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In the current study , a comprehensive , data driven , mathematical model for cholera transmission in Haiti is presented . Along with the inclusion of short cycle human-to-human transmission and long cycle human-to-environment and environment-to-human transmission , this novel dynamic model incorporates both the report...	Based on the model-fitted trend and the observed incidence , there is evidence that after an initial period of intense transmission , the cholera epidemic in Haiti stabilized during the third year of the outbreak and became endemic . The model estimates indicate that the proportion of the population susceptible to infe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Cholera Transmission in Ouest Department of Haiti: Dynamic Modeling and the Future of the Epidemic
The Rhox cluster on the mouse X chromosome contains reproduction-related homeobox genes expressed in a sexually dimorphic manner . We report that two members of the Rhox cluster , Rhox6 and 9 , are regulated by de-methylation of histone H3 at lysine 27 by KDM6A , a histone demethylase with female-biased expression . Co...	Homeobox ( HOX ) genes are known to be under epigenetic control during development . Here , we report that two mouse X-linked homeobox genes implicated in reproduction , Rhox6 and 9 , are activated by the histone demethylase KDM6A that removes methylation at lysine 27 of histone H3 . Kdm6a is one in a small group of ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "function", "developmental", "biology", "x", "chromosome", "inactivation", "rna", "interference", "stem", "cells", "chromosome", "biology", "embryonic", "stem", "cells", "genomic", "imprinting", "gene", "expression", "genetics", "gene", "regulation", "epigenetic...	2013	Female Bias in Rhox6 and 9 Regulation by the Histone Demethylase KDM6A
The infectious and diagnostic form of Entamoeba histolytica ( Eh ) , cause of amebic dysentery and liver abscess , is the quadranucleate cyst . The cyst wall of Entamoeba invadens ( Ei ) , a model for Eh , is composed of chitin fibrils and three sets of chitin-binding lectins that cross-link chitin fibrils ( multivalen...	For many years , we and others have used cysts of Entamoeba invadens ( Ei ) , a reptilian parasite , to model the infectious and diagnostic cysts of the human pathogen Entamoeba histolytica ( Eh ) . The Ei cyst wall is composed of chitin fibrils , as well as Jacob and Jessie lectins that have unique chitin-binding doma...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "cell", "biology/morphogenesis", "and", "cell", "biology", "immunology/immune", "response", "biochemistry/macromolecular", "assemblies", "and", "machines" ]	2010	The Jacob2 Lectin of the Entamoeba histolytica Cyst Wall Binds Chitin and Is Polymorphic
French Guiana , a French overseas department located in South America between Brazil and Surinam , is the only European territory geographically located in the Amazonian forest complex and is considered endemic for yellow fever ( YF ) . In the context of the emergent threat of YF in Latin America , we conducted a large...	Yellow fever ( YF ) is the most severe arbovirus to circulate in the Americas . French Guiana , a French overseas department located in South America between Brazil and Surinam , is the only European territory geographically located in the Amazonian forest complex and is considered endemic for YF . We conducted a large...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "education", "immunology", "geographical", "locations", "sociology", "social", "sciences", "ethnicities", "preventive", "medicine", "vaccination", "and", "immunization", "public", "and...	2019	Vaccination coverage in the context of the emerging Yellow Fever threat in French Guiana
We introduce a theory of sequential causal inference in which learners in a chain estimate a structural model from their upstream “teacher” and then pass samples from the model to their downstream “student” . It extends the population dynamics of genetic drift , recasting Kimura's selectively neutral theory as a specia...	Human knowledge is often transmitted orally within a group via a sequence of communications between individuals . The children's game of Telephone is a familiar , simplified version . A phrase is uttered , understood , and then transmitted to another . Genetic information is communicated in an analogous sequential comm...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neutral", "theory", "population", "genetics", "markov", "model", "mathematics", "effective", "population", "size", "stochastic", "processes", "emergence", "forms", "of", "evolution", "theoretical", "biology", "evolutionary", "modeling", "biology", "evolutionary", "theory...	2012	Structural Drift: The Population Dynamics of Sequential Learning
