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Prediction and control of the spread of infectious disease in human populations benefits greatly from our growing capacity to quantify human movement behavior . Here we develop a mathematical model for non-transmissible infections contracted from a localized environmental source , informed by a detailed description of ...	Public health strategies for infectious disease control can benefit greatly from our growing capacity to predict human movement behaviour . This is facilitated by modern methods of electronic data generation and storage that allow us to track detailed human movement patterns . Here we develop a mathematical model of th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "epidemiology", "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences", "computational", "biology" ]	2014	Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set
Leptospirosis is considered underdiagnosed because of its nonspecific presentation and lack of proper understanding of its epidemiology . Early diagnosis and treatment are crucial . However , few data are available on confirmed leptospirosis cases in children in industrialized countries . We therefore aimed to describe...	Leptospirosis is a bacterial disease that affects humans and animals . It is caused by Leptospira . Leptospira is a spiral-shaped Gram-negative spirochete with internal flagella , which enters the host through mucosa and broken skin . Leptospirosis is a worldwide zoonosis , but it is considered underdiagnosed because o...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "japan", "pathogens", "tropical", "diseases", "geographical", "locations", "microbiology", "pediatrics", "bacterial", "diseases", "age", "groups", "signs", "...	2018	Childhood leptospirosis in an industrialized country: Population-based study in Okinawa, Japan
Trypanosoma brucei ( T . b . ) rhodesiense is the cause of the acute form of human African trypanosomiasis ( HAT ) in eastern and southern African countries . There is some evidence that there is diversity in the disease progression of T . b . rhodesiense in different countries . HAT in Malawi is associated with a chro...	Though some work has been done on the genetics of trypanosome infections in animals , relatively little is known about the genetics of human African trypanosomiasis ( HAT ) infections . To test whether any variants are associated with reduced or increased risk of trypanosomiasis , 96 variants in 17 genes were genotyped...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "african", "trypanosomiasis", "variant", "genotypes", "tropical", "diseases", "geographical", "locations", "uganda", "parasitic", "diseases", "parasitic", "protozoans", "malawi", "genetic", "mapping", "trypanosoma", "brucei", "prot...	2019	Association of APOL1 renal disease risk alleles with Trypanosoma brucei rhodesiense infection outcomes in the northern part of Malawi
The nuclear pore complex ( NPC ) is responsible for nucleocytoplasmic transport and constitutes a hub for control of gene expression . The components of NPCs from several eukaryotic lineages have been determined , but only the yeast and vertebrate NPCs have been extensively characterized at the quaternary level . Signi...	Much of the core architecture of the eukaryotic cell was established over one billion years ago . Significantly , many cellular systems possess lineage-specific features , and architectural and compositional variation of complexes and pathways that are likely keyed to specific functional adaptations . The nuclear pore ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "organismal", "evolution", "vertebrates", "animals", "membrane", "proteins", "fungi", "phylogenetic", "analysis", "fungal", "evolution", "eukaryotic", "evolution", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles...	2016	Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex
Entry of hepatitis C virus ( HCV ) into hepatocytes is a complex process that involves numerous cellular factors , including the scavenger receptor class B type 1 ( SR-B1 ) , the tetraspanin CD81 , and the tight junction ( TJ ) proteins claudin-1 ( CLDN1 ) and occludin ( OCLN ) . Despite expression of all known HCV-ent...	Infection with hepatitis C virus ( HCV ) is associated with a high risk of developing hepatocellular carcinoma ( HCC ) . However , it is unknown whether HCV promotes HCC indirectly , through chronic inflammation , fibrosis and liver regeneration , or directly , in a manner similar to other oncogenic viruses . We recent...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "liver", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "hepacivirus", "pathogens", "biological", "cultures", "microbiology", "hepatoma", "cells", "viruses", "rna", "viruses", "immunoprecipitation", "cell", "...	2018	Infection with hepatitis C virus depends on TACSTD2, a regulator of claudin-1 and occludin highly downregulated in hepatocellular carcinoma
Carrion's disease affects small Andean communities in Peru , Colombia and Ecuador and is characterized by two distinct disease manifestations: an abrupt acute bacteraemic illness ( Oroya fever ) and an indolent cutaneous eruptive condition ( verruga Peruana ) . Case fatality rates of untreated acute disease can exceed ...	Carrion's disease is one of the truly neglected tropical diseases . It affects children predominantly in small Andean communities in Peru , Colombia and Ecuador . Case fatality rates of untreated acute disease can exceed 80% during outbreaks . Diagnostic and treatment guidelines are based on very low evidence reports a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bartonella", "medicine", "infectious", "diseases", "neglected", "tropical", "diseases" ]	2012	Bartonella bacilliformis: A Systematic Review of the Literature to Guide the Research Agenda for Elimination
Dengue virus ( DENV ) is primarily vectored by the mosquito Aedes aegypti , and is estimated to cause 390 million human infections annually . A novel method for DENV control involves stable transinfection of Ae . aegypti with the common insect endosymbiont Wolbachia , which mediates an antiviral effect . However , the ...	Dengue virus is transmitted by the mosquito Aedes aegypti and can cause dengue fever and dengue haemorrhagic fever in humans . The World Health Organization currently considers it as the most important mosquito-borne virus globally . One method to control dengue infection of Ae . aegypti is to infect the mosquito with ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "microbiome", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "enterobacter", "infections", "animals", "wolbachia", "viruses", "bacterial", "...	2017	The microbiome composition of Aedes aegypti is not critical for Wolbachia-mediated inhibition of dengue virus
Pulmonary epithelial cell responses can enhance type 2 immunity and contribute to control of nematode infections . An important epithelial product is the collectin Surfactant Protein D ( SP-D ) . We found that SP-D concentrations increased in the lung following Nippostrongylus brasiliensis infection; this increase was ...	Infections by parasitic worms are very common , and controlling them is a major medical and veterinary challenge . Very few drugs exist to treat them , and the parasites can develop resistance to these . In order to find new ways to control worm infections , understanding how our immune system responds to them is essen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immunology", "cell-mediated", "immunity", "parasitic", "diseases", "infectious", "disease", "immunology", "clinica...	2016	Surfactant Protein-D Is Essential for Immunity to Helminth Infection
Flaviviruses cause a wide range of severe diseases ranging from encephalitis to hemorrhagic fever . Discovery of host factors that regulate the fate of flaviviruses in infected cells could provide insight into the molecular mechanisms of infection and therefore facilitate the development of anti-flaviviral drugs . We p...	The Flavivirus genus includes several emergent and reemergent viruses , such as dengue and yellow fever viruses , which cause severe diseases in humans for which there is no approved treatment . Flaviviruses are transmitted to humans by arthropods and they rely on scores of vertebrate and invertebrate factors to replic...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology", "biology", "microbiology" ]	2012	G Protein-Coupled Receptor Kinase 2 Promotes Flaviviridae Entry and Replication
In human crowds as well as in many animal societies , local interactions among individuals often give rise to self-organized collective organizations that offer functional benefits to the group . For instance , flows of pedestrians moving in opposite directions spontaneously segregate into lanes of uniform walking dire...	A crowd of pedestrians is a complex system that exhibits a rich variety of self-organized collective behaviours . For instance , when two flows of people are walking in opposite directions in a crowded street , pedestrians spontaneously share the available space by forming lanes of uniform walking directions . This “pe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "social", "and", "behavioral", "sciences", "biology", "computational", "biology" ]	2012	Traffic Instabilities in Self-Organized Pedestrian Crowds
Typical enteropathogenic Escherichia coli ( tEPEC ) strains were associated with mortality in the Global Enteric Multicenter Study ( GEMS ) . Genetic differences in tEPEC strains could underlie some of the variability in clinical outcome . We produced draft genome sequences of all available tEPEC strains from GEMS leth...	Typical enteropathogenic E . coli ( tEPEC ) strains are associated with high mortality among infants with moderate-to-severe diarrhea , but most infants infected with tEPEC strains survive , and some have no symptoms . To investigate the bacterial factors associated with severe outcome , we determined the genomic seque...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Bacterial Factors Associated with Lethal Outcome of Enteropathogenic Escherichia coli Infection: Genomic Case-Control Studies
Ivermectin ( IVM ) has been used in Ghana for over two decades for onchocerciasis control . In recent years there have been reports of persistent microfilaridermias despite multiple treatments . This has necessitated a reexamination of its microfilaricidal and suppressive effects on reproduction in the adult female Onc...	Onchocerciasis , commonly known as river blindness , is caused by the filarial nematode Onchocerca volvulus and is transmitted by a blackfly vector . Over 37 million people are thought to be infected , with over 90 million at risk . Infection predominantly occurs in sub-Saharan Africa . Foci also exist in the Arabian P...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases", "infectious", "diseases/antimicrobials", "and", "drug", "resistance", "infectious", "diseases/neglected", "tropical", "diseases" ]	2011	Phenotypic Evidence of Emerging Ivermectin Resistance in Onchocerca volvulus
In contrast to most RNA viruses , influenza viruses replicate their genome in the nucleus of infected cells . As a result , newly-synthesized vRNA genomes , in the form of viral ribonucleoprotein complexes ( vRNPs ) , must be exported to the cytoplasm for productive infection . To characterize the composition of vRNP e...	Influenza viruses replicate their single-stranded RNA genomes in the nucleus of infected cells . Since new virus particles are formed at the plasma membrane , these genomes must be exported in the form of a viral ribonucleoprotein complex ( vRNP ) from the nucleus to the cytoplasm at a late point during infection . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "viral", "classification", "microbiology", "rna", "viruses", "emerging", "infectious", "diseases", "cell", "nucleus", "viral", "nucleic", "acid", "biology", "viral", "packaging", "viral", "replication", "complex", "viral", "replication", "cell"...	2011	Influenza Virus Ribonucleoprotein Complexes Gain Preferential Access to Cellular Export Machinery through Chromatin Targeting
