks , although no single species has emerged as a preferred organism . Moreover , adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate speci...	Algae are a highly diverse group of organisms that have become the focus of renewed interest due to their potential for producing biofuel feedstocks , nutraceuticals , and biomaterials . Their high photosynthetic yields and ability to grow in areas unsuitable for agriculture provide a potential sustainable alternative ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "systems", "biology", "plant", "science", "model", "organisms", "plant", "biology", "biology", "genomics", "genetics", "and", "genomics" ]	2012	Genome, Functional Gene Annotation, and Nuclear Transformation of the Heterokont Oleaginous Alga Nannochloropsis oceanica CCMP1779
The cohesin complex topologically encircles chromosomes and mediates sister chromatid cohesion to ensure accurate chromosome segregation upon cell division . Cohesin also participates in DNA repair and gene transcription . The Nipped-B–Mau2 protein complex loads cohesin onto chromosomes and the Pds5—Wapl complex remove...	The cohesin protein complex has multiple functions in eukaryotic cells . It ensures that when a cell divides , the two daughter cells receive the correct number of chromosomes . It does this by holding together the sister chromatids that are formed when chromosomes are duplicated by DNA replication . Cohesin also helps...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "gene", "regulation", "cancer", "risk", "factors", "chromatids", "animals", "oncology", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "dna", "replication", "experi...	2018	Brca2, Pds5 and Wapl differentially control cohesin chromosome association and function
The mechanisms by which receptors guide intracellular virus transport are poorly characterized . The murine polyomavirus ( Py ) binds to the lipid receptor ganglioside GD1a and traffics to the endoplasmic reticulum ( ER ) where it enters the cytosol and then the nucleus to initiate infection . How Py reaches the ER is ...	To cause infection , viruses must reach appropriate compartments within the cell where they undergo a programmed series of conformational changes that enable the viral genome to be exposed and released . The mechanisms that target viruses to these compartments are often not clear . Here we study the infectious pathway ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/host", "invasion", "and", "cell", "entry" ]	2009	A Lipid Receptor Sorts Polyomavirus from the Endolysosome to the Endoplasmic Reticulum to Cause Infection
Bovine cysticercosis is a worldwide distributed zoonosis caused by the larval form of Taenia saginata present in bovine muscles . The diagnosis is based on the postmortem inspection at slaughterhouses and consists of the macroscopic visualization of lesions caused by cysticercosis in muscle sites . However , parasitize...	Taenia saginata cysticercosis occurs worldwide . The prevalence related is higher mainly in developing countries , causing damage to public health and economic losses . Through our study , a new antigen with high diagnostic potential was developed for use in laboratory serological tests , aiming at the detection of bov...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "molecular", "probe", "techniques", "tropical", "diseases", "immunoblotting", "parasitic", "diseases", "biochemical", "analysis", "enzyme", "assays", "veterinary", "diagnostics", "neglected", "tropica...	2018	Development of the multi-epitope chimeric antigen rqTSA-25 from Taenia saginata for serological diagnosis of bovine cysticercosis
The impact of intestinal helminth infection on the clinical presentation and immune response during active tuberculosis ( TB ) infection is not well characterized . Our aim was to investigate whether asymptomatic intestinal helminth infection alters the clinical signs and symptoms as well as the cell mediated immune re...	The effects of helminth infection on chronic infectious diseases such as tuberculosis ( TB ) merit further characterization . There is limited data regarding the impact of helminth co-infection on clinical and immunological outcomes of TB from clinical field studies in high endemic areas . We tried to address some of t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Asymptomatic Helminth Infection in Active Tuberculosis Is Associated with Increased Regulatory and Th-2 Responses and a Lower Sputum Smear Positivity