Peripheral infection by Trypanosoma brucei , the protozoan responsible for sleeping sickness , activates lymphocytes , and , at later stages , causes meningoencephalitis . We have videoed the cortical meninges and superficial parenchyma of C56BL/6 reporter mice infected with T . b . brucei . By use of a two-photon micr...	African trypanosomes are motile parasites that cause sleeping sickness . They multiply first in the blood then cause death mainly by effects on the brain: immune system cells , including T cells and dendritic cells , play major roles in this . Thinking we might see the attack on the brain , we infected mice with trypan...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[]	2015	Intravital Imaging of a Massive Lymphocyte Response in the Cortical Dura of Mice after Peripheral Infection by Trypanosomes
In ecology , species can mitigate their extinction risks in uncertain environments by diversifying individual phenotypes . This observation is quantified by the theory of bet-hedging , which provides a reason for the degree of phenotypic diversity observed even in clonal populations . Bet-hedging in well-mixed populati...	Ecological populations are often exposed to unpredictable and variable environmental conditions . A number of strategies have evolved to cope with such uncertainty . One of them is stochastic phenotypic switching , by which some individuals in the community are enabled to tackle adverse conditions , even at the price o...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "bacteriology", "organismal", "evolution", "species", "colonization", "ecology", "and", "environmental", "sciences", "invasive", "species", "applied", "mathematics", "population", "genetics", "microbiology", "mathematics", "microbial", "evolution", "population", "biology", ...	2019	Bet-hedging strategies in expanding populations
Co-expression network analysis provides useful information for studying gene regulation in biological processes . Examining condition-specific patterns of co-expression can provide insights into the underlying cellular processes activated in a particular condition . One challenge in this type of analysis is that the sa...	Gene co-expression networks provide insights into the mechanism of cellular activity and gene regulation . Condition-specific mechanisms may be identified by constructing and comparing co-expression networks of multiple conditions . We propose a novel statistical method to jointly construct co-expression networks for g...	[ "Abstract", "Introduction", "Results", "Method" ]	[ "medicine", "and", "health", "sciences", "genetic", "networks", "breast", "tumors", "cardiovascular", "anatomy", "gene", "regulation", "cancers", "and", "neoplasms", "random", "variables", "covariance", "simulation", "and", "modeling", "oncology", "mathematics", "networ...	2018	Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network
Effector responses induced by polarized CD4+ T helper 2 ( Th2 ) cells drive nonhealing responses in BALB/c mice infected with Leishmania major . Th2 cytokines IL-4 and IL-13 are known susceptibility factors for L . major infection in BALB/c mice and induce their biological functions through a common receptor , the IL-4...	Leishmaniasis is a disease induced by a protozoan parasite and transmitted by the sandfly . Several forms of infection are identified , and the different diseases have wide-ranging symptoms from localized cutaneous sores to visceral disease affecting many internal organs . Animal models of human cutaneous leishmaniasis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mus", "(mouse)", "none", "infectious", "diseases", "immunology" ]	2007	Deletion of IL-4Rα on CD4 T Cells Renders BALB/c Mice Resistant to Leishmania major Infection
Safe treatment of Plasmodium vivax requires diagnosis of both the infection and status of erythrocytic glucose-6-phosphate dehydrogenase ( G6PD ) activity because hypnozoitocidal therapy against relapse requires primaquine , which causes a mild to severe acute hemolytic anemia in G6PD deficient patients . Many national...	G6PD deficiency affects over 400 million people worldwide . This enormously diverse disorder causes acute hemolytic anemia upon exposure to oxidizing chemicals , e . g . , naphthalene , some sulfa drugs , and certain antimalarials , including primaquine . The primary public health concern with G6PD deficiency involves ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	G6PD Deficiency at Sumba in Eastern Indonesia Is Prevalent, Diverse and Severe: Implications for Primaquine Therapy against Relapsing Vivax Malaria