The molecular mechanisms of plant recognition , colonization , and nutrient exchange between diazotrophic endophytes and plants are scarcely known . Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane . The genome of H . seropedicae str...	In this work we describe the genome of H . seropedicae SmR1 , a bacterium capable of fixing nitrogen and promoting the growth of important plant crops such as maize , rice , and sugar cane . Several investigations have shown that H . seropedicae supplies fixed nitrogen to the associated plant and increases grain produc...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "genome", "sequencing", "bacterial", "physiology", "microbial", "metabolism", "microbial", "physiology", "biology", "genomics", "microbiology", "bacterial", "biochemistry", "genetics", "and", "genomics" ]	2011	Genome of Herbaspirillum seropedicae Strain SmR1, a Specialized Diazotrophic Endophyte of Tropical Grasses
Hepatitis C is a pandemic human RNA virus , which commonly causes chronic infection and liver disease . The characterization of viral populations that successfully initiate infection , and also those that drive progression to chronicity is instrumental for understanding pathogenesis and vaccine design . A comprehensive...	Primary hepatitis C ( HCV ) infection is typically asymptomatic and commonly results in persistent infection . The characteristics of early infection remain undefined . Four subjects were studied longitudinally from within a few weeks of transmission until resolution of outcome , via a full genome analysis of viral evo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "transmission", "and", "infection", "microbiology", "host-pathogen", "interaction", "mutation", "hepatitis", "hepatitis", "c", "sequence", "analysis", "infectious", "diseases", "biology", "pathogenesis", "viral", "evolution", "genetic", "drift", "natu...	2011	Sequential Bottlenecks Drive Viral Evolution in Early Acute Hepatitis C Virus Infection
Adult humans possess a sophisticated repertoire of mathematical faculties . Many of these capacities are rooted in symbolic language and are therefore unlikely to be shared with nonhuman animals . However , a subset of these skills is shared with other animals , and this set is considered a cognitive vestige of our com...	Adult humans possess mathematical abilities that are unmatched by any other member of the animal kingdom . Yet , there is increasing evidence that the ability to enumerate sets of objects nonverbally is a capacity that humans share with other animal species . That is , like humans , nonhuman animals possess the ability...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "evolutionary", "biology" ]	2007	Basic Math in Monkeys and College Students
Cell entry of many enveloped viruses occurs by engagement with cellular receptors , followed by internalization into endocytic compartments and pH-induced membrane fusion . A previously unnoticed step of receptor switching was found to be critical during cell entry of two devastating human pathogens: Ebola and Lassa vi...	To infect , enveloped viruses need to fuse their membrane with the host membrane . Fusion is mediated by special glycoprotein machineries that must be triggered only at the right time and at the right place . A major cue that viruses utilize for triggering is acidic pH . Until recently , such pH-induced triggering was ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "chemical", "characterization", "crystal", "structure", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "co...	2017	Mapping of the Lassa virus LAMP1 binding site reveals unique determinants not shared by other old world arenaviruses
With the rapidly increasing volume of deep sequencing data , more efficient algorithms and data structures are needed . Minimizers are a central recent paradigm that has improved various sequence analysis tasks , including hashing for faster read overlap detection , sparse suffix arrays for creating smaller indexes , a...	High-throughput sequencing data has been accumulating at an extreme pace . The need to efficiently analyze and process it has become a critical challenge of the field . Many of the data structures and algorithms for this task rely on k-mer sets ( DNA words of length k ) to represent the sequences in a dataset . The run...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "bacteriology", "sequencing", "techniques", "applied", "mathematics", "microbiology", "human", "genomics", "invertebrate", "genomics", "simulation", "and", "modeling", "algorithms", "mathematics", "algebra", "bacterial", "genetics", "molecular", "biology", "techniques", "di...	2017	Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing
Buruli ulcer ( BU ) is an extensively damaging skin infection caused by Mycobacterium ulcerans , whose transmission mode is still unknown . The focal distribution of BU and the absence of interpersonal transmission suggest a major role of environmental factors , which remain unidentified . This study provides the first...	Buruli ulcer ( BU ) remains a mysterious disease without efficient prevention since the mode of transmission of its agent , Mycobacterium ulcerans , is still unknown . The disease is highly localised within countries and even at the village scale within endemic regions , but environmental factors explaining this focal ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "disease", "surveillance", "bacterial", "diseases", "infectious", "diseases", "buruli", "ulcer", "plant", "science", "medicine", "and", "health", "sciences", "public", "and", "occupational", "health", "disease", "ecology", "infectious", "disease", "epidemi...	2014	Spatio-temporal Patterns and Landscape-Associated Risk of Buruli Ulcer in Akonolinga, Cameroon
Borrelia hermsii , a causative agent of relapsing fever of humans in western North America , is maintained in enzootic cycles that include small mammals and the tick vector Ornithodoros hermsi . In mammals , the spirochetes repeatedly evade the host’s acquired immune response by undergoing antigenic variation of the va...	Borrelia hermsii , an agent of tick-borne relapsing fever when infecting humans , employs antigenic variation of the variable major proteins ( Vmps ) to escape the host immune response . This mechanism allows the bacteria to persist in the blood of a mammal , which increases their potential for acquisition by their tic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "microbiology" ]	2014	Inactivation of Genes for Antigenic Variation in the Relapsing Fever Spirochete Borrelia hermsii Reduces Infectivity in Mice and Transmission by Ticks
Innate immune sensing of viral infection results in type I interferon ( IFN ) production and inflammasome activation . Type I IFNs , primarily IFN-α and IFN-β , are produced by all cell types upon virus infection and promote an antiviral state in surrounding cells by inducing the expression of IFN-stimulated genes . Ty...	Pathogens are detected by the immune system in multiple ways that initiate responses to control infection . Two systems of first line defense against viruses are 1 ) the production of Type I interferons and 2 ) production of the cytokines IL-1β and IL-18 by the inflammasome . Type I interferons promote an antiviral sta...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "cytokines", "hiv", "immunopathogenesis", "immunology", "microbiology", "liver", "diseases", "immunodeficiency", "viruses", "developmental", "biology", "infectious", "hepatitis", "hep...	2014	HIV and HCV Activate the Inflammasome in Monocytes and Macrophages via Endosomal Toll-Like Receptors without Induction of Type 1 Interferon
Recently identified broadly neutralizing antibodies ( bnAbs ) show great potential for clinical interventions against HIV-1 infection . However , resistant strains may impose substantial challenges . Here , we report on the identification and characterization of a panel of HIV-1 strains with broad and potent resistance...	Recently identified broadly neutralizing antibodies ( bnAbs ) show great potential for clinical interventions against HIV-1 infection . Among the bnAbs isolated to date , those targeting the CD4bs are the most abundant and thoroughly studied as they disrupt the crucial step of viral interaction with the cellular recept...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "binding", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cloning", "retroviruses", "viruses", "immunodeficiency", "viruses", "mutatio...	2019	Broadly resistant HIV-1 against CD4-binding site neutralizing antibodies
Identification of pathways involved in the structural transitions of biomolecular systems is often complicated by the transient nature of the conformations visited across energy barriers and the multiplicity of paths accessible in the multidimensional energy landscape . This task becomes even more challenging in explor...	Most proteins are biomolecular machines . They perform their function by undergoing changes between different structures . Understanding the mechanism of transition between these structures is of major importance to design methods for controlling such transitions , and thereby modulating protein function . Although the...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biophysics/theory", "and", "simulation", "computational", "biology", "computational", "biology/molecular", "dynamics" ]	2009	Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL
Organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions . Cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence , human health , agricultural production and many other biological ...	The ability to adjust to changing osmotic conditions ( osmoadaptation ) is crucial to the survival of organisms across the tree of life . However , significant gaps still exist in our understanding of this important phenomenon . To help fill some of these gaps , we have produced high-quality draft genomes for 59 osmoad...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "organismal", "evolution", "ecology", "and", "environmental", "sciences", "astrobiology", "archaeal", "physiology", "microbiology", "extremophiles", "archaeal", "evolution", "microbial", "evolution", "microbial", "genomics", "bacterial", "genomics", "microbial...	2014	Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response
Periventricular nodular heterotopia ( PVNH ) is a malformation of cortical development commonly associated with epilepsy . We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci . We first performed a trio-based analysis and identified 219 de novo variants . Although no novel genes we...	Almost 20 years ago the first gene responsible for periventricular nodular heterotopia ( PVNH ) , a disorder that leads to abnormal migration of neurons during fetal brain development , was discovered . Since that time additional genes have been identified , but collectively they only explain a minority of cases . In t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "variant", "genotypes", "alleles", "genetic", "mapping", "genome", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "epilepsy", "bioinformatics", "genetic", "loci", "dna", "sequence", "analysis", "h...	2018	De novo and inherited private variants in MAP1B in periventricular nodular heterotopia
Human parasitic nematodes are the causative agents of lymphatic filariasis ( elephantiasis ) and onchocerciasis ( river blindness ) , diseases that are endemic to more than 80 countries and that consistently rank in the top ten for the highest number of years lived with disability . These filarial nematodes have evolve...	Wuchereria bancrofti , Brugia malayi , Brugia timori , and Onchocerca volvulus are human parasitic nematodes and causative agents of lymphatic filariasis ( LF , elephantiasis ) and onchocerciasis ( river blindness ) . These neglected tropical diseases are ranked in the top ten for the highest years lived with disabilit...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "metabolic", "processes", "ketones", "pathogens", "parasitic", "diseases", "animals", "pyruvate", "glycolysis", "...	2019	Pyruvate produced by Brugia spp. via glycolysis is essential for maintaining the mutualistic association between the parasite and its endosymbiont, Wolbachia
