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Ocular coloboma results from abnormal embryonic development and is often associated with additional ocular and systemic features . Coloboma is a highly heterogeneous disorder with many cases remaining unexplained . Whole exome sequencing from two cousins affected with dominant coloboma with microcornea , cataracts , an...	Coloboma is a hole or gap in one or more of the structures of the eye . Coloboma occurs when the eye is not formed properly during prenatal development . It is often associated with additional eye abnormalities and can result in significant loss of vision . Identification of the genetic causes of coloboma provides more...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Mutations in MAB21L2 Result in Ocular Coloboma, Microcornea and Cataracts
Large-scale codon re-encoding ( i . e . introduction of a large number of synonymous mutations ) is a novel method of generating attenuated viruses . Here , it was applied to the pathogenic flavivirus , tick-borne encephalitis virus ( TBEV ) which causes febrile illness and encephalitis in humans in forested regions of...	The arbovirus Tick-borne encephalitis virus ( TBEV; genus Flavivirus ) is transmitted by ticks of the Ixodes genus . TBEV causes febrile illness and encephalitis in humans in forested regions of Europe and Asia . The incidence of TBE is increasing across Central and Eastern European countries despite the availability o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Attenuation of Tick-Borne Encephalitis Virus Using Large-Scale Random Codon Re-encoding
Gene expression measurements are influenced by a wide range of factors , such as the state of the cell , experimental conditions and variants in the sequence of regulatory regions . To understand the effect of a variable of interest , such as the genotype of a locus , it is important to account for variation that is du...	Gene expression is a complex phenotype . The measured expression level in an experiment can be affected by a wide range of factors—state of the cell , experimental conditions , variants in the sequence of regulatory regions , and others . To understand genotype-to-phenotype relationships , we need to be able to disting...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "genetics", "and", "genomics/gene", "expression", "computational", "biology/transcriptional", "regulation" ]	2010	A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies
In operant learning , behaviors are reinforced or inhibited in response to the consequences of similar actions taken in the past . However , because in natural environments the “same” situation never recurs , it is essential for the learner to decide what “similar” is so that he can generalize from experience in one st...	According to the law of effect , formulated a century ago by Edward Thorndike , actions which are rewarded in a particular situation are more likely to be executed when that same situation recurs . However , in natural settings the same situation never recurs and therefore , generalization from one state of the world t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "psychology", "cognitive", "psychology", "behavior", "biology", "and", "life", "sciences", "social", "sciences", "cognitive", "science", "neuroscience" ]	2014	Spatial Generalization in Operant Learning: Lessons from Professional Basketball
Knowledge of the functional cis-regulatory elements that regulate constitutive and alternative pre-mRNA splicing is fundamental for biology and medicine . Here we undertook a genome-wide comparative genomics approach using available mammalian genomes to identify conserved intronic splicing regulatory elements ( ISREs )...	During RNA splicing , sequences ( introns ) in a pre-mRNA are excised and discarded , and the remaining sequences ( exons ) are joined to form the mature RNA . Splicing is regulated not only by the binding of the basic splicing machinery to splice sites located at the exon–intron boundaries , but also by the combined e...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "dog", "computational", "biology", "evolutionary", "biology", "molecular", "biology", "rattus", "(rat)", "mus", "(mouse)" ]	2007	Discovery and Analysis of Evolutionarily Conserved Intronic Splicing Regulatory Elements
Trans-sialidases are key enzymes in the life cycle of African trypanosomes in both , mammalian host and insect vector and have been associated with the disease trypanosomiasis , namely sleeping sickness and nagana . Besides the previously reported TconTS1 , we have identified three additional active trans-sialidases , ...	Trypanosomiasis is a disease also known as sleeping sickness in humans ( Human African Trypanosomiasis ) and nagana in animals ( Animal African Trypanosomiasis ) . This disease is caused by protozoan parasites of the genus Trypanosoma . Tsetse flies are responsible for the transmission of these parasites . Trypanosoma ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Biochemical Diversity in the Trypanosoma congolense Trans-sialidase Family
Varicella zoster virus ( VZV ) is a ubiquitous human alphaherpesvirus , responsible for varicella upon primary infection and herpes zoster following reactivation from latency . To establish lifelong infection , VZV employs strategies to evade and manipulate the immune system to its advantage in disseminating virus . As...	Varicella zoster virus ( VZV ) is a pervasive pathogen , causing chickenpox during primary infection and shingles when the virus reactivates from latency . VZV is therefore a lifelong infection for humans , warranting investigation of how this virus interacts with the immune system . One of the first immune cells to re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "epithelial", "cells", "viruses", "dna", "viruses", "herpesviruses", "research", ...	2018	Varicella zoster virus productively infects human natural killer cells and manipulates phenotype
In recent years , remarkable versatility of polyketide synthases ( PKSs ) has been recognized; both in terms of their structural and functional organization as well as their ability to produce compounds other than typical secondary metabolites . Multifunctional Type I PKSs catalyze the biosynthesis of polyketide produc...	Polyketide synthases ( PKSs ) form a large family of multifunctional proteins involved in the biosynthesis of diverse classes of natural products . Mycobacterium tuberculosis ( Mtb ) exploits these polyketide biosynthetic enzymes to synthesize complex lipids , many of which are essential for its virulence . PKSs utiliz...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "biology", "biochemistry" ]	2008	Novel Intermolecular Iterative Mechanism for Biosynthesis of Mycoketide Catalyzed by a Bimodular Polyketide Synthase
This paper explores the framings of trypanosomiasis , a widespread and potentially fatal zoonotic disease transmitted by tsetse flies ( Glossina species ) affecting both humans and livestock . This is a country case study focusing on the political economy of knowledge in Zambia . It is a pertinent time to examine this ...	This paper explores the differing opinions of various stakeholders in relation to trypanosomiasis , a widespread and potentially fatal disease spread by tsetse flies which affects both humans and animals . It is an important time to examine this issue as human population growth and other factors have led to migration i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Stakeholder Narratives on Trypanosomiasis, Their Effect on Policy and the Scope for One Health
Neuroinvasive viruses , such as alpha herpesviruses ( αHV ) and rabies virus ( RABV ) , initially infect peripheral tissues , followed by invasion of the innervating axon termini . Virus particles must undergo long distance retrograde axonal transport to reach the neuron cell bodies in the peripheral or central nervous...	Rabies virus ( RABV ) and alpha herpesviruses ( αHV ) ( e . g . herpes simplex virus ) evolved to enter the nervous system efficiently each time they infect a host . In most mammals , RABV reaches the brain , causing a fatal encephalitis . Whereas , αHV remain in the peripheral nervous system in a quiescent but reactiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "vesicles", "cell", "processes", "neuroscience", "protein", "synthesis", "nerve", "fibers", "bioassays", "and", "physiological", "analysis", "cellular", "structures", "and", "organelles", "chemical", "synthesis", "research", "and", "analysis", "methods", "transport", "i...	2018	Retrograde axonal transport of rabies virus is unaffected by interferon treatment but blocked by emetine locally in axons
Schistosomes are amongst the most important and neglected pathogens in the world , and schistosomiasis control relies almost exclusively on a single drug . The neuromuscular system of schistosomes is fertile ground for therapeutic intervention , yet the details of physiological events involved in neuromuscular function...	Schistosomiasis ( bilharzia ) is caused by infection with trematodes of the genus Schistosoma . The disease afflicts over 200 million people , with the bulk of the disease burden focused in some of the world's poorest countries . Schistosomiasis control rests largely on chemotherapy with a single drug , praziquantel , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "pharmacology/drug", "resistance", "physiology/motor", "systems", "physiology/cell", "signaling", "physiology/integrative", "physiology", "pharmacology", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2010	FMRFamide-Like Peptides (FLPs) Enhance Voltage-Gated Calcium Currents to Elicit Muscle Contraction in the Human Parasite Schistosoma mansoni
For encapsulated bacteria such as Streptococcus pneumoniae , asymptomatic carriage is more common and longer in duration than disease , and hence is often a more convenient endpoint for clinical trials of vaccines against these bacteria . However , using a carriage endpoint entails specific challenges . Carriage is alm...	Streptococcus pneumoniae , a bacterium carried in the nasopharynx of many healthy people , is also a leading cause of bacterial pneumonia , sepsis , and ear infections in children aged five years and younger . Vaccines targeting select strains of S . pneumoniae have been effective , and the development of new vaccines ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "children", "medicine", "and", "health", "sciences", "immunology", "simulation", "and", "modeling", "vaccines", "preventive", "medicine", "age", "groups", "infants", "infectious", "disease", "control", "vaccination", "and", "immunization", "families", "research", "and",...	2018	Use of an individual-based model of pneumococcal carriage for planning a randomized trial of a whole-cell vaccine
As a person learns a new skill , distinct synapses , brain regions , and circuits are engaged and change over time . In this paper , we develop methods to examine patterns of correlated activity across a large set of brain regions . Our goal is to identify properties that enable robust learning of a motor skill . We me...	When someone learns a new skill , his/her brain dynamically alters individual synapses , regional activity , and larger-scale circuits . In this paper , we capture some of these dynamics by measuring and characterizing patterns of coherent brain activity during the learning of a motor skill . We extract time-evolving c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Task-Based Core-Periphery Organization of Human Brain Dynamics