The study of Onchocerca volvulus has been limited by its host range , with only humans and non-human primates shown to be susceptible to the full life cycle infection . Small animal models that support the development of adult parasites have not been identified . We hypothesized that highly immunodeficient NSG mice wou...	Onchocerciasis , caused by the filarial parasitic nematode Onchocerca volvulus , remains a significant source of morbidity throughout sub-Saharan Africa and is a primary cause of infectious blindness . Research on this disease has been hindered by an absence of suitable small animal hosts . Here we describe the develop...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "onchocerca", "volvulus", "helminths", "immunology", "biomarkers", "parasitic", "diseases", "animals", "onchocerca", "animal", "models", "urine", "developmental", "biology", "model", "organisms", ...	2018	Development of Onchocerca volvulus in humanized NSG mice and detection of parasite biomarkers in urine and serum
The ultimate goal of metabolic engineering is to produce desired compounds on an industrial scale in a cost effective manner . To address challenges in metabolic engineering , computational strain optimization algorithms based on genome-scale metabolic models have increasingly been used to aid in overproducing products...	Computational strain design algorithms based on genome-scale metabolic models have increasingly been used to guide rational strain design for metabolic engineering . However , most strain optimization algorithms only utilize a metabolic network alone and cannot provide strategies that also involve transcriptional regul...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "chemical", "compounds", "gene", "regulation", "applied", "mathematics", "metabolic", "networks", "organic", "compounds", "simulation", "and", "modeling", "algorithms", "fungi", "model", "organisms", "mathematics", "simulated", "annealing", "network", "analysis", "experim...	2019	OptRAM: In-silico strain design via integrative regulatory-metabolic network modeling
Antigenic variation to evade host immunity has long been assumed to be a driving force of diversifying selection in pathogens . Colonization by Streptococcus pneumoniae , which is central to the organism's transmission and therefore evolution , is limited by two arms of the immune system: antibody- and T cell- mediated...	Streptococcus pneumoniae , or pneumococcus , is a leading cause of morbidity and mortality in young children and elderly persons worldwide . Current pneumococcus vaccines target a limited number of clinically important serotypes , while strains with serotypes not targeted by current vaccines are increasing in importanc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "of", "the", "immune", "system", "genomic", "evolution", "immunity", "evolutionary", "immunology", "biology", "evolutionary", "biology", "comparative", "genomics", "immunology", "evolutionary", "processes", "immune", "response" ]	2012	Distinct Effects on Diversifying Selection by Two Mechanisms of Immunity against Streptococcus pneumoniae
Innate lymphoid cells ( ILCs ) are severely depleted during chronic HIV-1 infection by unclear mechanisms . We report here that human ILC1s comprising of CD4+ and CD4- subpopulations were present in various human lymphoid organs but with different transcription programs and functions . Importantly , CD4+ ILC1s expresse...	Innate lymphoid cells ( ILCs ) , including ILC1 , ILC2 and ILC3 populations , represent a novel cellular family of the immune system and have potentials to produce large amounts of T cell-associated cytokines in response to innate stimulation in the absence of specific antigen stimulation . ILCs have emerged as central...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "highly-active", "antiretroviral", "therapy", "immune", "physiology", "cytokines", "antiviral", ...	2018	Infection and depletion of CD4+ group-1 innate lymphoid cells by HIV-1 via type-I interferon pathway
Infection with human BK polyomavirus , a small double-stranded DNA virus , potentially results in severe complications in immunocompromised patients . Here , we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing . Our data reveal the highest genomic evolutionary rate described in d...	Little is known about the mechanisms of evolution and viral immune escape in double-stranded DNA ( dsDNA ) viruses . Here , we study the evolution of BK polyomavirus and observe the highest genomic evolutionary rate described so far for a dsDNA virus , in the range of RNA viruses , which usually evolve rapidly . Furthe...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "taxonomy", "organismal", "evolution", "medicine", "and", "health", "sciences", "body", "fluids", "genome", "evolution", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "microbiology", "organic", "compounds", "viruses", "urine", "phyl...	2018	An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides
KSHV is the causative agent of Kaposi sarcoma ( KS ) , a spindle-shaped endothelial cell neoplasm accompanied by an inflammatory infiltrate . To evaluate the role of KSHV vFLIP in the pathogenesis of KS , we constructed mice with inducible expression of vFLIP in endothelial cells . Abnormal cells with endothelial marke...	Kaposi’s sarcoma ( KS ) is the most common cancer in men infected with HIV , and also among the most frequent malignancies in Sub-Equatorial Africa . KS is a tumor of endothelial cell origin that is caused by infection with a gamma-herpesvirus , called KS herpesvirus ( KSHV ) or human herpesvirus 8 ( HHV-8 ) . KSHV vFL...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Systemic Expression of Kaposi Sarcoma Herpesvirus (KSHV) Vflip in Endothelial Cells Leads to a Profound Proinflammatory Phenotype and Myeloid Lineage Remodeling In Vivo
Crossovers ( COs ) are at the origin of genetic variability , occurring across successive generations , and they are also essential for the correct segregation of chromosomes during meiosis . Their number and position are precisely controlled , however the mechanisms underlying these controls are poorly understood . Ne...	During meiosis , two successive chromosomal divisions follow a single S phase , resulting in the formation of four haploid cells , each with half of the parental genetic material . This reduction in chromosome number occurs during the first meiotic division , when homologous chromosomes ( paternal and maternal ) are se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "brassica", "gene", "function", "plant", "science", "model", "organisms", "molecular", "genetics", "plants", "arabidopsis", "thaliana", "research", "and", "analysis", "methods", "chromosome", ...	2014	Crossover Localisation Is Regulated by the Neddylation Posttranslational Regulatory Pathway
In eutherian mammals , embryonic growth and survival is dependent on the formation of the placenta , an organ that facilitates the efficient exchange of oxygen , nutrients , and metabolic waste between the maternal and fetal blood supplies . Key to the placenta's function is the formation of its vascular labyrinth , a ...	Defects in placental development are a common cause of mid-gestational lethality . Key to the placenta's function is its vascular labyrinth , a series of finely branched vessels that facilitate the efficient exchange of gases , nutrients , and metabolic waste between the maternal and fetal blood supplies . In this stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "developmental", "biology/molecular", "development", "developmental", "biology/developmental", "evolution", "developmental", "biology/developmental", "molecular", "mechanisms" ]	2008	HOXA13 Is Essential for Placental Vascular Patterning and Labyrinth Endothelial Specification
The initial response to Leishmania parasites is essential in determining disease development or resistance . In vitro , a divergent response to Leishmania , characterized by high or low IFN-γ production has been described as a potential tool to predict both vaccine response and disease susceptibility in vivo . We ident...	Control and development of Cutaneous Leishmaniasis ( CL ) are dependent on the host immunological response . One of the key molecules in determining elimination of Leishmania parasites from the infected host cell is the cytokine interferon gamma ( IFN-γ ) . The aim of this study was to investigate which immune response...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "signs", "and", "symptoms", "leishmania", ...	2016	Gene Expression Profile of High IFN-γ Producers Stimulated with Leishmania braziliensis Identifies Genes Associated with Cutaneous Leishmaniasis
Human TRIM5α potently restricts particular strains of murine leukemia viruses ( the so-called N-tropic strains ) but not others ( the B- or NB-tropic strains ) during early stages of infection . We show that overexpression of SUMO-1 in human 293T cells , but not in mouse MDTF cells , profoundly blocks N-MLV infection ....	TRIM5α is an intrinsic immunity protein that provides a post-entry block of retroviral infection , which depends on its specific ability to recognize retroviral capsid ( CA ) . Human TRIM5α is able to recognize and block infection by N-tropic murine leukemia virus ( N-MLV ) as well as other viruses . The exact mechanis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "molecular", "cell", "biology", "virology", "genetics", "biology", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics" ]	2011	SUMO-Interacting Motifs of Human TRIM5α are Important for Antiviral Activity