During viral infection , tight regulation of CD8+ T-cell functions determines the outcome of the disease . Recently , others and we determined that the natural killer ( NK ) cells kill hyperproliferative CD8+ T cells in the context of viral infection , but molecules that are involved in shaping the regulatory capabilit...	FcRγ is a signaling molecule for Fc receptors and NK cell killer activating receptor ( KAR ) complex . FcRγ is highly expressed by NK cells and involved in NK cell activity . NK cells are widely defined to regulate the expansion of T cells . Here using chronic LCMV model , we described the role of FcRγ in NK cell media...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "viral", "transmission", "and", "infection", "spleen", "immunology", "microbiology", "cytotoxic", "t", "cells", "antibodies", "research", "and", "analysis", "methods"...	2019	NK cell–intrinsic FcεRIγ limits CD8+ T-cell expansion and thereby turns an acute into a chronic viral infection
In all tetrapods examined thus far , the development and patterning of limbs require the activation of gene members of the HoxD cluster . In mammals , they are regulated by a complex bimodal process that controls first the proximal patterning and then the distal structure . During the shift from the former to the latte...	The shapes of limbs vary greatly among tetrapod species , even between the forelimbs and hindlimbs of the same animal . Hox genes regulate the proper growth and patterning of tetrapod limbs . In order to evaluate whether variations in the complex regulation of a cluster of Hox genes—the Hoxd genes—during limb developme...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "gene", "regulation", "chickens", "vertebrates", "animals", "developmental", "biology", "mammalian", "genomics", "molecular", "biology", "techniques", "rna", "sequencing", "body", "limbs", "research", ...	2018	Similarities and differences in the regulation of HoxD genes during chick and mouse limb development
The type I interferons ( IFN-Is ) are critical not only in early viral control but also in prolonged T-cell immune responses . However , chronic viral infections such as those of human immunodeficiency virus ( HIV ) and hepatitis C virus ( HCV ) in humans and lymphocytic choriomeningitis virus ( LCMV ) in mice overcome...	Chronic viral infections , such as those of human immunodeficiency virus ( HIV ) and hepatitis C virus ( HCV ) in humans , remain serious health problems worldwide , necessitating alternative targets/reagents for better treatment . Although the production of and/or response to type I interferon ( IFN-I ) , a critical a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "adaptive", "immunity", "immune", "cells", "viral", "immune", "evasion", "immunity", "viral", "persistence", "and", "latency", "virology", "innate", "immunity", "antigen-presenting", "cells", "t", "cells", "immunology", "immune", "suppression", "biology", "immune", "t...	2013	Negative Regulation of Type I IFN Expression by OASL1 Permits Chronic Viral Infection and CD8+ T-Cell Exhaustion
The fidelity of epigenetic inheritance or , the precision by which epigenetic information is passed along , is an essential parameter for measuring the effectiveness of the process . How the precision of the process is achieved or modulated , however , remains largely elusive . We have performed quantitative measuremen...	In this study , we found replication stresses reduce the fidelity of nucleosome-mediated epigenetic inheritance . Using Position Effect Variegation ( PEV ) in centromere as an indicator of chromatin epigenetic stability , we quantified the precision of nucleosomal inheritance and found replication stresses reduce the f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "dna", "replication", "epigenetics", "dna", "synthesis", "phase", "chromatin", "heterochromatin", "chromosome", "biology", "proteins", "gene", "expression", "histones", "genetic"...	2017	Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance
Lowered insulin/insulin-like growth factor ( IGF ) signaling ( IIS ) can extend healthy lifespan in worms , flies , and mice , but it can also have adverse effects ( the “insulin paradox” ) . Chronic , moderately lowered IIS rescues age-related decline in neurotransmission through the Drosophila giant fiber system ( GF...	Insulin and insulin-like growth factors play an important role in the nervous system development and function . Reduced insulin signaling , however , can improve symptoms of neurodegenerative diseases in different model organisms and protect against age-associated decline in neuronal function extending lifespan . Here ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "nervous", "system", "junctional", "complexes", "electrophysiology", "neuroscience", "animals", "hormones", "endocrine", "physiology", "animal", "models", "gap", "...	2017	Reduced insulin signaling maintains electrical transmission in a neural circuit in aging flies
Salmonella enterica serovar Typhimurium Sequence Type ( ST ) 313 is a major cause of invasive non-Typhoidal salmonellosis in sub-Saharan Africa . No animal reservoir has been identified , and it has been suggested that ST313 is adapted to humans and transmission may occur via person-to-person spread . Here , we show th...	Salmonella enterica serovar Typhimurium usually causes foodborne diarrheal infections in humans . Recently variants of S . Typhimurium have emerged in Africa associated with invasive and often fatal disease , especially in adults infected by HIV and children with malaria or malnutrition . Analysis of these Sequence Typ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Invasive Non-Typhoidal Salmonella Typhimurium ST313 Are Not Host-Restricted and Have an Invasive Phenotype in Experimentally Infected Chickens
Two-component signal transduction systems enable bacteria to sense and respond to a wide range of environmental stimuli . Sensor histidine kinases transmit signals to their cognate response regulators via phosphorylation . The faithful transmission of information through two-component pathways and the avoidance of unwa...	Maintaining the specificity of signal transduction pathways is critical to the ability of cells to process information , make decisions , and regulate their behavior . Preventing cross-talk often relies predominantly on molecular recognition and a set of specificity-determining residues in cognate proteins . Identifyin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/molecular", "evolution", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "cell", "biology/cell", "signaling", "molecular", "biology/molecular", "evolution", "microbiology...	2010	Systematic Dissection and Trajectory-Scanning Mutagenesis of the Molecular Interface That Ensures Specificity of Two-Component Signaling Pathways
Gut microbiota facilitate many aspects of human health and development , but dysbiotic microbiota can promote hyperplasia and inflammation and contribute to human diseases such as cancer . Human patients infected with the gastric cancer-causing bacterium Helicobacter pylori have altered microbiota; however , whether dy...	Microbial communities in the gut , termed microbiota are important for human health , and when altered can sometimes promote disease . Infections , such as with the cancer-causing bacterium Helicobacter pylori , can cause altered gut microbiota , but why these alterations occur and whether the altered communities contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "gut", "bacteria", "microbiome", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "microbiology", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", ...	2017	The bacterial virulence factor CagA induces microbial dysbiosis that contributes to excessive epithelial cell proliferation in the Drosophila gut
Previous studies have shown maternal , inflammatory , and socioeconomic variables to be associated with growth and neurodevelopment in children from low-income countries . However , these outcomes are multifactorial and work describing which predictors most strongly influence them is lacking . We conducted a longitudin...	Children from low-income settings experience linear growth faltering and neurodevelopmental delay that have been associated with maternal , socioeconomic , and infectious/inflammatory variables . Given the interdependent nature of these associations , understanding which variables are the best predictors of poor outcom...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "social", "sciences", "neuroscience", "reoviruses", "vaccines", "viruses", "age", "groups", "developmental", "biology", "cognitive...	2018	Role of maternal health and infant inflammation in nutritional and neurodevelopmental outcomes of two-year-old Bangladeshi children
A common occurrence in metazoan development is the rise of multiple tissues/organs from a single uniform precursor field . One example is the anterior forebrain of vertebrates , which produces the eyes , hypothalamus , diencephalon , and telencephalon . Another instance is the Drosophila wing disc , which generates the...	A battery of transcription factors collectively called the retinal determination ( RD ) network controls the earliest steps in the specification of the fruit fly compound eye . Loss-of-function mutations lead to the loss of the compound eyes while over-expression of RD network members in non-retinal tissues induces the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "skin", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "integumentary", "system", "engineering", "and", "technology", "light", "microscopy", "cloning", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "...	2018	Allocation of distinct organ fates from a precursor field requires a shift in expression and function of gene regulatory networks
Highly virulent Helicobacter pylori cause proinflammatory signaling inducing the transcriptional activation and secretion of cytokines such as IL-8 in epithelial cells . Responsible in part for this signaling is the cag pathogenicity island ( cagPAI ) that codetermines the risk for pathological sequelae of an H . pylor...	The Cag Type IV secretion system , which contributes to inflammation and cancerogenesis during chronic infection , is one of the major virulence and fitness factors of the bacterial gastric pathogen Helicobacter pylori . Up to now , the mechanisms leading to cagPAI-dependent signal transduction and cytokine secretion w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "cell", "metabolism", "physiological", "processes", "helicobacter", "mole...	2017	Helicobacter pylori modulates host cell responses by CagT4SS-dependent translocation of an intermediate metabolite of LPS inner core heptose biosynthesis
Individuals diagnosed with neurocysticercosis often present with epilepsy and sometimes with progressively worsening severe chronic headaches ( WSCH ) . While cross-sectional associations between seropositivity to cysticercal antigens and epilepsy have been reported , few large scale studies have been conducted in West...	Taenia solium is a parasite that can be transmitted between humans and pigs in areas with poor sanitation and pig management practices . When this parasite infects the human brain , it can cause epilepsy or severe headaches . Our study aimed to measure the association between being seropositive to cysticercal antigens ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "physicians", "medical", "doctors", "pathology", "and", "laboratory", "medicine", "education", "medical", "personnel", "sociology", "tropical", "diseases", "diet", "social", "sciences", "vertebrates", "parasitic", "diseases", "mi...	2019	Estimating the association between being seropositive for cysticercosis and the prevalence of epilepsy and severe chronic headaches in 60 villages of rural Burkina Faso
Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations . An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours...	Understanding the evolution of cooperation is a persistent challenge to evolutionary theorists . A contemporary take on this subject is to model populations with interactions structured as close as possible to actual social networks . These networks are heterogeneous in the number and type of contact each member has . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "game", "theory", "mathematics", "theoretical", "biology", "evolutionary", "modeling", "applied", "mathematics", "biology", "and", "life", "sciences", "physical", "sciences", "evolutionary", "theory", "evolutionary", "biology", "computational", "biology" ]	2014	Evolutionary Game Dynamics in Populations with Heterogenous Structures
Eukaryotic cells have evolved to use complex pathways for DNA damage signaling and repair to maintain genomic integrity . RNF168 is a novel E3 ligase that functions downstream of ATM , γ-H2A . X , MDC1 , and RNF8 . It has been shown to ubiquitylate histone H2A and to facilitate the recruitment of other DNA damage respo...	The repair of DNA damage is fundamental as illustrated by the many human syndromes , immunodeficiencies , and cancers associated with defects in DNA damage signaling and repair . RIDDLE syndrome , caused by mutations of the human RNF168 , is a novel hereditary disease clinically characterized by radiosensitivity , immu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/animal", "genetics" ]	2011	Genomic Instability, Defective Spermatogenesis, Immunodeficiency, and Cancer in a Mouse Model of the RIDDLE Syndrome
During neuronal development , β-actin serves an important role in growth cone mediated axon guidance . Consistent with this notion , in vivo ablation of the β-actin gene leads to abnormalities in the nervous system . However , whether β-actin is involved in the regulation of neuronal gene programs is not known . In thi...	Although β-actin plays an important role in growth cone mediated axon guidance in neurons , the potential role of β-actin in controlling neuron differentiation remains unknown . Here , we converted β-actin+/+ WT , β-actin+/- HET and β-actin-/- KO mouse embryonic fibroblast ( MEFs ) into chemically induced neurons ( CiN...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "neuroscience", "fibroblasts", "connective", "tissue", "cells", "genome", "analysis", "epigenetics", "chromatin", "heterochromatin", "genomics", "animal", "cells", "chromosome", "biology", "gene", "expression", "connective", "tissu...	2018	β-actin regulates a heterochromatin landscape essential for optimal induction of neuronal programs during direct reprograming
Noroviruses , an important cause of acute gastroenteritis in humans , recognize the histo-blood group antigens ( HBGAs ) as host susceptible factors in a strain-specific manner . The crystal structures of the HBGA-binding interfaces of two A/B/H-binding noroviruses , the prototype Norwalk virus ( GI . 1 ) and a predomi...	The interactions of noroviruses with histo-blood group antigens ( HBGAs ) are diverse , in which strains in both genogroups I and II ( GI and GII ) recognizing either the secretor or the non-secretor ( Lewis ) HBGAs have been reported . The crystal structures of the HBGA binding interfaces of two secretor binders ( Nor...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "viral", "diseases", "calicivirus", "infection" ]	2011	Crystallography of a Lewis-Binding Norovirus, Elucidation of Strain-Specificity to the Polymorphic Human Histo-Blood Group Antigens
Many organisms divide chromosomes within the confines of the nuclear envelope ( NE ) in a process known as closed mitosis . Thus , they must ensure coordination between segregation of the genetic material and division of the NE itself . Although many years of work have led to a reasonably clear understanding of mitotic...	Chromosomes replicate in the nucleus , which is surrounded by the double-layered nuclear envelope ( NE ) . During so-called open mitosis , the NE breaks down to allow spindle microtubules ( which do the work of pulling the replicated chromosomes apart ) access to the nuclear interior . Alternatively , in closed mitosis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "yeast", "and", "fungi", "eukaryotes" ]	2007	The Spindle Pole Bodies Facilitate Nuclear Envelope Division during Closed Mitosis in Fission Yeast
A multi-mode nonlinear constitutive model for mucus is constructed directly from micro- and macro-rheology experimental data on cell culture mucus , and a numerical algorithm is developed for the culture geometry and idealized cilia driving conditions . This study investigates the roles that mucus rheology , wall effec...	In the lungs , the airway surface liquid protects the airway epithelium from inhaled pathogens and particulates . It is well known that failure to properly clear mucus from the airways leads to chronic , even fatal , lung infections . To date , there is no validated constitutive model capable of recapitulating mucus rh...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "drug", "absorption", "body", "fluids", "classical", "mechanics", "fluid", "mechanics", "biological", "cultures", "cell", "cultures", "damage", "mechanics", "pharmacology", "cellular", "structures", "and", "organelles", "research...	2016	Modeling and Simulation of Mucus Flow in Human Bronchial Epithelial Cell Cultures – Part I: Idealized Axisymmetric Swirling Flow
Case notifications of pertussis have shown an increase in a number of countries with high rates of routine pediatric immunization . This has led to significant public health concerns over a possible pertussis re-emergence . A leading proposed explanation for the observed increase in incidence is the loss of immunity to...	The eradication of vaccine-preventable infectious diseases remains an important public health priority . To achieve this goal , the level of immunity afforded needs to be high and long-lasting . For pertussis , one of the leading causes of mortality in infants , immunity has been shown to wane in some individuals . The...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2009	Estimating the Duration of Pertussis Immunity Using Epidemiological Signatures
We were interested in gaining insight into the functional properties of frontal networks based upon their anatomical inputs . We took a neuroinformatics approach , carrying out maximum likelihood hierarchical cluster analysis on 25 frontal cortical areas based upon their anatomical connections , with 68 input areas rep...	The anatomical input to a cortical area defines , to a large extent , the functions that the area can perform . For example , if an area has no visual inputs , it cannot carry out computations on visual information . Therefore , understanding the inputs to a patch of cortex can provide fundamental insight into the func...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience" ]	2008	The Statistical Neuroanatomy of Frontal Networks in the Macaque
In crowding , perception of an object deteriorates in the presence of nearby elements . Although crowding is a ubiquitous phenomenon , since elements are rarely seen in isolation , to date there exists no consensus on how to model it . Previous experiments showed that the global configuration of the entire stimulus mus...	Visual crowding highlights interactions between elements in the visual field . For example , an object is more difficult to recognize if it is presented in clutter . Crowding is one of the most fundamental aspects of vision , playing crucial roles in object recognition , reading and visual perception in general , and i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "fourier", "analysis", "medicine", "and", "health", "sciences", "neural", "networks", "social", "sciences", "neuroscience", "human", "performance", "vision", "research", "and", "analysis", "methods", "sensory", "physiology", "computer", "and", "information", "sciences",...	2019	Beyond Bouma's window: How to explain global aspects of crowding?
In order to assess whether gene expression variability could be influenced by several SNPs acting in cis , either through additive or more complex haplotype effects , a systematic genome-wide search for cis haplotype expression quantitative trait loci ( eQTL ) was conducted in a sample of 758 individuals , part of the ...	In order to assess whether gene expression variability could be influenced by the presence of more than one cis-acting SNP , we have conducted a systematic genome-wide search for haplotypic cis eQTL effects in a sample of 758 individuals and replicated the findings in an independent sample of 1 , 374 subjects . In both...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "immune", "cells", "population", "genetics", "quantitative", "traits", "immunology", "gene", "expression", "biology", "haplotypes", "monocytes", "heredity", "genetics", "genomics", "genetics", "a...	2013	Genome-Wide Haplotype Analysis of Cis Expression Quantitative Trait Loci in Monocytes
Strongyloides stercoralis infection is a neglected tropical disease which can lead to severe symptoms and even death in immunosuppressed people . Unfortunately , its diagnosis is hampered by the lack of a gold standard , as the sensitivity of traditional parasitological tests ( including microscopic examination of stoo...	Strongyloides stercoralis is a worm that can potentially kill affected immunosuppressed individuals . The parasite is not easily detected with stool microscopy , hence novel tests have been implemented , such as polymerase chain reaction ( PCR ) , that can detect the DNA of the parasite . This work aims at evaluating t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "parasitic", "diseases", "animals", "parasitology", "organisms", "molecular", "biology", "techniques", "strongyloides", "stercoralis", "cellular", "structures", "and", ...	2018	Accuracy of molecular biology techniques for the diagnosis of Strongyloides stercoralis infection—A systematic review and meta-analysis
We investigated the efficacy , safety and cost of lime wash of household walls plus treatment of sand fly breeding places with bleach ( i . e . environmental management or EM ) , insecticide impregnated durable wall lining ( DWL ) , and bed net impregnation with slow release insecticide ( ITN ) for sand fly control in ...	Sand fly control is one of the main priorities of the Visceral Leishmaniasis ( VL ) Elimination Program in Bangladesh , India and Nepal . Currently , indoor residual spraying with insecticides ( IRS ) is the most effective method available for sand fly control . The efficacy of other methods of vector control remains p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "demography", "geographical", "locations", "tropical", "diseases", "india", "sand", "flies", "parasitic", "diseases", "neglected", "tropical", "diseases", "populati...	2016	Efficacy, Safety and Cost of Insecticide Treated Wall Lining, Insecticide Treated Bed Nets and Indoor Wall Wash with Lime for Visceral Leishmaniasis Vector Control in the Indian Sub-continent: A Multi-country Cluster Randomized Controlled Trial