Attractor neural networks are thought to underlie working memory functions in the cerebral cortex . Several such models have been proposed that successfully reproduce firing properties of neurons recorded from monkeys performing working memory tasks . However , the regular temporal structure of spike trains in these mo...	The basic computational principles of the brain are still unknown , and one major reason for this is related to the difficulties in simultaneously measuring detailed data from a sufficiently large number of cells . In techniques where populations of cells are monitored , resolution is low . Computational models have no...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2010	Bistable, Irregular Firing and Population Oscillations in a Modular Attractor Memory Network
Ecological communities are structured in part by evolutionary interactions among their members . A number of recent studies incorporating phylogenetics into community ecology have upheld the paradigm that competition drives ecological divergence among species of the same guild . However , the role of other interspecifi...	What governs the composition of communities of species ? Competition promotes divergence in behavior and habitat , allowing species to co-exist . But the effects of other interactions , such as mutualism , are less well understood . We examined the interplay between mutualistic interactions , common ancestry and compet...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "ecology" ]	2008	Mutualistic Interactions Drive Ecological Niche Convergence in a Diverse Butterfly Community
The length of cilia is controlled by a poorly understood mechanism that involves members of the conserved RCK kinase group , and among them , the LF4/MOK kinases . The multiciliated protist model , Tetrahymena , carries two types of cilia ( oral and locomotory ) and the length of the locomotory cilia is dependent on th...	Cilia are conserved organelles that generate motility and mediate vital sensory functions , including olfaction and vision . Cilia that are either too short or too long fail to generate proper forces or responses to extracellular signals . Several cilia-based diseases ( ciliopathies ) are associated with defects in cil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "cloning", "biological", "locomotion", "protozoans", "protein", "structure", "prediction", "protein", "structure", "ciliate", "protozoans", "molecular", "biology", "techniques", "cellular", "structures", "and", "...	2019	LF4/MOK and a CDK-related kinase regulate the number and length of cilia in Tetrahymena
Dengue virus causes ∼50–100 million infections per year and thus is considered one of the most aggressive arthropod-borne human pathogen worldwide . During its replication , dengue virus induces dramatic alterations in the intracellular membranes of infected cells . This phenomenon is observed both in human and vector-...	Dengue virus is one of the most aggressive human pathogens worldwide . It causes 50–100 million infections per year but there is no vaccine or antiviral that is currently effective against the disease . The virus is spread by Aedes aegyptii and Aedes albopictus mosquitoes and viral replication within the mosquito vecto...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Materials" ]	[ "biotechnology", "systems", "biology", "biochemistry", "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "epidemiology", "biology", "microbiology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides . However , the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary tra...	We present an approach to evolutionary analysis of bacterial pathogens combining core genome , accessory genome , and gene regulatory region analyses . This enables unparalleled resolution of the evolution of a multi-drug resistant pandemic pathogen that would remain invisible to a core genome phylogenetic analysis alo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "taxonomy", "genome", "evolution", "gene", "regulation", "microbiology", "animal", "phylogenetics", "genomic", "databases", "phylogenetics", "data", "management", "genome", "analysis", "bacterial", "genetics", "mammalian", "genomics", "microbial", "genetics"...	2016	Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations
African trypansomiases of humans and animals can be controlled by attacking the vectors , various species of tsetse fly . Treatment of cattle with pyrethroids to kill tsetse as they feed is the most cost-effective method . However , such treatments can contaminate cattle dung , thereby killing the fauna which disperse ...	In Zimbabwe , we treated cattle with spray or pour-on formulations of deltamethrin , as recommended by the manufacturers for control of tsetse flies . We then gauged the degree of dung contamination , using field bioassays involving adult beetles ( Coleoptera: Scarabaeidae ) . In the first 16 days after whole-body spra...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Pyrethroid Treatment of Cattle for Tsetse Control: Reducing Its Impact on Dung Fauna
The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies , mainly using mitochondrial genome diversity . Here we address the age of P . vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci . Analysis of ten house...	Plasmodium vivax is the most prevalent human malaria parasite outside Africa , responsible for significant morbidity , although it is commonly referred to as a benign malaria agent with respect to P . falciparum . Inferring the evolutionary history of an infectious agent provides important information for designing con...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Neutral Polymorphisms in Putative Housekeeping Genes and Tandem Repeats Unravels the Population Genetics and Evolutionary History of Plasmodium vivax in India
Domestication is one of the strongest forms of short-term , directional selection . Although selection is typically only exerted on one or a few target traits , domestication can lead to numerous changes in many seemingly unrelated phenotypes . It is unknown whether such correlated responses are due to pleiotropy or li...	The genetic analysis of phenotypes and the identification of the causative underlying genes remain central to molecular and evolutionary biology . By utilizing the domestication process , it is possible to exploit the large differences between domesticated animals and their wild counterparts to study both this and the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "genomics", "functional", "genomics", "gene", "expression", "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "genetics", "and", "genomics" ]	2012	A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication
The cell envelope of gram-negative bacteria , a structure comprising an outer ( OM ) and an inner ( IM ) membrane , is essential for life . The OM and the IM are separated by the periplasm , a compartment that contains the peptidoglycan . The OM is tethered to the peptidoglycan via the lipoprotein , Lpp . However , the...	Antibiotic resistance is one of the greatest threats that humanity faces today . In particular , the emergence of multidrug-resistant gram-negative bacteria has become a pressing issue . Infections caused by resistant gram-negative bacteria are indeed difficult to treat because of the presence of a double-membraned env...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "periplasm", "cell", "physiology", "engineering", "and", "technology", "molecular", "probe", "techniques", "signal", "processing", "microbiology", "immunoblotting", "electron", "cryo-microscopy", "microscopy", "materials", "science", "molecular", "biology", "techniques", "m...	2017	Communication across the bacterial cell envelope depends on the size of the periplasm
VRC01 protects macaques from vaginal SHIV infection after a single high-dose challenge . Infusion of a simianized anti-α4β7 mAb ( Rh-α4β7 ) just prior to , and during repeated vaginal exposures to SIVmac251 partially protected macaques from vaginal SIV infection and rescued CD4+ T cells . To investigate the impact of c...	Broadly neutralizing antibodies ( bNAbs ) constitute a promising new strategy to prevent and/or treat HIV-1 acquisition . However , it is clear that individual bNAbs cannot be used alone as a single intervention . α4β7 blockade with a monoclonal antibody ( mAb ) similar to a drug approved for treatment of inflammatory ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "pathogens", "immunology", "microbiology", "vertebrates", "animals", "mammals", "retroviruses", "primate...	2019	Delayed vaginal SHIV infection in VRC01 and anti-α4β7 treated rhesus macaques
Budding yeast cells exist in two mating types , a and α , which use peptide pheromones to communicate with each other during mating . Mating depends on the ability of cells to polarize up pheromone gradients , but cells also respond to spatially uniform fields of pheromone by polarizing along a single axis . We used qu...	Budding yeast cells exist in two mating types , a and α , which use peptide pheromones to communicate with each other during mating . Mating depends on the ability of cells to polarize up pheromone gradients , but cells also respond to spatially uniform fields of pheromone by polarizing along a single axis . We used qu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "cell", "processes", "mathematical", "models", "cell", "polarity", "fungi", "model", "organisms", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "saccharomyces", "pheromone", "receptors", "mathematical", "a...	2016	A Predictive Model for Yeast Cell Polarization in Pheromone Gradients
In eukaryotes , fumarase ( FH in human ) is a well-known tricarboxylic-acid-cycle enzyme in the mitochondrial matrix . However , conserved from yeast to humans is a cytosolic isoenzyme of fumarase whose function in this compartment remains obscure . A few years ago , FH was surprisingly shown to underlie a tumor suscep...	Fumarate hydratase ( FH; also known as fumarase ) is an enzyme found in both the cytoplasm and mitochondria of all eukaryotes . In mitochondria , FH is involved in generating energy for the cell through a metabolic pathway called the Krebs cycle . Its role in the cytoplasm , however , is unclear . FH can function as a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "molecular", "biology/dna", "repair" ]	2010	Fumarase: A Mitochondrial Metabolic Enzyme and a Cytosolic/Nuclear Component of the DNA Damage Response
The genomic information of microbes is a major determinant of their phenotypic properties , yet it is largely unknown to what extent ecological associations between different species can be explained by their genome composition . To bridge this gap , this study introduces two new genome-wide pairwise measures of microb...	It is still unknown to what extent ecological associations between microbes , as measured by co-occurrence of different taxa in 16S rRNA surveys , can be explained , or predicted , using composition and structure of microbial genomes alone . Here I introduce two new genome-wide , pairwise indices for quantifying the pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "ecology", "and", "environmental", "sciences", "functional", "genomics", "microbiology", "genomic", "databases", "phylogenetics", "data", "management", "genome", "analysis", "research", "and", "analysis", "methods", "ecological", "metrics", "computer", "and", ...	2017	Genome composition and phylogeny of microbes predict their co-occurrence in the environment