Metachondromatosis ( MC ) is a rare , autosomal dominant , incompletely penetrant combined exostosis and enchondromatosis tumor syndrome . MC is clinically distinct from other multiple exostosis or multiple enchondromatosis syndromes and is unlinked to EXT1 and EXT2 , the genes responsible for autosomal dominant multip...	Children with cartilage tumor syndromes form multiple tumors of cartilage next to joints . These tumors can occur inside the bones , as with Ollier disease and Maffuci syndrome , or on the surface of bones , as in the Multiple Osteochondroma syndrome ( MO ) . In a hybrid syndrome , called metachondromatosis ( MC ) , pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cancer", "genetics", "pediatric", "oncology", "pediatrics", "molecular", "genetics", "pediatric", "orthopedics", "pediatrics", "and", "child", "health", "biology", "autosomal", "dominant", "clinical", "genetics", "gene", "identification", "and", "analysis", ...	2011	Loss-of-Function Mutations in PTPN11 Cause Metachondromatosis, but Not Ollier Disease or Maffucci Syndrome
Deleterious mutations appearing in a population increase in frequency until stopped by natural selection . The ensuing equilibrium creates a stable frequency of deleterious mutations or the mutational load . Here I develop the comparable concept of a damage load , which is caused by harmful non-heritable changes to the...	Almost all living organisms deteriorate with time through the process of aging or senescence . Because most studies on senescence examined organisms possessing a juvenile state , it was thought that bacteria , which reproduce by producing two apparently identical daughter cells , were immortal and not senescent . Recen...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "computational", "biology/population", "genetics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/evolutionary", "ecology", "microbiology/microbial", "evolution...	2010	A Model for Damage Load and Its Implications for the Evolution of Bacterial Aging
The proteasome inhibitor MG132 had been shown to prevent galactose induction of the S . cerevisiae GAL1 gene , demonstrating that ubiquitin proteasome-dependent degradation of transcription factors plays an important role in the regulation of gene expression . The deletion of the gene encoding the F-box protein Mdm30 h...	The expression levels of proteins are tightly regulated , not only via their production but also via their degradation . Genes are transcribed only if their encoded proteins are required by the environmental or developmental conditions of a cell , and once a certain protein is no longer needed , it is rapidly degraded ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "proteins", "genetics", "molecular", "genetics", "biology", "genetics", "and", "genomics" ]	2012	Mediator Acts Upstream of the Transcriptional Activator Gal4
The Second Heart Field ( SHF ) has been implicated in several forms of congenital heart disease ( CHD ) , including atrioventricular septal defects ( AVSDs ) . Identifying the SHF gene regulatory networks required for atrioventricular septation is therefore an essential goal for understanding the molecular basis of AVS...	Atrioventricular septal defects ( AVSDs ) are a common severe class of congenital heart defects . Recent work demonstrates that events in the second heart field ( SHF ) progenitors , rather than in the heart , drive atrioventricular ( AV ) septation . Our laboratory has shown that both Hedgehog signaling and the T-box ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "organism", "development", "heart", "development", "organogenesis", "biology", "and", "life", "sciences", "morphogenesis" ]	2014	Foxf Genes Integrate Tbx5 and Hedgehog Pathways in the Second Heart Field for Cardiac Septation
Dengue has become a major concern for international public health . Frequent epidemic outbreaks are believed to be driven by a complex interplay of immunological interactions between its four co-circulating serotypes and large fluctuations in mosquito densities . Viral lineage replacement events , caused for example by...	Dengue fever and the more severe dengue haemorrhagic fever and dengue shock syndrome are mosquito borne viral infections that have seen a major increase in terms of global distribution and total case numbers over the last few decades . There are currently four antigenically distinct and potentially co-circulating dengu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "infectious", "diseases" ]	2010	Viral and Epidemiological Determinants of the Invasion Dynamics of Novel Dengue Genotypes