The expression of the human papillomavirus ( HPV ) E6/E7 oncogenes is crucial for HPV-induced malignant cell transformation . The identification of cellular targets attacked by the HPV oncogenes is critical for our understanding of the molecular mechanisms of HPV-associated carcinogenesis and may open novel therapeutic...	Specific types of human papillomaviruses ( HPVs ) are closely linked to the development of malignant tumors , such as cervical cancer . Virtually all cervical cancers contain HPV DNA and the tumorigenic growth behavior of cervical cancer cells is dependent on the activity of two viral oncogenes , called E6 and E7 . It ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "gynecological", "tumors", "viruses", "and", "cancer", "virology", "cervical", "cancer", "biology", "microbiology", "cancers", "and", "neoplasms" ]	2014	Oncogenic Human Papillomaviruses Activate the Tumor-Associated Lens Epithelial-Derived Growth Factor (LEDGF) Gene
Bloodstream form African trypanosomes are thought to rely exclusively upon glycolysis , using glucose as a substrate , for ATP production . Indeed , the pathway has long been considered a potential therapeutic target to tackle the devastating and neglected tropical diseases caused by these parasites . However , plasma ...	Trypanosomes are the etiological agents of human sleeping sickness and animal African trypanosomiases , a range of diseases in cattle , other livestock and horses caused by several Trypanosoma subspecies . The mammalian stage of the parasite circulates in the bloodstream , a nutrient-rich environment with constant temp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "carbohydrate", "metabolism", "chemical", "compounds", "monomers", "metabolic", "processes", "carbohydrates", "glucose", "metabolism", "parasitic", "protozoans", "organic", "compounds", "glucose", "glycolysis", "trypanosoma", "brucei", "protozoans", "molecular", "biology", ...	2018	Gluconeogenesis using glycerol as a substrate in bloodstream-form Trypanosoma brucei
Sexual reproduction in an environmental pathogen helps maximize its lineage fitness to changing environment and the host . For the fungal pathogen Cryptococcus neoformans , sexual reproduction is proposed to have yielded hyper virulent and drug resistant variants . The life cycle of this pathogen commences with mating ...	Sex , despite its cost , is an important means to maximize species fitness in coping with unpredictable environmental challenges . In the human fungal pathogen Cryptococcus neoformans , sexual reproduction has yielded hyper virulent and drug resistant variants , and produces airborne infectious spores . Developmentally...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "mycology", "fungi", "sexual", "differentiation", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "microbial", "growth", "and", "development", "microbiology", "fungal", "reproduction", "morphogenesis", "fungal", "stru...	2014	Morphotype Transition and Sexual Reproduction Are Genetically Associated in a Ubiquitous Environmental Pathogen
The causative agent of Lyme borreliosis , the spirochete Borrelia burgdorferi , has been shown to induce expression of the urokinase receptor ( uPAR ) ; however , the role of uPAR in the immune response against Borrelia has never been investigated . uPAR not only acts as a proteinase receptor , but can also , dependent...	Lyme borreliosis is caused by the spirochete Borrelia burgdorferi and is transmitted through ticks . Since its discovery approximately 30 years ago it has become the most important vector-borne disease in the Western world . The pathogenesis of this complex zoonosis is still not entirely understood . We here demonstrat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections", "cardiovascular", "disorders", "immunology/leukocyte", "activation" ]	2009	The Urokinase Receptor (uPAR) Facilitates Clearance of Borrelia burgdorferi
Sister kinetochores are connected to the same spindle pole during meiosis I and to opposite poles during meiosis II . The molecular mechanisms controlling the distinct behavior of sister kinetochores during the two meiotic divisions are poorly understood . To study kinetochore behavior during meiosis , we have optimize...	For production of oocytes and sperm , cells have to complete meiosis which includes two successive divisions . These divisions convert diploid cells with a maternal and a paternal copy of each chromosome into haploid cells with only one copy of each chromosome . Chromosome copy reduction requires regulation of sister k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "spermatocytes", "anaphase", "chromosome", "structure", "and", "function", "metaphase", "centromeres", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animal...	2018	Dynamics and control of sister kinetochore behavior during the meiotic divisions in Drosophila spermatocytes
Computational studies as well as in vivo and in vitro results have shown that many cortical neurons fire in a highly irregular manner and at low average firing rates . These patterns seem to persist even when highly rhythmic signals are recorded by local field potential electrodes or other methods that quantify the sum...	The gamma rhythm is a prominent , 30–80-Hz EEG signal that is associated with cognition . Several classes of computational models have been posited to explain the gamma rhythm mechanistically . We study a particular class in which the gamma rhythm arises from delayed negative feedback . Our study is unique in that we c...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "neuroscience", "biology", "neuroscience", "neurophysiology" ]	2012	Membrane Properties and the Balance between Excitation and Inhibition Control Gamma-Frequency Oscillations Arising from Feedback Inhibition
Central questions to epigenome evolution include whether interspecies changes of histone modifications are independent of evolutionary changes of DNA , and if there is dependence whether they depend on any specific types of DNA sequence changes . Here , we present a likelihood approach for testing hypotheses on the co-...	Epigenetic modifications play a significant role in gene regulations and thus heavily influence phenotypic outcomes . Whereas cross-species epigenomic comparisons have been fruitful in revealing the function of epigenetic modifications , it still remains unclear how the epigenome changes across species . A central ques...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome", "evolution", "applied", "mathematics", "histone", "modification", "algorithms", "simulation", "and", "modeling", "mathematics", "genetic", "elements", "sequence", "motif", "analysis", "epigenetics", "epigenomics", "chromatin", "research", "and", "analysis", "met...	2018	A likelihood approach to testing hypotheses on the co-evolution of epigenome and genome
Precise control of cell cycle regulators is critical for normal development and tissue homeostasis . E2F transcription factors are activated during G1 to drive the G1-S transition and are then inhibited during S phase by a variety of mechanisms . Here , we genetically manipulate the single Drosophila activator E2F ( E2...	Rapidly growing tissues provide an excellent opportunity to study the careful balance between cell proliferation and apoptosis needed for normal organ structure and function in developing organisms . We present evidence that a transcription factor critical for regulating progression of the Drosophila melanogaster cell ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	S Phase–Coupled E2f1 Destruction Ensures Homeostasis in Proliferating Tissues
Bangladesh had one of the highest burdens of lymphatic filariasis ( LF ) at the start of the Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) with an estimated 70 million people at risk of infection across 34 districts . In total 19 districts required mass drug administration ( MDA ) to interrupt transmissi...	Lymphatic filariasis ( LF ) was highly endemic in Bangladesh at the start of the Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) in 2000 , with approximately 70 million people at risk . To address this burden , the National LF Programme implemented mass drug administration ( MDA ) in 19 highly endemic dist...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "education", "population", "dynamics", "sociology", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "filariasis", "pharmaceutics", "d...	2017	The significant scale up and success of Transmission Assessment Surveys 'TAS' for endgame surveillance of lymphatic filariasis in Bangladesh: One step closer to the elimination goal of 2020
Broadly neutralizing antibodies ( bnAbs ) to HIV-1 can evolve after years of an iterative process of virus escape and antibody adaptation that HIV-1 vaccine design seeks to mimic . To enable this , properties that render HIV-1 envelopes ( Env ) capable of eliciting bnAb responses need to be defined . Here , we followed...	HIV-1 infected individuals rarely develop broadly neutralizing antibodies ( bnAbs ) that inhibit diverse HIV-1 subtypes . As activity against the majority of HIV-1 isolates is necessary for effective immunization against HIV-1 , current vaccine development seeks to generate regimens that evoke bnAb responses . Delineat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "organismal", "evolution", "medicine", "and", "health", "sciences", "luciferase", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "viral", "transmission", "and", "infection", "enzymes", "pathogens", ...	2018	Phenotypic deficits in the HIV-1 envelope are associated with the maturation of a V2-directed broadly neutralizing antibody lineage
The two-component system PhoP-PhoQ is highly conserved in bacteria and regulates virulence in response to various signals for bacteria within the mammalian host . Here , we demonstrate that PhoP could be acetylated by Pat and deacetylated by deacetylase CobB enzymatically in vitro and in vivo in Salmonella Typhimurium ...	Salmonella Typhimurium is a facultative intracellular pathogen capable of survival within host phagocytic cells . The crucial two-component system regulator PhoP-PhoQ is involved in response to different stresses and essential for the virulence of S . Typhimurium . In this study , we show that PhoP can be acetylated by...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "immunology", "microbiology", "organic", "compounds", "dna", "transcription", "animal", "models", "bacterial...	2016	Acetylation of Lysine 201 Inhibits the DNA-Binding Ability of PhoP to Regulate Salmonella Virulence
Temperature potently modulates various physiologic processes including organismal motility , growth rate , reproduction , and ageing . In ectotherms , longevity varies inversely with temperature , with animals living shorter at higher temperatures . Thermal effects on lifespan and other processes are ascribed to passiv...	Temperature is a critical environmental factor that affects ageing in both cold-blooded and warm-blooded species . In invertebrate animals , lifespan varies inversely with temperature , with higher temperature resulting in faster development but shorter lifespan . This phenomenon has been usually attributed to passive ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Co-chaperone p23 Regulates C. elegans Lifespan in Response to Temperature
Endemic mycoses are systemic fungal infections . Histoplasmosis is endemic in all temperate areas of the world; coccidioidomycosis and paracoccidioidomycosis are only present in the American continent . These pathogens are not present in Spain , but in the last years there has been an increase of reported cases due to ...	Histoplasmosis , coccidioidomycosis and paracoccidioidomycosis are infections produced by environmental fungi . Despite the fact that these pathogens are not found in Spain , these diseases are an important health problem in many countries of the world , especially in Latin America . Due to the increased migration from...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "hiv", "infections", "medicine", "and", "health", "sciences", "european", "union", "evolutionary", "biology", "histoplasmosis", "geographical", "locations", "tropical", "diseases", "paracoccidioidomycosis", "neglected", "tropical", "diseases", "fungal", ...	2018	Imported endemic mycoses in Spain: Evolution of hospitalized cases, clinical characteristics and correlation with migratory movements, 1997-2014