Congenital Zika virus ( ZIKV ) infection was first linked to birth defects during the American outbreak in 2015/2016 . It has been proposed that mutations unique to the Asian/American-genotype explain , at least in part , the ability of Asian/American ZIKV to cause congenital Zika syndrome ( CZS ) . Recent studies iden...	Zika virus ( ZIKV ) was first discovered in Uganda in 1947 , and is thought to have spread from Africa through equatorial Asia in the middle of the 20th century . Along the way the virus diversified , so that now two genetic lineages , African and Asian/American , are recognized . Congenital Zika syndrome ( CZS ) , the...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion", "Conclusions" ]	[]	2019	Zika viruses of African and Asian lineages cause fetal harm in a mouse model of vertical transmission
Kaposi’s Sarcoma-Associated Herpesvirus ( KSHV ) is an oncogenic virus which has adapted unique mechanisms to modulate the cellular microenvironment of its human host . The pathogenesis of KSHV is intimately linked to its manipulation of cellular signaling pathways , including the extracellular signal-regulated kinase ...	Kaposi’s sarcoma-associated herpesvirus ( KSHV ) is a human tumor virus which hijacks the host signaling pathways in order to maintain persistent infection . We previously discovered that the KSHV protein ORF45 binds to and activates the cellular kinase RSK ( p90 ribosomal S6 kinase ) , and that this activation is vita...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication
Analysis of the transcriptome of Borrelia burgdorferi , the causative agent of Lyme disease , during infection has proven difficult due to the low spirochete loads in the mammalian tissues . To overcome this challenge , we have developed an In Vivo Expression Technology ( IVET ) system for identification of B . burgdor...	Lyme disease is caused by tick-bite transmission of the pathogenic spirochete Borrelia burgdorferi . An increased understanding of how B . burgdorferi survives throughout its infectious cycle is critical for the development of innovative diagnostic and therapeutic protocols to reduce the incidence of Lyme disease . One...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "borrelia", "infection", "bacterial", "diseases", "infectious", "diseases", "lyme", "disease" ]	2013	In Vivo Expression Technology Identifies a Novel Virulence Factor Critical for Borrelia burgdorferi Persistence in Mice
Coma complicates Plasmodium falciparum infection but is uncommonly associated with P . vivax . Most series of vivax coma have been retrospective and have not utilized molecular methods to exclude mixed infections with P . falciparum . We prospectively enrolled patients hospitalized in Timika , Indonesia , with a Glasgo...	An estimated 132 to 391 million cases of Plasmodium vivax occur annually , accounting for up to 50% of malaria cases in South and East Asia . Vivax malaria is called “benign tertian malaria” and is not considered to be associated with life threatening or severe complications . Recently , observational studies and case ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Acknowledgments" ]	[ "medicine", "infectious", "diseases", "global", "health" ]	2011	Coma Associated with Microscopy-Diagnosed Plasmodium vivax: A Prospective Study in Papua, Indonesia
The area of Walikale in North Kivu , Democratic Republic of Congo , is intensely affected by conflict and population displacement . Médecins-Sans-Frontières ( MSF ) returned to provide primary healthcare in July 2012 . To better understand the impact of the ongoing conflict and displacement on the population , a retros...	The area of Walikale , in the eastern province of North Kivu , Democratic Republic of Congo has been experiencing ongoing conflict , violence and population displacement in recent years . Médecins Sans Frontières ( MSF ) has been working in this part of DRC since July 2012 and decided to document the impact of the conf...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "socioeconomic", "aspects", "of", "health", "medicine", "and", "health", "sciences", "epidemiology", "global", "health", "health", "care" ]	2014	Mortality Rates above Emergency Threshold in Population Affected by Conflict in North Kivu, Democratic Republic of Congo, July 2012–April 2013
Genomic imprinting is an epigenetic process leading to parent-of-origin–specific DNA methylation and gene expression . To date , ∼60 imprinted human genes are known . Based on genome-wide methylation analysis of a patient with multiple imprinting defects , we have identified a differentially methylated CpG island in in...	Genomic imprinting is an epigenetic process leading to parent-of-origin–specific DNA methylation and gene expression . Defects in this process lead to abnormal development , growth , or behavior . It is still unclear why and how imprinting evolved and how many human genes are imprinted . Based on genome-wide DNA methyl...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/gene", "expression" ]	2009	The Human Retinoblastoma Gene Is Imprinted
To date , there has been no standardized approach to the assessment of aerobic fitness among children who harbor parasites . In quantifying the disability associated with individual or multiple chronic infections , accurate measures of physical fitness are important metrics . This is because exercise intolerance , as s...	Reduced physical fitness , which is a manifestation of the body's inability to maintain adequate oxygen supply to the tissues , can have many causes . In developing countries , a person's low physical fitness is often the result of anemia and undernutrition , which have multifactorial etiologies including poor diet and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "growth", "retardation", "sports", "and", "exercise", "medicine", "parasitic", "diseases", "anemia", "pediatrics", "test", "evaluation", "filariasis", "nutrition", "hookworm", "infection", "neglected", "tropical", "...	2011	Measuring Fitness of Kenyan Children with Polyparasitic Infections Using the 20-Meter Shuttle Run Test as a Morbidity Metric
The human fungal pathogen , Cryptococcus neoformans , dramatically alters its cell wall , both in size and composition , upon entering the host . This cell wall remodeling is essential for host immune avoidance by this pathogen . In a genetic screen for mutants with changes in their cell wall , we identified a novel pr...	Disease causing microorganisms have adapted many strategies to avoid host immune detection in order to facilitate their survival . Pathogenic fungi alter their cell surface in order to mask immune stimulatory epitopes in their cell wall . We have identified a novel protein involved in this host-induced cell wall remode...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "walls", "chitin", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "light", "microscopy", "fungi"...	2018	Defects in intracellular trafficking of fungal cell wall synthases lead to aberrant host immune recognition
Meiotic recombination is a mandatory process for sexual reproduction . We identified a protein specifically implicated in meiotic homologous recombination that we named: meiosis specific with OB domain ( MEIOB ) . This protein is conserved among metazoan species and contains single-strand DNA binding sites similar to t...	Homologous recombination allows faithful repair of damaged DNA; in mitotic cells , it necessitates the formation of single strand DNA ( ssDNA ) , which is first protected by RPA and then coated by the RAD51 recombinase to mediate homology search . Specific modifications are made to this mechanism during meiosis , a spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	MEIOB Targets Single-Strand DNA and Is Necessary for Meiotic Recombination
Innate antiviral immunity is the first line of the host defense system that rapidly detects invading viruses . Mitochondria function as platforms for innate antiviral signal transduction in mammals through the adaptor protein , MAVS . Excessive activation of MAVS-mediated antiviral signaling leads to dysfunction of mit...	Pattern recognition receptors are vital to innate immunity . In the antiviral innate immunity , retinoic acid-inducible gene-I ( RIG-I ) -like receptors ( RLRs ) , such as RIG-I and MDA5 , sense viral RNAs through their C-terminal helicase domains , then initiate the antiviral response through interaction with the esse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	COX5B Regulates MAVS-mediated Antiviral Signaling through Interaction with ATG5 and Repressing ROS Production
Transmembrane α-helices play a key role in many receptors , transmitting a signal from one side to the other of the lipid bilayer membrane . Bacterial chemoreceptors are one of the best studied such systems , with a wealth of biophysical and mutational data indicating a key role for the TM2 helix in signalling . In par...	Understanding the physical mechanisms by which signals are transduced across a lipid bilayer is central to an account of cell signalling . We have used a novel technique for performing simulations to model the interactions of transmembrane ( TM ) helices from bacterial methyl accepting chemoreceptor proteins with lipid...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "transmembrane", "proteins", "molecular", "dynamics", "proteins", "chemistry", "biology", "computational", "chemistry", "biophysics", "simulations", "biophysics" ]	2011	Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling
Accurate prediction of dengue incidence levels weeks in advance of an outbreak may reduce the morbidity and mortality associated with this neglected disease . Therefore , models were developed to predict high and low dengue incidence in order to provide timely forewarnings in the Philippines . Model inputs were chosen ...	A largely automated methodology is described for creating models that use past and recent data to predict dengue incidence levels several weeks in advance for a specific time period and a geographic region that can be sub-national . The input data include historical and recent dengue incidence , socioeconomic factors ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "algorithms", "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "mathematics", "epidemiology", "remote", "sensing", "imagery", "applied", "mathematics", "computing", "methods", "physical", "sciences", "geoinformatics", "fuzzy", "logic"...	2014	Prediction of High Incidence of Dengue in the Philippines
Reinforcement learning has been widely used in explaining animal behavior . In reinforcement learning , the agent learns the value of the states in the task , collectively constituting the task state space , and uses the knowledge to choose actions and acquire desired outcomes . It has been proposed that the orbitofron...	Many studies employ reinforcement learning models to explain human or animal behavior , in which it is assumed that the animals know the task structure . Yet in the real life , the task structure also has to be acquired through learning . The orbitofrontal cortex has been proposed to play important roles in representin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "decision", "making", "neural", "networks", "prefrontal", "cortex", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "cognitive", "psychology", "animal", "behavior", "cognition", "network", ...	2018	A neural network model for the orbitofrontal cortex and task space acquisition during reinforcement learning