Optimal sensory decision-making requires the combination of uncertain sensory signals with prior expectations . The effect of prior probability is often described as a shift in the decision criterion . Can observers track sudden changes in probability ? To answer this question , we used a change-point detection paradig...	We demonstrate how people learn and adapt to changes to the probability of occurrence of one of two categories on decision-making under uncertainty . The study combined psychophysical behavioral tasks with computational modeling . We used two behavioral tasks: a typical forced-choice categorization task as well as one ...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Methods" ]	[ "learning", "ellipses", "decision", "making", "statistics", "social", "sciences", "geometry", "neuroscience", "learning", "and", "memory", "cognitive", "psychology", "mathematics", "probability", "distribution", "cognition", "research", "and", "analysis", "methods", "beha...	2019	Human online adaptation to changes in prior probability
Cells of the spinal cord and somites arise from shared , dual-fated precursors , located towards the posterior of the elongating embryo . Here we show that these neuromesodermal progenitors ( NMPs ) can readily be generated in vitro from mouse and human pluripotent stem cells by activating Wnt and Fgf signalling , time...	Stem cells are providing insight into embryo development and offering new approaches to clinical and therapeutic research . In part this progress arises from “directed differentiation” – artificially controlling the types of cells produced from stem cells . Here we describe the directed differentiation of mouse and hum...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "cell", "differentiation", "developmental", "biology", "neuronal", "differentiation" ]	2014	In Vitro Generation of Neuromesodermal Progenitors Reveals Distinct Roles for Wnt Signalling in the Specification of Spinal Cord and Paraxial Mesoderm Identity
Primary effusion lymphoma ( PEL ) is an aggressive B-cell lymphoma with poor prognosis caused by Kaposi’s sarcoma-associated herpesvirus ( KSHV ) . Previous studies have revealed that HIF-1α , which mediates much of the cellular response to hypoxia , plays an important role in life cycle of KSHV . KSHV infection promot...	Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is an oncogenic herpesvirus that causes several malignancies including primary effusion lymphoma ( PEL ) . PEL is an aggressive B-cell lymphoma that usually develops in a hypoxic environment . There is no standard treatment for PEL and it carries a poor prognosis . Previ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "metabolic", "processes", "pathogens", "immunology", "microbiology", "glycolysis", "viruses", "oncology", "micrornas", "dna"...	2017	Hypoxia-inducible factor-1 alpha as a therapeutic target for primary effusion lymphoma
Transcription factors ( TFs ) regulate gene expression in both prokaryotes and eukaryotes by recognizing and binding to specific DNA promoter sequences . In higher eukaryotes , it remains unclear how the duration of TF binding to DNA relates to downstream transcriptional output . Here , we address this question for the...	To control the rate of transcription of genes , both eukaryotes and prokaryotes express specialized proteins , transcription factors ( TF ) , that bind promoter sequences to mark them for the transcriptional machinery including DNA polymerase II . TFs are often multi-subunit proteins containing a DNA-binding domain ( D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "interactions", "hela", "cells", "gene", "regulation", "biological", "cultures", "dna-binding", "proteins", "light", "microscopy", "dna", "transcription", "microscopy", "cell", "cultures", "research", "and", "analysis", "methods", "transcriptional", "control", ...	2019	Single-molecule dynamics and genome-wide transcriptomics reveal that NF-kB (p65)-DNA binding times can be decoupled from transcriptional activation
How the innate immune system tailors specific responses to diverse microbial infections is not well understood . Cells use a limited number of host receptors and signaling pathways to both discriminate among extracellular and intracellular microbes , and also to generate responses commensurate to each threat . Here , w...	Macrophages are critical cells of the innate immune system , contributing to immediate and robust defense against microbial infections . Macrophages detect pathogens using host receptors located on the cell surface , in phagosomal vacuoles , and in the cytosol . While fundamental to innate immunity , it is not clear if...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "microbiology", "animals", "genetics", "and", "genomics", "eubacteria" ]	2008	Distinct TLR- and NLR-Mediated Transcriptional Responses to an Intracellular Pathogen

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