Neuronal migration during embryonic development contributes to functional brain circuitry . Many neurons migrate in morphologically distinct stages that coincide with differentiation , requiring tight spatial regulation . It had been proposed that neurotransmitter-mediated activity could exert this control . Here , we ...	Postmitotic neurons migrate from their site of origin to their final destination in the developing brain to form functional structures . These neurons typically follow defined routes through the tissue . Previous studies investigating progress along such route have identified neurotransmitters—chemicals that transmit t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "motility", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "optogenetics", "aliphatic", "amino", "acids", "brain", "neuroscience", "organic", "compounds", "developmental", "biology", "hindbrain", "brain", "mapping", "amino", ...	2018	Neurotransmitter-mediated activity spatially controls neuronal migration in the zebrafish cerebellum
In many motor tasks , optimal performance presupposes that human movement planning is based on an accurate internal model of the subject's own motor error . We developed a motor choice task that allowed us to test whether the internal model implicit in a subject's choices differed from the actual in isotropy ( elongati...	When you play darts , which part of the dartboard do you aim at ? The tiny bull's eye is worth 50 points . The 20-point section is much larger . If you're not very good at dart throwing you may want to take that into account . Your choice of target depends not on how good you are but on how good you think you are – you...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "social", "and", "behavioral", "sciences", "experimental", "psychology", "psychophysics", "psychology" ]	2013	Testing Whether Humans Have an Accurate Model of Their Own Motor Uncertainty in a Speeded Reaching Task
The cohesin complex is crucial for chromosome segregation during mitosis and has recently also been implicated in transcriptional regulation and chromatin architecture . The NIPBL protein is required for the loading of cohesin onto chromatin , but how and where cohesin is loaded in vertebrate cells is unclear . Heteroz...	The cohesin complex is crucial for chromosome segregation during cell divisions but was recently also implicated in transcriptional regulation and chromatin architecture . Cohesin's binding to chromatin depends on NIPBL , a factor that was found to be mutated in 50% of the cases of the human developmental disorder Corn...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mitosis", "developmental", "biology", "chromosome", "biology", "chromosome", "structure", "and", "function", "birth", "defects", "gene", "expression", "genetics", "biology", "genomics", "molecular", "cell", "biology", "morphogenesis", "genetics", "of", "disease", "chro...	2014	A Cohesin-Independent Role for NIPBL at Promoters Provides Insights in CdLS
Positive-strand RNA viruses assemble numerous membrane-bound viral replicase complexes within large replication compartments to support their replication in infected cells . Yet the detailed mechanism of how given subcellular compartments are subverted by viruses is incompletely understood . Although , Tomato bushy stu...	Viral replication organelles are formed in subcellular compartments during positive-strand RNA virus infections to support robust virus replication . TBSV induces multivesicular body-like structures consisting of aggregated peroxisomes . However , endoplasmic reticulum ( ER ) and early endosomal proteins and membranes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protein", "interactions", "microbiology", "light", "microscopy", "membrane", "proteins", "fungi", "confocal", "laser", "microscopy", "microscopy", "confocal", "microscopy", "peroxisomes", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "meth...	2018	Assembly-hub function of ER-localized SNARE proteins in biogenesis of tombusvirus replication compartment
An ongoing challenge in protein chemistry is to identify the underlying interaction energies that capture protein dynamics . The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed force fields are typically well-parameterized , ob...	All-atom biomolecular simulations are useful but often take months to simulate biologically relevant reactions . Coarse-grain folding simulations reduce the computational requirements; however , they typically have reduced accuracy and knowledge of the native state is required . Here , we show that a properly formulate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "chemical", "bonding", "crystal", "structure", "condensed", "matter", "physics", "simulation", "and", "modeling", "protein", "structure", "prediction", "protein", "structure", "crystallography", "thermodynamics", "hydrogen", "bonding", "physical", "chemistry", "research", ...	2018	Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours
Taenia solium cysticercosis is a zoonotic neglected disease responsible for severe health disorders such as seizures and death . Understanding the epidemiology of human cysticercosis ( HCC ) in endemic regions will help to expose critical information about the transmission of the disease , which could be used to design...	Human cysticercosis is a neglected zoonotic disease caused by the larval stage of the parasite Taenia solium . This disease is responsible for severe health disorders such as seizures , and in some cases even death . T . solium cysticercosis is endemic in countries in Africa , Latin America and Asia where conditions su...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Taenia solium Human Cysticercosis: A Systematic Review of Sero-epidemiological Data from Endemic Zones around the World
Genetic linkage maps are cornerstones of a wide spectrum of biotechnology applications , including map-assisted breeding , association genetics , and map-assisted gene cloning . During the past several years , the adoption of high-throughput genotyping technologies has been paralleled by a substantial increase in the d...	Genetic linkage maps are cornerstones of a wide spectrum of biotechnology applications . In recent years , new high-throughput genotyping technologies have substantially increased the density and diversity of genetic markers , creating new algorithmic challenges for computational biologists . In this paper , we present...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "computational", "biology/population", "genetics", "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "genetics", "and", "genomics/bioinformatics", "genetics", "and", "genomics/population", "genetics" ]	2008	Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph
Neural oscillations have been recorded and implicated in many different basic brain and cognitive processes . For example , oscillatory neural activity has been suggested to play a role in binding and in the maintenance of information in working memory . With respect to the latter , the majority of work has focused pri...	Working memory is a form of limited-capacity short term memory that is relevant to cognition . Various studies have shown that ensembles of neurons oscillate during working memory retention , and cross-frequency coupling ( between , e . g . , theta and gamma frequencies ) has been conjectured as underlying the observed...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "nervous", "system", "population", "dynamics", "electrophysiology", "neuroscience", "learning", "and", "memory", "cognitive", "neuroscience", "cognition", "network", "analysis", "memory", "population", "biolog...	2018	Oscillations in working memory and neural binding: A mechanism for multiple memories and their interactions
Polymicrobial interactions play an important role in shaping the outcome of antibiotic treatment , yet how multispecies communities respond to antibiotic assault is still little understood . Here we use an individual-based simulation model of microbial biofilms to investigate how competitive and mutualistic interaction...	Pathogens -microorganisms that make us sick- often live within dynamic and complex multispecies communities , where they may not only compete for limiting resources but also exchange beneficial resources or services with other resident species . While antibiotics are commonly used to get rid of such harmful microbes , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biofilms", "antimicrobials", "medicine", "and", "health", "sciences", "toxins", "microbiome", "pathology", "and", "laboratory", "medicine", "drugs", "microbiology", "toxicology", "toxic", "agents", "antibiotic", "resistance", "nutrition", "antibiotics", "pharmacology", "...	2018	Community interactions and spatial structure shape selection on antibiotic resistant lineages
A large number of alternative exons are spliced with tissue-specific patterns , but little is known about how such patterns have evolved . Here , we study the conservation of the neuron-specific splicing factors Nova1 and Nova2 and of the alternatively spliced exons they regulate in mouse brain . Whereas Nova RNA bindi...	Alternative splicing generates different mRNA isoforms from a single gene and thus increases the number of proteins a cell can produce . This is particularly important in the brain , which possesses a number of brain-specific splicing factors . In this study , we have looked at evolution of brain-specific splicing regu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "chicken", "homo", "(human)", "danio", "(zebrafish)", "vertebrates", "evolutionary", "biology", "molecular", "biology", "mus", "(mouse)" ]	2007	Evolution of Nova-Dependent Splicing Regulation in the Brain
The versatile functions of the heat shock protein 70 ( Hsp70 ) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains , NBD and SBD . Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators . Yet , de...	The Hsp70 family of molecular chaperones assists in protein folding , degradation , assembly/disassembly of some complexes , and intracellular trafficking . These activities in the cell are accomplished by coupled conformational switches/signals between their nucleotide-binding and substrate-binding domains ( NBD and S...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "sequence", "analysis", "biochemistry", "proteins", "chaperone", "proteins", "biology", "and", "life", "sciences", "molecular", "biology", "techniques", "computational", "biology", "molecular", "biology" ]	2014	ATPase Subdomain IA Is a Mediator of Interdomain Allostery in Hsp70 Molecular Chaperones
Wolbachia , an endosymbiont of filarial nematode , is considered a promising target for therapy against lymphatic filariasis . Transcription elongation factor GreA is an essential factor that mediates transcriptional transition from abortive initiation to productive elongation by stimulating the escape of RNA polymeras...	Diethylcarbamazine and ivermectin , the conventional antifilarial drugs , exert poor activity on adult filarial worms . Brugia malayi , a causative agent of human lymphatic filariasis , harbors an obligate alpha-proteobacterium , Wolbachia . Because the endosymbiont is required for the development , viability , and fer...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences" ]	2014	Wolbachia Transcription Elongation Factor “Wol GreA” Interacts with α2ββ′σ Subunits of RNA Polymerase through Its Dimeric C-Terminal Domain