This study was conducted to assess the impact of chikungunya on health costs during the epidemic that occurred on La Réunion in 2005–2006 . From data collected from health agencies , the additional costs incurred by chikungunya in terms of consultations , drug consumption and absence from work were determined by a comp...	For a long time , studies of chikungunya virus infection have been neglected , but since its resurgence in the south-western Indian Ocean and on La Réunion Island , this disease has been paid greater amounts of attention . The economic and social impacts of chikungunya epidemics are poorly documented , including in dev...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "socioeconomic", "aspects", "of", "health", "public", "health", "and", "epidemiology", "epidemiology", "neglected", "tropical", "diseases", "arboviral", "infections", "economic", "epidemiology", "public", "health" ]	2011	The Chikungunya Epidemic on La Réunion Island in 2005–2006: A Cost-of-Illness Study
A new generation of strategies is evolving that aim to block malaria transmission by employing genetically modified vectors or mosquito pathogens or symbionts that express anti-parasite molecules . Whilst transgenic technologies have advanced rapidly , there is still a paucity of effector molecules with potent anti-mal...	Breaking the complex life cycle of malaria by blocking its development in the mosquito is one area of research being pursued for malaria control . Currently , the mosquito itself , or microbes that live within it , are being genetically modified to provide toxic or lethal outcomes to the parasite . However , this usual...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Killer Bee Molecules: Antimicrobial Peptides as Effector Molecules to Target Sporogonic Stages of Plasmodium
Neisseria meningitidis ( Nm ) and N . gonorrhoeae ( Ng ) are adapted to different environments within their human host . If the basis of this difference has not yet been fully understood , previous studies ( including our own data ) have reported that , unlike Ng , Nm tolerates high manganese concentrations . As transi...	Neisseria meningitidis is an obligate resident of the human nasopharynx but can also be responsible for septicemia and meningitis . During our efforts to understand the specific selective pressure underwent by N . meningitidis to survive in its human niche , we have brought to light a new family of bacterial manganese-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "evolutionary", "biology" ]	2011	A Novel Metal Transporter Mediating Manganese Export (MntX) Regulates the Mn to Fe Intracellular Ratio and Neisseria meningitidis Virulence
The most immediate and evident effect of mucosal exposure to semen in vivo is a local release of proinflammatory mediators accompanied by an influx of leukocytes into the female genital mucosa ( FGM ) . The implication of such response in HIV-1 transmission has never been addressed due to limitations of currently avail...	The majority of HIV-1 transmissions worldwide occur via unprotected vaginal intercourse , with semen and the female genital mucosa ( FGM ) being the main vector and recipient of virus acquisition in women . It is well known that mucosal exposure to semen via vaginal intercourse or artificial fertilization results in tr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods", "Accession", "numbers" ]	[ "blood", "cells", "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "body", "fluids", "immune", "cells", "pathogens", "sexual", "and", "gender...	2017	Seminal plasma induces inflammation and enhances HIV-1 replication in human cervical tissue explants
The Drosophila spermatogenesis cell differentiation pathway involves the activation of a large set of genes in primary spermatocytes . Most of these genes are activated by testis-specific TATA-binding protein associated factors ( tTAFs ) . In the current model for the activation mechanism , Polycomb plays a key role si...	How are developmental gene expression programs activated ? An interesting activation mechanism has been suggested by studies of the switch-on of the genes required for sperm differentiation in Drosophila; the spermatogenesis genes . These studies indicated that removal of the Polycomb protein from spermatogenesis genes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genome-Wide and Cell-Specific Epigenetic Analysis Challenges the Role of Polycomb in Drosophila Spermatogenesis
Chirality in shape and motility can evolve rapidly in microbes and cancer cells . To determine how chirality affects cell fitness , we developed a model of chiral growth in compact aggregates such as microbial colonies and solid tumors . Our model recapitulates previous experimental findings and shows that mutant cells...	Is it better to be left- or right-handed ? The answer depends on whether the goal is making a handshake or winning a boxing match . The need for coordination favors the handedness of the majority , but being different could also provide an advantage . The same rules could apply to microbial colonies and cancer tumors ....	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "distance", "measurement", "organismal", "evolution", "ecology", "and", "environmental", "sciences", "engineering", "and", "technology", "population", "dynamics", "population", "genetics", "microbiology", "simulation", "and", "modeling", "microbial", "evolution", "populatio...	2018	Chirality provides a direct fitness advantage and facilitates intermixing in cellular aggregates
The methylation of lysine 4 of Histone H3 ( H3K4me ) is an important component of epigenetic regulation . H3K4 methylation is a consequence of transcriptional activity , but also has been shown to contribute to “epigenetic memory”; i . e . , it can provide a heritable landmark of previous transcriptional activity that ...	The germ line transmits both genetic and epigenetic information between and across generations . The germ line uniquely retains developmental totipotency , and this property of germ cells is likely embedded in epigenetic information that is retained throughout the germ line cycle , within and across each generation . T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "developmental", "biology/embryology", "developmental", "biology/stem", "cells", "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/epigenetics" ]	2011	A Role for Set1/MLL-Related Components in Epigenetic Regulation of the Caenorhabditis elegans Germ Line
Oxidative stress is linked to many pathological conditions including the loss of dopaminergic neurons in Parkinson’s disease . The vast majority of disease cases appear to be caused by a combination of genetic mutations and environmental factors . We screened for genes protecting Caenorhabditis elegans dopaminergic neu...	Animals employ multiple mechanisms to prevent their cells from damage by reactive oxygen species , chemically reactive molecules containing oxygen . Oxidative stress , caused by the overabundance of reactive oxygen species or a decreased cellular defence against these chemicals , is linked to a variety of neurodegenera...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "cell", "death", "neurochemistry", "caenorhabditis", "oxidative", "stress", "dopaminergics", "cell", "processes", "neuroscience", "animals", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "experimental", "...	2018	6-OHDA-induced dopaminergic neurodegeneration in Caenorhabditis elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33
Streptococcus gallolyticus subsp . gallolyticus ( Sg ) has long been known to have a strong association with colorectal cancer ( CRC ) . This knowledge has important clinical implications , and yet little is known about the role of Sg in the development of CRC . Here we demonstrate that Sg promotes human colon cancer c...	Colorectal cancer ( CRC ) is a leading cause of cancer-related death . The recognition that microbial agents can contribute to the development of CRC raises hope for improving CRC diagnosis and treatment by incorporating both microbial and patient characteristics into clinical strategies . S . gallolyticus subsp . gall...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "lactococcus", "lactis", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "cancer", "treatment", "cell", "processes", "biological", "cultures", "cancers", "and", "neoplasms", "microbiology", "oncology", "animal", "model...	2017	Streptococcus gallolyticus subsp. gallolyticus promotes colorectal tumor development
In Escherichia coli , damage to the chromosomal DNA induces the SOS response , setting in motion a series of different DNA repair and damage tolerance pathways . DNA polymerase IV ( pol IV ) is one of three specialised DNA polymerases called into action during the SOS response to help cells tolerate certain types of DN...	Translesion DNA polymerases play a critical role in DNA damage tolerance in all cells . In Escherichia coli , the translesion polymerases include DNA polymerases II , IV , and V . At stalled replication forks , DNA polymerase IV is thought to compete with , and perhaps displace the polymerizing subunits of DNA polymera...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cell", "binding", "cell", "physiology", "fluorescence", "imaging", "dna-binding", "proteins", "light", "microscopy", "dna", "damage", "polymerases", "dna", "replication", "microscopy", "dna", "bright", "field", "imaging", "research", "and", "analysis", "methods", "im...	2018	DNA polymerase IV primarily operates outside of DNA replication forks in Escherichia coli
All four serotypes of dengue virus are endemic in Indonesia , where the population at risk for infection exceeds 200 million people . Despite continuous control efforts that were initiated more than four decades ago , Indonesia still suffers from multi-annual cycles of dengue outbreak and dengue remains as a major publ...	While methods for vector control such as mosquito breeding source reduction and focal insecticide spraying that have been practiced to reduce dengue transmission in Indonesia have had limited success , dengue vaccines are expected to be an effective control method . However , even if an efficacious vaccine is developed...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Public Acceptance and Willingness-to-Pay for a Future Dengue Vaccine: A Community-Based Survey in Bandung, Indonesia
Extended-spectrum beta-lactamases ( ESBL ) constitute a key antibiotic-resistance mechanism affecting Gram-negative bacteria , and also an excellent model for studying evolution in real time . A shift in the epidemiology of ESBLs is being observed , which is characterized by the explosive diversification and increase i...	Antimicrobial resistance in bacterial organisms is a worldwide problem widely discussed from clinical , economical and social points of view . The number of new resistance mechanisms and microorganisms resistant to new drugs is increasing all over the world . The development and spread of antibiotic resistance in bacte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "evolutionary", "biology/bioinformatics" ]	2010	Evolutionary Trajectories of Beta-Lactamase CTX-M-1 Cluster Enzymes: Predicting Antibiotic Resistance