The mammalian Y chromosome plays a critical role in spermatogenesis . However , the exact functions of each gene in the Y chromosome have not been completely elucidated , partly owing to difficulties in gene targeting analysis of the Y chromosome . Zfy was first proposed to be a sex determination factor , but its funct...	The Y chromosome is known to play a critical role in spermatogenesis based on human genetic evidence . However , specific Y chromosome genes responsible for spermatogenesis have not been fully elucidated yet , because the targeted deletion of Y chromosome genes is difficult owing to its unique structure . In this study...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "medicine", "and", "health", "sciences", "reproductive", "system", "cell", "cycle", "and", "cell", "division", "cell", "processes", "reproductive", "physiology", "germ", "cells", "developmental", "biology", "oocytes", "epididymis", "embryos", "cellular", "s...	2017	Complementary Critical Functions of Zfy1 and Zfy2 in Mouse Spermatogenesis and Reproduction
Visceral Leishmaniasis ( VL ) , a severe parasitic disease , could be fatal if diagnosis and treatment is delayed . Post kala-azar dermal leishmaniasis ( PKDL ) , a skin related outcome , is a potential reservoir for the spread of VL . Diagnostic tests available for VL such as tissue aspiration are invasive and painful...	Visceral leishmaniasis ( VL ) , one of the most prevalent parasitic diseases in the developing world causes serious health concerns . Post kala-azar dermal leishmaniasis ( PKDL ) is a skin disease which occurs after treatment as a sequel to VL . Parasitological diagnosis involves invasive tissue aspiration which is ted...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "kala-azar", "medicine", "and", "health", "sciences", "body", "fluids", "enzyme-linked", "immunoassays", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "urine", "protozoans", "leishmania", "neglected", "tropical", "diseases", "immunologic", "t...	2016	Noninvasive Diagnosis of Visceral Leishmaniasis: Development and Evaluation of Two Urine-Based Immunoassays for Detection of Leishmania donovani Infection in India
The development of effective immunoprophylaxis against tuberculosis ( TB ) remains a global priority , but is hampered by a partially protective Bacillus Calmette-Guérin ( BCG ) vaccine and an incomplete understanding of the mechanisms of immunity to Mycobacterium tuberculosis . Although host genetic factors may be a p...	Tuberculosis ( TB ) is one of the leading infectious causes of death worldwide . The current vaccine for TB , BCG , is widely used but it is not highly effective in preventing disease . We investigated the role of host genetics in the immune response to BCG vaccination . We found that variants of innate immunity genes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "genetic", "mutation", "immunology", "gene", "function", "bacterial", "diseases", "global", "health", "infectious", "disease", "control", "immunizations", "infectious", "diseases", "tuberculosis", "biology", "immune", "response", "immunity", "genetic", "associ...	2011	Association of Human TLR1 and TLR6 Deficiency with Altered Immune Responses to BCG Vaccination in South African Infants
Epstein-Barr virus lytic replication is accomplished by an intricate cascade of gene expression that integrates viral DNA replication and structural protein synthesis . Most genes encoding structural proteins exhibit “true” late kinetics–their expression is strictly dependent on lytic DNA replication . Recently , the E...	A strict linkage between viral DNA replication and the onset of late gene expression is commonly found in DNA viruses . In herpesviruses , the precise mechanism for this requirement remains elusive . Competing models are titration of putative repressors as a result of increase in template copy number and the requiremen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hek", "293", "cells", "pathogens", "biological", "cultures", "microbiology", "plasmid", "construction", "viruses", "dna", "replication", "dna", "viruses", "dna", "c...	2016	An Epstein-Barr Virus-Encoded Protein Complex Requires an Origin of Lytic Replication In Cis to Mediate Late Gene Transcription
During development , proper differentiation and final organ size rely on the control of territorial specification and cell proliferation . Although many regulators of these processes have been identified , how both are coordinated remains largely unknown . The homeodomain Iroquois/Irx proteins play a key , evolutionari...	The correct development of body organs , with their characteristic size and shape , requires the coordination of cell division and cell differentiation . Here we show that the Iroquois proteins ( Irx in vertebrates ) slow down cell division in the Drosophila imaginal discs , in addition to their well-known role in cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Homeodomain Iroquois Proteins Control Cell Cycle Progression and Regulate the Size of Developmental Fields
The temporal and spatial change in trends of antimicrobial resistance ( AMR ) in typhoid have not been systematically studied , and such information will be critical for defining intervention , as well as planning sustainable prevention strategies . To identify the phenotypic trends in AMR , 13 , 833 individual S . Typ...	Typhoid is an invasive bacterial disease causing 26 million illness episodes globally , each year particularly in South Asia and sub-Saharan Africa afflicting children and poorer sections of society disproportionally . AMR is increasingly recognized among S . Typhi lineages spreading from South Asia to Africa , with re...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "antimicrobials", "gram", "negative", "bacteria", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "geographical", "locations", "microbiology", "salmonella", "typhi", "bacterial", "diseases", "sig...	2018	A systematic review of antimicrobial resistance in Salmonella enterica serovar Typhi, the etiological agent of typhoid
HCV infection is a major risk factor for liver cancer and liver transplantation worldwide . Overstimulation of host lipid metabolism in the liver by HCV-encoded proteins during viral infection creates a favorable environment for virus propagation and pathogenesis . In this study , we hypothesize that targeting cellular...	Chronic hepatitis C virus ( HCV ) infection is one of the leading causes of liver cancer and liver transplantation worldwide . No vaccine is available for preventing the spread of HCV , and the current therapeutic regimen is only moderately effective and causes serious side effects . New antiviral agents are required t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cellular", "structures", "subcellular", "organelles", "viral", "classification", "drugs", "and", "devices", "microbiology", "host-pathogen", "interaction", "viral", "structure", "hepatitis", "rna", "viruses", "pharmacology", "hepatitis", "c", "infectious", "d...	2012	Human Subtilase SKI-1/S1P Is a Master Regulator of the HCV Lifecycle and a Potential Host Cell Target for Developing Indirect-Acting Antiviral Agents
Despite their classical role as transcriptional repressors , several histone deacetylases , including the baker's yeast Set3/Hos2 complex ( Set3C ) , facilitate gene expression . In the dimorphic human pathogen Candida albicans , the homologue of the Set3C inhibits the yeast-to-filament transition , but the precise mol...	Many human pathogenic fungi are able to change their morphological properties , including their size and shape , in response to their outside environment . This ability , which is key for infection , is not completely understood on the molecular level . We have previously shown that not just DNA–binding transcription f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genomics", "functional", "genomics", "molecular", "cell", "biology", "gene", "expression", "genetics", "epigenetics", "biology", "microbial", "growth", "and", "development", "microbiology", "gene", "networks", "molecular", "biology", "genetics...	2012	A Histone Deacetylase Adjusts Transcription Kinetics at Coding Sequences during Candida albicans Morphogenesis
Varicella-zoster virus ( VZV ) causes varicella , establishes a life-long latent infection of ganglia and reactivates to cause herpes zoster . The cell types that transport VZV from the respiratory tract to skin and ganglia during primary infection are unknown . Clinical , pathological , virological and immunological f...	Varicella-zoster virus ( VZV ) causes varicella , establishes life-long latent infection in ganglia and reactivates later in life to cause zoster . VZV is acquired via the respiratory route , with skin rash occurring up to 3 weeks after exposure . The cell types that transport VZV to skin and ganglia during primary inf...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "histology", "pathogenesis", "neurobiology", "of", "disease", "and", "regeneration", "model", "organisms", "immune", "cells", "virology", "immunology", "host-pathogen", "interaction", "biology", "anatomy", "and", "physiology", "immunologic", "technique...	2013	T-Cell Tropism of Simian Varicella Virus during Primary Infection
A well-established notion in cognitive neuroscience proposes that multiple brain systems contribute to choice behaviour . These include: ( 1 ) a model-free system that uses values cached from the outcome history of alternative actions , and ( 2 ) a model-based system that considers action outcomes and the transition st...	In this paper , we report a reliability analysis for the estimation of “model basedness”—a psychological construct that informs a wealth of studies in animal , human and clinical research . We consider an exemplar paradigm , the two-step task , widely used in the recent literature . We report low reliability for model-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "learning", "decision", "making", "applied", "mathematics", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "algorithms", "cognitive", "psychology", "systems", "science", "mathematics", "cognition", "research", "and", ...	2019	Improving the reliability of model-based decision-making estimates in the two-stage decision task with reaction-times and drift-diffusion modeling
Type VI secretion systems ( T6SSs ) are widespread multi-component machineries that translocate effectors into either eukaryotic or prokaryotic cells , for virulence or for interbacterial competition . Herein , we report that the T6SS-4 from Yersinia pseudotuberculosis displays an unexpected function in the transportat...	One unique feature of type VI secretion system is the presence of multiple distinct systems in certain bacterial species . It is well established that some of these systems function to compete for their living niches among diverse bacterial species , whilst the activity of many such transporters remains unknown . Becau...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Type VI Secretion System Transports Zn2+ to Combat Multiple Stresses and Host Immunity
Proteins from halophilic organisms , which live in extreme saline conditions , have evolved to remain folded at very high ionic strengths . The surfaces of halophilic proteins show a biased amino acid composition with a high prevalence of aspartic and glutamic acids , a low frequency of lysine , and a high occurrence o...	Life on earth exhibits an enormous adaptive capacity and living organisms can be found even in extreme environments . The halophilic archea are a group of microorganisms that grow best in highly salted lakes ( with KCl concentrations between 2 and 6 molar ) . To avoid osmotic shock , halophilic archea have the same ion...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/environmental", "microbiology", "biophysics", "biochemistry/protein", "chemistry", "chemistry/biochemistry" ]	2009	Structural Basis for the Aminoacid Composition of Proteins from Halophilic Archea
DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA . However , the number and the location of DNase I ion-binding sites remain unclear , as well as the role of these counter-ions . Using molecular dynamics simulations , we show that bovine pancreatic ( bp ) DNase I contains four ion-binding pockets . Tw...	DNase I requires Ca2+ and Mg2+ for hydrolyzing double-stranded DNA . Here , we show that bovine pancreatic ( bp ) DNase I contains four ion-binding pockets . Two of them , previously observed in the crystallographic structure of free bpDNase I , strongly bind Ca2+ . The other two sites bind Mg2+ and are described in de...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biochemistry/biocatalysis", "cell", "biology/cellular", "death", "and", "stress", "responses", "computational", "biology/transcriptional", "regulation", "computational", "biology/comparative", "sequence", "analysi...	2010	How Cations Can Assist DNase I in DNA Binding and Hydrolysis