We previously reported that TR2 and TR4 orphan nuclear receptors bind to direct repeat ( DR ) elements in the ε- and γ-globin promoters , and act as molecular anchors for the recruitment of epigenetic corepressors of the multifaceted DRED complex , thereby leading to ε- and γ-globin transcriptional repression during de...	Sequential genome-wide binding studies investigated by deep sequencing ( ChIP-seq ) represent a powerful tool for investigating the temporal sequence of gene activation and repression events that take place as cells differentiate . Here , we report the binding of an “orphan” nuclear receptor ( one for which no ligand h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Biased, Non-equivalent Gene-Proximal and -Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells
Response of cells to changing environmental conditions is governed by the dynamics of intricate biomolecular interactions . It may be reasonable to assume , proteins being the dominant macromolecules that carry out routine cellular functions , that understanding the dynamics of protein∶protein interactions might yield ...	Many cellular processes and the response of cells to environmental cues are determined by the intricate protein∶protein interactions . These cellular protein interactions can be represented in the form of a graph , where the nodes represent the proteins and the edges signify the interactions between them . However , th...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "computational", "biology/genomics" ]	2008	Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data
While schistosomiasis remains a significant health problem in low to middle income countries , it also represents a recently recognised threat to more economically-developed regions . Until a vaccine is developed , this neglected infectious disease is primarily controlled by praziquantel , a drug with a currently unkno...	Schistosomiasis , caused by infection with blood fluke worms , is responsible for chronic disability and debilitating pathology in millions of infected individuals living in deprived regions of the developing world . Currently , schistosomiasis is primarily controlled by administration of a single drug ( praziquantel )...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "helminths", "gene", "regulation", "dna-binding", "proteins", "animals", "epigenetics", "dna", "molecular", "biology", "techniques", "dna", "methylation", "chromatin", "research", "and", "analysis", "methods", "sma...	2018	Methyl-CpG-binding (SmMBD2/3) and chromobox (SmCBX) proteins are required for neoblast proliferation and oviposition in the parasitic blood fluke Schistosoma mansoni
The genus Leishmania includes approximately 53 species , 20 of which cause human leishmaniais; a significant albeit neglected tropical disease . Leishmaniasis has afflicted humans for millennia , but how ancient is Leishmania and where did it arise ? These questions have been hotly debated for decades and several theor...	The genus Leishmania includes approximately 53 species , 20 of which cause human leishmaniais , a significant disease that has afflicted humans for millennia . But how ancient is Leishmania and where did it arise ? Some suggest Leishmania originated in the Palearctic . Others suggest it appeared in the Neotropics . The...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results" ]	[ "taxonomy", "invertebrates", "parasite", "evolution", "microbiology", "protozoan", "life", "cycles", "parasitic", "protozoans", "parasitology", "animals", "organisms", "developmental", "biology", "phylogenetics", "data", "management", "protozoans", "leishmania", "phylogenetic...	2017	Isolation of Novel Trypanosomatid, Zelonia australiensis sp. nov. (Kinetoplastida: Trypanosomatidae) Provides Support for a Gondwanan Origin of Dixenous Parasitism in the Leishmaniinae
Gravity models have a long history of use in describing and forecasting the movements of people as well as goods and services , making them a natural basis for disease transmission rates over distance . In agent-based micro-simulations , gravity models can be directly used to represent movement of individuals and hence...	An accurate representation of disease transmission between spatially-distinct regions is an essential part of modelling epidemic behaviour on a national or international scale . Gravity models , which describe movement fluxes between regions in terms of their populations and distance from each other , have a history of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "distance-decay", "models", "medicine", "public", "health", "and", "epidemiology", "geography", "social", "and", "behavioral", "sciences", "epidemiology", "infectious", "disease", "epidemiology", "human", "geography" ]	2012	Evaluating the Adequacy of Gravity Models as a Description of Human Mobility for Epidemic Modelling
Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function . Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic da...	Genomic data are becoming increasingly valuable as we develop methods to utilize the information at scale and gain a greater understanding of how genetic information relates to biological function . Advances in synthetic biology and the decreased cost of sequencing are increasing the amount of privately held genomic da...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "pathogens", "synthetic", "biology", "microbiology", "staphylococcus", "aureus", "genomic", "databases", "mutation", "mathematics", "genome", "analys...	2018	SIG-DB: Leveraging homomorphic encryption to securely interrogate privately held genomic databases
The ~1 . 6 Ga Tirohan Dolomite of the Lower Vindhyan in central India contains phosphatized stromatolitic microbialites . We report from there uniquely well-preserved fossils interpreted as probable crown-group rhodophytes ( red algae ) . The filamentous form Rafatazmia chitrakootensis n . gen , n . sp . has uniserial ...	The last common ancestor of modern eukaryotes is generally believed to have lived during the Mesoproterozoic era , about 1 . 6 to 1 billion years ago , or possibly somewhat earlier . We studied exquisitely preserved fossil communities from ~1 . 6 billion-year-old sedimentary rocks in central India representing a shallo...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "engineering", "and", "technology", "manufacturing", "processes", "fossil", "record", "fossil", "calibration", "materials", "science", "marine", "fossils", "paleontology", "plants", "bacteria", "coatings", "materials", "by", "attribute", "cyanobacteria", "algae", "paleobi...	2017	Three-dimensional preservation of cellular and subcellular structures suggests 1.6 billion-year-old crown-group red algae
In an active , self-ubiquitinated state , the Ring1B ligase monoubiquitinates histone H2A playing a critical role in Polycomb-mediated gene silencing . Following ubiquitination by external ligases , Ring1B is targeted for proteosomal degradation . Using biochemical data and computational modeling , we show that the Rin...	The generation of polyubiquitin chains on target proteins as a degradation signal was a landmark discovery rewarded by the 2004 Nobel Prize in Chemistry . However , emerging evidence suggests that protein ubiquitination is more versatile . Different types of ubiquitin chains serve numerous non-proteolytic functions , a...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "systems", "biology", "biology", "genetics", "and", "genomics" ]	2011	Switches, Excitable Responses and Oscillations in the Ring1B/Bmi1 Ubiquitination System
The mammalian Msx homeobox genes , Msx1 and Msx2 , encode transcription factors that control organogenesis and tissue interactions during embryonic development . We observed overlapping expression of these factors in uterine epithelial and stromal compartments of pregnant mice prior to embryo implantation . Conditional...	During implantation , various tissue compartments within the uterus , including epithelium and stroma , undergo sequential proliferation and differentiation as the embryo attaches to the uterus and invades into the maternal tissue . There is only limited understanding of the molecular signaling pathways that interconne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Msx Homeobox Genes Critically Regulate Embryo Implantation by Controlling Paracrine Signaling between Uterine Stroma and Epithelium
Biological data sets are typically characterized by high dimensionality and low effect sizes . A powerful method for detecting systematic differences between experimental conditions in such multivariate data sets is multivariate pattern analysis ( MVPA ) , particularly pattern classification . However , in virtually al...	When data are analyzed using multivariate pattern classification , any systematic similarities between subsets of trials ( e . g . shared physical properties among a subgroup of stimuli , trials belonging to the same session or subject , etc . ) form distinct nested subclasses within each class . Pattern classification...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "statistics", "experimental", "design", "brain", "electrophysiology", "electrophysiology", "neuroscience", "research", "design", "clinical", "medicine", "probability", "distribution", "mathematics", "artificial", "intelligence", "brain...	2018	Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing
Epigenetic mechanisms are implicated in gene regulation and the development of different diseases . The epigenome differs between cell types and has until now only been characterized for a few human tissues . Environmental factors potentially alter the epigenome . Here we describe the genome-wide pattern of DNA methyla...	Given the important role of epigenetics in gene regulation and disease development , we here present the genome-wide DNA methylation pattern of 476 , 753 CpG sites in adipose tissue obtained from healthy men . Since environmental factors potentially change metabolism through epigenetic modifications , we examined if a ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "diabetes", "mellitus", "type", "2", "diabetic", "endocrinology", "endocrinology", "gene", "expression", "genetics", "epigenetics", "sports", "and", "exercise", "medicine", "biology", "dna", "modification" ]	2013	A Six Months Exercise Intervention Influences the Genome-wide DNA Methylation Pattern in Human Adipose Tissue
Several naked virus species , including members of the Picornaviridae family , have recently been described to escape their host cells and spread infection via enclosure in extracellular vesicles ( EV ) . EV are 50–300 nm sized lipid membrane-enclosed particles produced by all cells that are broadly recognized for play...	Picornaviruses constitute a family of viruses that cause many human and animal diseases . These ‘naked’ viruses are known to spread by causing infected cell to burst open . However , challenging recent data indicate that virions also escape intact cells enclosed in small lipid membrane-enclosed particles , called ‘extr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "density", "microbiology", "viral", "structure", "membrane", "proteins", "materials", "science", "centrifugation", "materials", "physics", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "separation", "processe...	2019	Picornavirus infection induces temporal release of multiple extracellular vesicle subsets that differ in molecular composition and infectious potential
Kleefstra syndrome , caused by haploinsufficiency of euchromatin histone methyltransferase 1 ( EHMT1 ) , is characterized by intellectual disability ( ID ) , autism spectrum disorder ( ASD ) , characteristic facial dysmorphisms , and other variable clinical features . In addition to EHMT1 mutations , de novo variants w...	Neurodevelopmental disorders ( NDDs ) like intellectual disability ( ID ) and autism spectrum disorder ( ASD ) present an enormous challenge to affected individuals , their families , and society . Understanding the mechanisms underlying NDDs may lead to the development of targeted therapeutics , but this is complicate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "gene", "regulation", "dna-binding", "proteins", "animals", "invertebrate", "genomics", "animal", "models", "mutation", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "genome", "analysis", "nonsense", "mutation", ...	2017	Functional convergence of histone methyltransferases EHMT1 and KMT2C involved in intellectual disability and autism spectrum disorder
The major environmental determinants of honeybee caste development come from larval nutrients: royal jelly stimulates the differentiation of larvae into queens , whereas beebread leads to worker bee fate . However , these determinants are not fully characterized . Here we report that plant RNAs , particularly miRNAs , ...	How caste has formed in honeybees is an enduring puzzle . The prevailing view is that royal jelly stimulates the differentiation of larvae into queen . Here , we uncover a new mechanism that plant miRNAs in worker bee’s food postpone larval development , thereby inducing sterile worker bees . Thus , the theories about ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "plant", "anatomy", "medicine", "and", "health", "sciences", "honey", "bees", "gene", "regulation", "rna", "extraction", "diet", "animals", "animal", "products", "pollen", "animal", "models", "developmental", "biology", "micrornas", "plant", "science"...	2017	Plant microRNAs in larval food regulate honeybee caste development
Snakebites are a public health problem in Nicaragua: it is a tropical developing country , venomous snakes are present and there are reports of snakebites treated both in the formal and informal health care system . We aimed to produce an incidence map using data reported by the health care system that would be used to...	Snakebites have recently been recognized as a neglected cause of human suffering and death worldwide . Many bites are treated by traditional practitioners and thereby not recorded by the health care system . This leads to a lack of reliable epidemiological data and is identified as a major obstacle in dealing with this...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology" ]	2010	Mapping Snakebite Epidemiology in Nicaragua – Pitfalls and Possible Solutions
Androgenetic alopecia ( AGA ) is a highly heritable condition and the most common form of hair loss in humans . Susceptibility loci have been described on the X chromosome and chromosome 20 , but these loci explain a minority of its heritable variance . We conducted a large-scale meta-analysis of seven genome-wide asso...	While most genome-wide association studies ( GWAS ) focus on the identification of susceptibility loci for a specific disease , this hypothesis-free approach also enables the identification of unexpected associations between different diseases by taking advantage of the previously published GWAS associations . Androgen...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "public", "health", "and", "epidemiology", "epidemiology", "genetics", "biology", "genetics", "and", "genomics" ]	2012	Six Novel Susceptibility Loci for Early-Onset Androgenetic Alopecia and Their Unexpected Association with Common Diseases
Coarse-grained molecular dynamics simulations of the E . coli outer membrane proteins FhuA , LamB , NanC , OmpA and OmpF in a POPE/POPG ( 3∶1 ) bilayer were performed to characterise the diffusive nature of each component of the membrane . At small observation times ( <10 ns ) particle vibrations dominate phospholipid ...	Biological membranes are selective barriers which control the entry/exit of molecules to/from the interior of a cell . They are composed of a lipid bilayer in which are embedded many membrane proteins . Whilst the individual components of membranes are relatively well characterised , the lateral organization and dynami...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "molecular", "dynamics", "chemistry", "biology", "computational", "chemistry", "biophysics", "simulations", "biophysics" ]	2013	Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes
Dengue fever is a major public health concern in many parts of the tropics and subtropics . The first dengue vaccine has already been licensed in six countries . Given the growing interests in the effective use of the vaccine , it is critical to understand the economic burden of dengue fever to guide decision-makers in...	Dengue fever has been prevalent in South-East Asia and South America . Despite the increase of dengue fever cases , there continues to be a lack of economic assessment partly due to the absence of vaccines until recent times . Many of the previous economic burden studies for dengue fever were not standardized , making ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "tropical", "diseases", "geographical", "locations", "social", "sciences", "health", "care", "inpatients", "neglected", "tropical", "diseases", "patients", "infectious", "diseases", "health", "economics", "south", "america", "den...	2017	A multi-country study of the economic burden of dengue fever: Vietnam, Thailand, and Colombia
Despite the increasing availability of typhoid vaccine in many regions , global estimates of mortality attributable to enteric fever appear stable . While both Salmonella enterica serovar Typhi ( S . Typhi ) and serovar Paratyphi ( S . Paratyphi ) cause enteric fever , limited data exist estimating the burden of S . Pa...	Enteric fever due to Salmonella enterica serovar Typhi ( S . Typhi ) and serovar Paratyphi ( S . Paratyphi A , B , C ) remains a global public health concern . While numerous studies have estimated the levels or burden of S . Typhi , there are only limited data estimating the burden of S . Paratyphi A , particularly in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "medicine", "and", "health", "sciences", "epidemiology", "infectious", "disease", "epidemiology", "global", "health" ]	2014	Estimating the Burden of Paratyphoid A in Asia and Africa
The phytohormone abscisic acid ( ABA ) is an important regulator of plant development and response to environmental stresses . In this study , we identified two ABA overly sensitive mutant alleles in a gene encoding Auxin Response Factor2 ( ARF2 ) . The expression of ARF2 was induced by ABA treatment . The arf2 mutants...	Abscisic acid is a phytohormone that regulates many aspects in plant growth and development and response to different biotic and abiotic stresses . Research on ABA inhibiting seed germination , controlling stomatal movement , and regulating gene expression has been widely performed . However , the molecular mechanism f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2011	Auxin Response Factor2 (ARF2) and Its Regulated Homeodomain Gene HB33 Mediate Abscisic Acid Response in Arabidopsis
Herpes simplex virus ( HSV ) entry is associated with Akt translocation to the outer leaflet of the plasma membrane to promote a complex signaling cascade . We hypothesized that phospholipid scramblase-1 ( PLSCR1 ) , a calcium responsive enzyme that flips phosphatidylserines between membrane leaflets , might redistribu...	Defining the mechanisms by which herpes simplex viruses ( HSV ) enter cells will facilitate the development of new strategies to prevent or treat infections and provide insights into cell biology . We report the novel observation that HSV activates the enzyme , scramblase , which redistributes phosphatidylserines , the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "nuclear", "staining", "viral", "transmission", "and", "infection", "gene", "regulation", "microbiology", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "specimen", "preparation", "and", "treatmen...	2018	Herpes simplex viruses activate phospholipid scramblase to redistribute phosphatidylserines and Akt to the outer leaflet of the plasma membrane and promote viral entry
If insufficiently treated , Lyme borreliosis can evolve into an inflammatory disorder affecting skin , joints , and the CNS . Early innate immunity may determine host responses targeting infection . Thus , we sought to characterize the immediate cytokine storm associated with exposure of PBMC to moderate levels of live...	Lyme borreliosis displays multifaceted clinical manifestations caused by the Borrelia burgdorferi sensu lato complex . If insufficiently treated , infection may proceed to inflammatory complications of chronic infection . Th17-like cytokines , foremost IL-17 and IL-22 , are crucial for host defense against extracellula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "microbiology/innate", "immunity", "immunology/immune", "response", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections" ]	2010	Early Production of IL-22 but Not IL-17 by Peripheral Blood Mononuclear Cells Exposed to live Borrelia burgdorferi: The Role of Monocytes and Interleukin-1
Live-cell imaging by light microscopy has demonstrated that all cells are spatially and temporally organized . Quantitative , computational image analysis is an important part of cellular imaging , providing both enriched information about individual cell properties and the ability to analyze large datasets . However ,...	Recent studies have shown that all cells , including bacteria , are highly spatially organized . However , many questions about bacterial organization remain unanswered , often due to difficulties associated with visualizing and analyzing structures within such small and variably shaped cells . We have overcome these l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "computational", "biology" ]	2008	PSICIC: Noise and Asymmetry in Bacterial Division Revealed by Computational Image Analysis at Sub-Pixel Resolution
Plants recognize pathogen-associated molecular patterns ( PAMPs ) via cell surface-localized pattern recognition receptors ( PRRs ) , leading to PRR-triggered immunity ( PTI ) . The Arabidopsis cytoplasmic kinase BIK1 is a downstream substrate of several PRR complexes . How plant PTI is negatively regulated is not full...	Plants use immune receptors at the cell surface to perceive microbial molecules and initiate a broad-spectrum defence response against pathogens . However , the induction and amplitude of immune signalling must be tightly regulated . Immune responses are triggered by ligand binding to a cognate receptor , which is pres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "enzymes", "brassica", "enzymology", "phosphatases", "immune", "receptor", "signaling", "membrane", "proteins", "model", "organisms", "immunoprecipitation", "membrane", "receptor", "signaling", "molecular", "biology", "techniques", "co-immunoprecipitation", ...	2016	The Arabidopsis Protein Phosphatase PP2C38 Negatively Regulates the Central Immune Kinase BIK1