Cells employ a myriad of signaling circuits to detect environmental signals and drive specific gene expression responses . A common motif in these circuits is inducible auto-activation: a transcription factor that activates its own transcription upon activation by a ligand or by post-transcriptional modification . Exam...	Different times call for different measures . Therefore , cells adjust their protein levels depending on their environment . Upon the detection of certain environmental signals , transcription factors are activated , which activate or inhibit the production of specific sets of proteins . As it turns out , these transcr...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "gene", "regulation", "signaling", "networks", "dna", "transcription", "mathematics", "molecular", "genetics", "stochastic", "processes", "biophysics", "simulations", "theoretical", "biology", "gene", "expression", "biophysics", "theory", "regulatory", "networks", "biology"...	2011	Speed, Sensitivity, and Bistability in Auto-activating Signaling Circuits
The locus coeruleus ( LC ) in the pons is the major source of noradrenaline ( NA ) in the brain . Two modes of LC firing have been associated with distinct cognitive states: changes in tonic rates of firing are correlated with global levels of arousal and behavioural flexibility , whilst phasic LC responses are evoked ...	The brain uses sensory information to build internal models and make predictions about the world . When errors of prediction occur , models must be updated to ensure desired outcomes are still achieved . Neuromodulator chemicals provide a possible pathway for triggering such changes in brain state . One such neuromodul...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "learning", "medicine", "and", "health", "sciences", "decision", "making", "brain", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "psychology", "systems", "science", "mathematics", "probability", "distri...	2019	Locus Coeruleus tracking of prediction errors optimises cognitive flexibility: An Active Inference model
Metastasis is the principal cause of cancer death and occurs through multiple , complex processes that involve the concerted action of many genes . A number of studies have indicated that the Fragile Histidine Triad ( FHIT ) gene product , FHIT , functions as a tumor suppressor in a variety of common human cancers . Al...	Although Fragile Histidine Triad ( FHIT ) is known as a potential tumor suppressor gene in terms of tumor initiation and progression , the role of FHIT in the metastatic process is not well characterized . Here it is shown that FHIT reduces the motility and invasiveness of lung cancer cells in vitro and ability to meta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	FHIT Suppresses Epithelial-Mesenchymal Transition (EMT) and Metastasis in Lung Cancer through Modulation of MicroRNAs
Impaired acrosomal reaction ( IAR ) of sperm causes male subfertility in humans and animals . Despite compelling evidence about the genetic control over acrosome biogenesis and function , the genomics of IAR is as yet poorly understood , providing no molecular tools for diagnostics . Here we conducted Equine SNP50 Bead...	Impaired acrosomal reaction ( IAR ) of sperm causes male subfertility in humans and animals , and currently the molecular causes of the condition are not known . Here we report the mapping , identification , and functional analysis of a susceptibility locus for IAR in stallions . The candidate region was mapped to hors...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "animal", "genetics", "functional", "genomics", "gene", "function", "genome", "analysis", "tools", "molecular", "genetics", "structural", "genomics", "gene", "expression", "gene", "splicing", "comparative", "genomics", "biology", ...	2012	Genome-Wide Association Study Implicates Testis-Sperm Specific FKBP6 as a Susceptibility Locus for Impaired Acrosome Reaction in Stallions
Chronic chagasic cardiomyopathy ( CCM ) is presented by increased oxidative/inflammatory stress and decreased mitochondrial bioenergetics . SIRT1 senses the redox changes and integrates mitochondrial metabolism and inflammation; and SIRT1 deficiency may be a major determinant in CCM . To test this , C57BL/6 mice were i...	In this study , we determined whether enhancing the activity of sirtuin 1 ( SIRT1 ) would be beneficial in maintaining heart health in Chagas disease . SIRT1 senses the redox shifts and integrates mitochondrial metabolism and inflammation . We found that treatment with SIRT1 agonists , given in a therapeutic window of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "inflammatory", "diseases", "medicine", "and", "health", "sciences", "respiratory", "infections", "pathology", "and", "laboratory", "medicine", "mitochondrial", "dna", "cardiovascular", "anatomy", "immunology", "parasitic", "protozoans", "pulmonology", "protozoans", "heart"...	2016	SIRT1-PGC1α-NFκB Pathway of Oxidative and Inflammatory Stress during Trypanosoma cruzi Infection: Benefits of SIRT1-Targeted Therapy in Improving Heart Function in Chagas Disease
The number and distribution of crossover events are tightly regulated at prophase of meiosis I . The resolution of Holliday junctions by structure-specific endonucleases , including MUS-81 , SLX-1 , XPF-1 and GEN-1 , is one of the main mechanisms proposed for crossover formation . However , how these nucleases coordina...	Abnormalities in the number and/or structure of the chromosomes can result in cancer , birth defects , miscarriages and infertility . In particular , the exchange of genetic material ( crossover formation ) between maternal and paternal chromosomes during the cell division program of meiosis is essential to produce nor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Interplay between Structure-Specific Endonucleases for Crossover Control during Caenorhabditis elegans Meiosis
In many parts of sub-Saharan Africa , urogenital and intestinal schistosomiasis co-occur , and mixed species infections containing both Schistosoma haematobium and S . mansoni can be common . During co-infection , interactions between these two species are possible , yet the extent to which such interactions influence ...	In many parts of Africa both urinary and intestinal schistosomiasis are endemic , and mixed species infections can be common . However , little is known about potential within-host interactions between the causative parasites , S . haematobium and S . mansoni , and how these might influence treatment success and post-t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Epidemiological Interactions between Urogenital and Intestinal Human Schistosomiasis in the Context of Praziquantel Treatment across Three West African Countries
The skeleton is one of the most important features for the reconstruction of vertebrate phylogeny but few data are available to understand its molecular origin . In mammals the Runt genes are central regulators of skeletogenesis . Runx2 was shown to be essential for osteoblast differentiation , tooth development , and ...	Important molecular mechanisms underlying mammalian skeletogenesis have been described but knowledge about the evolutionary origin of these gene networks is limited . The Runt gene family ( Runx1–3 ) is of extraordinary importance for skeletogenesis . Runx2 deficient mice completely lack bone . Runx2 and Runx3 are esse...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology", "evolutionary", "biology/developmental", "molecular", "mechanisms" ]	2008	Evolution of a Core Gene Network for Skeletogenesis in Chordates
Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus that is causally linked to severe neonatal birth defects , including microcephaly , and is associated with Guillain-Barre syndrome in adults . Dendritic cells ( DCs ) are an important cell type during infection by multiple mosquito-borne flaviviruses , includ...	Zika virus ( ZIKV ) is an emerging mosquito-borne flavivirus that , upon congenital infection , can cause severe neonatal birth defects . To better understand the early innate immune response to ZIKV , we compared infection of human dendritic cells ( DCs ) between a contemporary Puerto Rican isolate and historic isolat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "phosphorylation", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immune", "cells", "pathogens", "immunology", "microbiology", "viruses", "physi...	2017	Zika Virus Antagonizes Type I Interferon Responses during Infection of Human Dendritic Cells
Ciliopathies are pleiotropic and genetically heterogeneous disorders caused by defective development and function of the primary cilium . Bardet-Biedl syndrome ( BBS ) proteins localize to the base of cilia and undergo intraflagellar transport , and the loss of their functions leads to a multisystemic ciliopathy . Here...	Bardet-Biedl syndrome ( BBS ) is a genetically heterogeneous , multisystemic disorder . Defects to the cilium , an evolutionarily conserved organelle , cause ciliopathies , a growing class of diseases that includes BBS . BBS proteins are involved in the vesicular transport of proteins to the cilium and in the process o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "molecular", "neuroscience", "clinical", "research", "design", "cgmp", "signaling", "animal", "models", "of", "disease", "anatomy", "and", "physiology", "signaling", "in", "selected", "disciplines", "neuroscience", "animal", "models", "developmental", "biolo...	2011	Mutations in a Guanylate Cyclase GCY-35/GCY-36 Modify Bardet-Biedl Syndrome–Associated Phenotypes in Caenorhabditis elegans
Exploiting pathogen genomes to reconstruct transmission represents a powerful tool in the fight against infectious disease . However , their interpretation rests on a number of simplifying assumptions that regularly ignore important complexities of real data , in particular within-host evolution and non-sampled patient...	We present a new tool , SCOTTI , to efficiently reconstruct transmission events within outbreaks . Our approach combines genetic information from infection samples with epidemiological information of patient exposure to infection . While epidemiological information has been traditionally used to understand who infected...	[ "Abstract", "Introduction", "Results", "Discussion", "Software", "Availability", "Materials", "and", "Methods" ]	[ "taxonomy", "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "spatial", "epidemiology", "microbiology", "simulation", "and", "modeling", "phylogenetics", "data", "management", "phylogenetic", "a...	2016	SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent
Macrophages play a central role in host defense against mycobacterial infection and anti- TNF therapy is associated with granuloma disorganization and reactivation of tuberculosis in humans . Here , we provide evidence for the presence of a T cell receptor ( TCR ) αβ based recombinatorial immune receptor in subpopulati...	Infection with mycobacteria results in a host response which results in the formation of granulomas , highly organized structures characterized by the presence of macrophages , which are considered to rely solely on invariant immune receptors . On the other hand , the presence of variable immune receptors is required f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunology" ]	2011	A TNF-Regulated Recombinatorial Macrophage Immune Receptor Implicated in Granuloma Formation in Tuberculosis

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