TORC1 is a central regulator of cell growth in response to amino acid availability , yet little is known about how it is regulated . Here , we performed a reverse genetic screen in yeast for genes necessary to inactivate TORC1 . The screen consisted of monitoring the expression of a TORC1 sensitive GFP-based transcript...	Before a eukaryotic cell commits to cell division it must be large enough so that both daughter cells would be of viable size . The control of cell size is largely mediated by nutritional input signals via an evolutionarily conserved protein complex termed TORC1 . In particular , TORC1 has been shown to sense the level...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "cell", "biology/cell", "signaling", "genetics", "and", "genomics/functional", "genomics", "cell", "biology/cell", "growth", "and", "division", "biochemistry/chemical", "biology", "of", "the", "cell", "biochemistry/cell", "...	2009	A Genome-Wide Screen for Regulators of TORC1 in Response to Amino Acid Starvation Reveals a Conserved Npr2/3 Complex
Fluctuations in the copy number of key regulatory macromolecules ( “noise” ) may cause physiological heterogeneity in populations of ( isogenic ) cells . The kinetics of processes and their wiring in molecular networks can modulate this molecular noise . Here we present a theoretical framework to study the principles o...	Within cells , fluctuations in molecule numbers are inevitable , since the synthesis and degradation of molecules are not synchronised . Such molecular noise can be transferred to other molecules through regulatory interactions . Noise in molecular networks , and especially in gene expression , has been studied extensi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/transcriptional", "regulation", "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology", "computational", "biology/signaling", "networks" ]	2009	Noise Management by Molecular Networks
Poliovirus is an enteric virus that rarely invades the human central nervous system ( CNS ) . To identify barriers limiting poliovirus spread from the periphery to CNS , we monitored trafficking of 10 marked viruses . After oral inoculation of susceptible mice , poliovirus was present in peripheral neurons , including ...	Neurotropic viruses , including herpesviruses , rabies virus , and poliovirus , initiate infection in the periphery and can move through peripheral neurons to reach the central nervous system ( CNS ) . Since peripheral neurons can be up to one meter long , inefficient neural transport could dramatically affect pathogen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "virology/virulence", "factors", "and", "mechanisms", "virology/viral", "replication", "and", "gene", "regulation", "microbiology/innate", "immunity", "virology/animal", "models", "of", "infe...	2010	Limited Trafficking of a Neurotropic Virus Through Inefficient Retrograde Axonal Transport and the Type I Interferon Response
Melioidosis is a serious infectious disease caused by the Category B select agent and environmental saprophyte , Burkholderia pseudomallei . Most cases of naturally acquired infection are assumed to result from skin inoculation after exposure to soil or water . The aim of this study was to provide evidence for inoculat...	Melioidosis is a serious infectious disease caused by the environmental saprophyte , Burkholderia pseudomallei . The infection is potentially preventable , but developing prevention guidelines is hampered by a lack of evidence on which to base them . The purpose of this study was to provide evidence for inoculation , i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "melioidosis" ]	2013	Activities of Daily Living Associated with Acquisition of Melioidosis in Northeast Thailand: A Matched Case-Control Study
Chagas disease , caused by the protozoan parasite Trypanosoma cruzi , represents a very important public health problem in Latin America where it is endemic . Although mostly asymptomatic at its initial stage , after the disease becomes chronic , about a third of the infected patients progress to a potentially fatal ou...	Chagas disease is a zoonosis caused by the protozoan parasite Trypanosoma cruzi . Endemic to Central and South America , it affects over 10 million people and many more live in risk transmission areas . Although mostly asymptomatic at its initial acute stage in humans , damages can occur over the years in many tissues ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Automated High-Content Assay for Compounds Selectively Toxic to Trypanosoma cruzi in a Myoblastic Cell Line
The Structural Maintenance of Chromosome ( SMC ) complex , termed cohesin , is essential for sister chromatid cohesion . Cohesin is also important for chromosome condensation , DNA repair , and gene expression . Cohesin is comprised of Scc3 , Mcd1 , Smc1 , and Smc3 . Scc3 also binds Pds5 and Wpl1 , cohesin-associated p...	Cohesin is a four-subunit complex that tethers distinct regions of chromatin either intra- or inter-molecularly . Cohesin is essential for mediating proper chromosome structure and dynamics and to maintain genome stability . In humans , mutations in cohesin are associated with several developmental disorders and cancer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Conserved Domain in the Scc3 Subunit of Cohesin Mediates the Interaction with Both Mcd1 and the Cohesin Loader Complex
The Rif1 protein is a negative regulator of DNA replication initiation in eukaryotes . Here we show that budding yeast Rif1 inhibits DNA replication initiation at the rDNA locus . Absence of Rif1 , or disruption of its interaction with PP1/Glc7 phosphatase , leads to more intensive rDNA replication . The effect of Rif1...	Rif1 is a conserved eukaryotic protein implicated in regulation of both the temporal pattern of DNA replication initiation and the DNA damage response ( DDR ) . We found that in budding yeast several of Rif1’s DDR-related phenotypes stem from its ability to interact with the Glc7/PP1 phosphatase and inhibit DNA replica...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "networks", "chromosome", "structure", "and", "function", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "damage", "telomeres", "fungi", "model", "organisms", "dna", "replication", "network", "analysis", "genome", "analysis", "pro...	2016	Budding Yeast Rif1 Controls Genome Integrity by Inhibiting rDNA Replication
Identifying the targets of broadly neutralizing antibodies to HIV-1 and understanding how these antibodies develop remain important goals in the quest to rationally develop an HIV-1 vaccine . We previously identified a participant in the CAPRISA Acute Infection Cohort ( CAP257 ) whose plasma neutralized 84% of heterolo...	Four sites of vulnerability for broadly neutralizing antibodies to HIV-1 have been identified thus far . How these broadly reactive antibodies arise , and the host-pathogen interactions that drive the affinity maturation necessary for neutralization breadth are poorly understood . This study details the sequential deve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Viral Escape from HIV-1 Neutralizing Antibodies Drives Increased Plasma Neutralization Breadth through Sequential Recognition of Multiple Epitopes and Immunotypes
Recurrent networks of non-linear units display a variety of dynamical regimes depending on the structure of their synaptic connectivity . A particularly remarkable phenomenon is the appearance of strongly fluctuating , chaotic activity in networks of deterministic , but randomly connected rate units . How this type of ...	Electrophysiological recordings from cortical circuits reveal strongly irregular and highly complex temporal patterns of in-vivo neural activity . In the last decades , a large number of theoretical studies have speculated on the possible sources of fluctuations in neural assemblies , pointing out the possibility of se...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "electrophysiology", "neuroscience", "systems", "science", "mathematics", "algebra", "white", "noise...	2017	Intrinsically-generated fluctuating activity in excitatory-inhibitory networks
Bacillus anthracis and Yersinia pestis are zoonotic bacteria capable of causing severe and sometimes fatal infections in animals and humans . Although considered as diseases of antiquity in industrialized countries due to animal and public health improvements , they remain endemic in vast regions of the world dispropor...	Anthrax and plague are ancient infectious diseases that continue to affect people living in poor , endemic regions and to threaten industrialized nations due to their potential use in biowarfare . Candidate vaccines need improvement to minimize non-desirable effects and increase their efficacy . The purpose of this wor...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "bacillus", "microbiology", "vaccines", "bacterial", "diseases", "yersinia", "infectious", "disease", ...	2019	Development of a multiple-antigen protein fusion vaccine candidate that confers protection against Bacillus anthracis and Yersinia pestis
The detailed knowledge of C . elegans connectome for 3 decades has not contributed dramatically to our understanding of worm’s behavior . One of main reasons for this situation has been the lack of data on the type of synaptic signaling between particular neurons in the worm’s connectome . The aim of this study was to ...	Neural connectomes , i . e . neural connectivity maps , are important for understanding the design principles of nervous systems . However , they are not sufficient for understanding network dynamics , which in turn are related to animal’s behavior . To understand behavior , we need additionally to know the type of sig...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "caenorhabditis", "nervous", "system", "electrical", "circuits", "electrophysiology", "neuroscience", "animals", "biological", "locomotion", "motor", "neurons", "animal", "models",...	2017	Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost
Emerging B . cereus strains that cause anthrax-like disease have been isolated in Cameroon ( CA strain ) and Côte d’Ivoire ( CI strain ) . These strains are unusual , because their genomic characterisation shows that they belong to the B . cereus species , although they harbour two plasmids , pBCXO1 and pBCXO2 , that a...	Anthrax is caused by the bacterium Bacillus anthracis that affects all mammals worldwide . It emerged more than 10 , 000 years ago from a Bacillus cereus precursor . In the past decade , B . cereus bacteria were isolated in the USA from anthrax-like pneumonia cases . They harbour one virulence plasmid very similar to t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Capsules, Toxins and AtxA as Virulence Factors of Emerging Bacillus cereus Biovar anthracis
Interruptions of microsatellite sequences impact genome evolution and can alter disease manifestation . However , human polymorphism levels at interrupted microsatellites ( iMSs ) are not known at a genome-wide scale , and the pathways for gaining interruptions are poorly understood . Using the 1000 Genomes Phase-1 var...	Microsatellites are short tandem repeat DNA sequences located throughout the human genome that display a high degree of inter-individual variation . This characteristic makes microsatellites an attractive tool for population genetics and forensics research . Some microsatellites affect gene expression , and mutations w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "genetic", "dominance", "population", "genetics", "cancer", "risk", "factors", "oncology", "genome", "sequencing", "mutation", "dna", "replication", "dna", "molecular", "biology", "techniques", "autoso...	2014	Microsatellite Interruptions Stabilize Primate Genomes and Exist as Population-Specific Single Nucleotide Polymorphisms within Individual Human Genomes
The objective of this study is to report the costs of Chagas disease in Colombia , in terms of vector disease control programmes and the costs of providing care to chronic Chagas disease patients with cardiomyopathy . Data were collected from Colombia in 2004 . A retrospective review of costs for vector control program...	Chagas disease is one of the most important vector-transmitted diseases in Latin America . Many patients with Chagas go undiagnosed for years , and because symptoms of the chronic condition are similar to those of other cardiac conditions , the burden of the disease is not evident . This leads to underestimation of the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "evidence-based", "healthcare/health", "services", "research", "and", "economics", "non-clinical", "medicine/health", "economics", "public", "health", "and", "epidemiology/health", "services", "research", "and", "economics" ]	2008	The Costs of Preventing and Treating Chagas Disease in Colombia
The Drosophila embryo proceeds through thirteen mitotic divisions as a syncytium . Its nuclei distribute in the embryo's interior during the first six divisions , dividing synchronously with a cycle time of less than ten minutes . After seven divisions ( nuclear cycle 8 ) , the syncytial blastoderm forms as the nuclei ...	Genetic studies identified many genes that are required during Drosophila oogenesis to endow the embryo with structures and components it will need to develop; they have also identified many genes that the embryo must express . However , measures of transcription have detected zygotic transcripts only after seven nucle...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "organism", "development", "genetics", "biology", "pattern", "formation" ]	2013	An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo
Gene expression is regulated by the complex interaction between transcriptional activators and repressors , which function in part by recruiting histone-modifying enzymes to control accessibility of DNA to RNA polymerase . The evolutionarily conserved family of Groucho/Transducin-Like Enhancer of split ( Gro/TLE ) prot...	Repression by transcription factors plays a central role in gene regulation . The Groucho/Transducin-Like Enhancer of split ( Gro/TLE ) family of co-repressors interacts with many different transcription factors and has many essential roles during animal development . Groucho/TLE proteins form oligomers that are necess...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "genome", "expression", "analysis", "invertebrates", "gene", "regulation", "dna-binding", "proteins", "animals", "next-generation", "sequencing", "genome", "analysis", "transcription", "factors", "molecular", "biology", "techniques", "drosophila", ...	2014	The Groucho Co-repressor Is Primarily Recruited to Local Target Sites in Active Chromatin to Attenuate Transcription
The telomere-ending binding protein complex CST ( Cdc13-Stn1-Ten1 ) mediates critical functions in both telomere protection and replication . We devised a co-expression and affinity purification strategy for isolating large quantities of the complete Candida glabrata CST complex . The complex was found to exhibit a 2∶4...	Telomeres are the special structures that protect the chromosomal ends against aberrant rearrangements . The most distal portion of a telomere is bound by the CST ( Cdc13-Stn1-Ten1 ) complex , which is critical for telomere protection . By preparing and analyzing large quantities of the CST complex derived from a fungu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "biophysics", "genetics", "and", "genomics" ]	2013	The Telomere Capping Complex CST Has an Unusual Stoichiometry, Makes Multipartite Interaction with G-Tails, and Unfolds Higher-Order G-Tail Structures
B-cell activation yields abundant cell death in parallel to clonal amplification and remodeling of immunoglobulin ( Ig ) genes by activation-induced deaminase ( AID ) . AID promotes affinity maturation of Ig variable regions and class switch recombination ( CSR ) in mature B lymphocytes . In the IgH locus , these proce...	Class switch recombination , initiated by the activation-induced deaminase enzyme rearranges immunoglobulin ( Ig ) genes in order to replace expression of IgM by IgG , IgA or IgE . A variant form of this event , locus suicide recombination ( LSR ) , was previously reported in mouse B-lymphocytes and simply deletes all ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "cell", "differentiation", "throat", "developmental", "biology", "molecular", "biology", "techniques", "memory", "b", "cells", "research", "and", "analysis", "methods", "white"...	2019	Locus suicide recombination actively occurs on the functionally rearranged IgH allele in B-cells from inflamed human lymphoid tissues
There are two major pathways leading to induction of NF-κB subunits . The classical ( or canonical ) pathway typically leads to the induction of RelA or c-Rel containing complexes , and involves the degradation of IκBα in a manner dependent on IκB kinase ( IKK ) β and the IKK regulatory subunit NEMO . The alternative (...	Although the classical NF-κB pathway is frequently associated with the induction of cellular senescence and the senescence associated secretory phenotype ( SASP ) , the role of the alternative NF-κB pathway , which is frequently activated in hematological malignancies as well as some solid tumors , has not been defined...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "biochemistry", "medicine", "and", "health", "sciences", "cell", "biology", "biology", "and", "life", "sciences", "molecular", "biology" ]	2014	Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence
Cystic hydatid disease ( CHD ) is a global parasitic zoonosis caused by the dog tapeworm , Echinococcus granulosus . The disease is hyperendemic in western China because of poor economic development; limited community knowledge of CHD; widespread , small-scale household animal production; home killing of livestock; and...	Cystic hydatid disease ( CHD ) , caused by the dog tapeworm , Echinococcus granulosus , is hyperendemic in western China . However , until recently the disease had been grossly neglected there due primarily to a weak economy and the primitive control measures used . The situation is now changing because of China's grow...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	A Pilot Study for Control of Hyperendemic Cystic Hydatid Disease in China
Flexibility in biomolecular recognition is essential and critical for many cellular activities . Flexible recognition often leads to moderate affinity but high specificity , in contradiction with the conventional wisdom that high affinity and high specificity are coupled . Furthermore , quantitative understanding of th...	Flexibility in biomolecular recognition is crucial for the function . Flexibility often leads to moderate binding affinity but high binding specificity , challenging the conventional wisdom that high specificity is guaranteed by high affinity . Currently , understanding of the relationship between affinity and specific...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "dimers", "(chemical", "physics)", "biochemistry", "protein-protein", "interactions", "protein", "interactions", "molecular", "dynamics", "proteins", "chemical", "physics", "biophysics", "theory", "biology", "and", "life", "sciences", "chemistry", "physical", "...	2014	Specificity and Affinity Quantification of Flexible Recognition from Underlying Energy Landscape Topography
Recombination is one of the main forces shaping genome diversity , but the information it generates is often overlooked . A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations . Just like mutations , these junctions carry evidence of the shared pas...	Recombination brings together DNA sequences that can be very distantly related , and , thus , quite different from each other . This is often cited as a main hurdle for using recombining regions ( that is , most of the genome ) to reconstruct sequence phylogeny . We have turned this argument around: chromosomes carryin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genome", "projects", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/population", "genetics" ]	2010	A New Method to Reconstruct Recombination Events at a Genomic Scale
Mass drug administration ( MDA ) for lymphatic filariasis ( LF ) programs has delivered more than 2 billion treatments of albendazole , in combination with either ivermectin or diethylcarbamazine , to communities co-endemic for soil-transmitted helminthiasis ( STH ) , reducing the prevalence of both diseases . A transm...	Since 2000 , some 2 billion preventive chemotherapy treatments have been delivered for lymphatic filariasis ( LF ) , many in areas co-endemic for soil-transmitted helminthiasis ( STH ) . A transmission assessment survey ( TAS ) is recommended to determine if such ‘mass drug administration ( MDA ) ’ for LF can be stoppe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "soil-transmitted", "helminths", "global", "health", "neglected", "tropical", "diseases", "lymphatic", "filariasis" ]	2014	Pilot Assessment of Soil-Transmitted Helminthiasis in the Context of Transmission Assessment Surveys for Lymphatic Filariasis in Benin and Tonga
During organogenesis , PAX6 is required for establishment of various progenitor subtypes within the central nervous system , eye and pancreas . PAX6 expression is maintained in a variety of cell types within each organ , although its role in each lineage and how it acquires cell-specific activity remain elusive . Herei...	It is currently poorly understood how a single developmental transcription regulator controls early specification as well as a broad range of highly specialized differentiation schemes . PAX6 is one of the most extensively investigated factors in central nervous system development , yet its role in execution of lineage...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "systems", "biology", "biochemistry", "developmental", "biology", "model", "organisms", "cell", "biology", "evolutionary", "biology", "genetics", "biology", "and", "life", "sciences", "molecular", "cell", "biology", "research", "and", "analysis", "methods" ]	2014	PAX6 Regulates Melanogenesis in the Retinal Pigmented Epithelium through Feed-Forward Regulatory Interactions with MITF
CtIP plays an important role in homologous recombination ( HR ) –mediated DNA double-stranded break ( DSB ) repair and interacts with Nbs1 and BRCA1 , which are linked to Nijmegen breakage syndrome ( NBS ) and familial breast cancer , respectively . We identified new CDK phosphorylation sites on CtIP and found that pho...	DNA double-strand break ( DSB ) repair plays a critical role in the maintenance of genome stability , and mutations in key regulators in the DSB repair pathway are often associated with cancers and human diseases exhibiting chromosomal aberrations . CtIP is an essential DNA repair factor participating in homologous rec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "stress", "responses", "molecular", "cell", "biology", "cell", "biology", "nucleic", "acids", "genetics", "dna", "biology", "dna", "repair", "molecular", "biology", "genetics", "and", "genomics", "gene", "function" ]	2013	The Interaction of CtIP and Nbs1 Connects CDK and ATM to Regulate HR–Mediated Double-Strand Break Repair

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