Rift Valley fever ( RVF ) is a major zoonotic and arboviral hemorrhagic fever . The conditions leading to RVF epidemics are still unclear , and the relative role of climatic and anthropogenic factors may vary between ecosystems . Here , we estimate the most likely scenario that led to RVF emergence on the island of May...	Rift Valley fever ( RVF ) is an arboviral hemorrhagic fever affecting primarily livestock in Africa and in the Arabian Peninsula . The conditions leading to RVF emergence are not fully understood , mainly because of data scarcity . Applied to the island of Mayotte ( our ecosystem under study ) , for which 12 years RVF ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "animal", "models", "of", "disease", "tropical", "diseases", "microbiology", "seasons", "rift", "valley", "fever", "age",...	2017	Drivers for Rift Valley fever emergence in Mayotte: A Bayesian modelling approach
Amyloids are highly organized protein aggregates that are associated with both neurodegenerative diseases such as Alzheimer disease and benign functions like skin pigmentation . Amyloids self-polymerize in a nucleation-dependent manner by recruiting their soluble protein/peptide counterpart and are stable against harsh...	Amyloids are highly organized protein aggregates that are associated with both neurodegenerative diseases such as Alzheimer disease and benign functions such as skin pigmentation . Amyloids self-polymerize by recruiting their soluble protein counterpart and remain stable against harsh physical , chemical , and biochemi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "neurological", "disorders", "pharmacology", "biophysics" ]	2008	Amyloid as a Depot for the Formulation of Long-Acting Drugs
HIV-1 entry requires the cell surface expression of CD4 and either the CCR5 or CXCR4 coreceptors on host cells . Individuals homozygous for the ccr5Δ32 polymorphism do not express CCR5 and are protected from infection by CCR5-tropic ( R5 ) virus strains . As an approach to inactivating CCR5 , we introduced CCR5-specifi...	For HIV to enter T cells , the virus first binds to a primary surface receptor CD4 and then to a coreceptor , either CCR5 or CXCR4 . Previously we engineered zinc-finger nucleases ( ZFNs ) to specifically disrupt the CCR5 gene in primary human T cells , the predominant cell type infected and killed by HIV . This makes ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biology" ]	2011	Engineering HIV-Resistant Human CD4+ T Cells with CXCR4-Specific Zinc-Finger Nucleases
Network robustness is a crucial property of the plant immune signaling network because pathogens are under a strong selection pressure to perturb plant network components to dampen plant immune responses . Nevertheless , modulation of network robustness is an area of network biology that has rarely been explored . Whil...	Robustness of a network is defined by how consistently it performs upon removal of some of its components . It is a common strategy for plant pathogens to attack components of the plant immune signaling network in an attempt to dampen plant immunity . Therefore , it is crucial for the plant immune signaling network to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Dual Regulation of Gene Expression Mediated by Extended MAPK Activation and Salicylic Acid Contributes to Robust Innate Immunity in Arabidopsis thaliana
Latent Epstein-Barr virus ( EBV ) infection contributes to both B-cell and epithelial-cell malignancies . However , whether lytic EBV infection also contributes to tumors is unclear , although the association between malaria infection and Burkitt lymphomas ( BLs ) may involve excessive lytic EBV replication . A particu...	Whether excessive lytic EBV infection increases the risk of EBV-induced cancers is not clear . A particular variant ( Zp-V3 ) of the viral promoter driving expression of the EBV immediate-early BZLF1 ( Z ) protein that mediates lytic viral reactivation has been reported to be over-represented ( relative to the prototyp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "luciferase", "milk", "immune", "cells", "breast", "milk", "pathology", "and", "laboratory", "medicine", "body", "fluids", "enzymes", "pathogens", "gene", "regulation", "immunology", "carcinomas", "enzymology"...	2018	A cancer-associated Epstein-Barr virus BZLF1 promoter variant enhances lytic infection
In many animal embryos , a specific gene expression pattern is established along the animal-vegetal axis soon after zygotic transcription begins . In the embryo of the ascidian Ciona intestinalis , soon after the division that separates animal and vegetal hemispheres into distinct blastomeres , maternal Gata . a and β-...	In embryogenesis of most animals , a specific gene expression pattern is established along the animal-vegetal axis first . In the embryo of the ascidian Ciona intestinalis , the activity of the maternal factor Gata . a is suppressed by β-catenin , which is active only in the vegetal hemisphere , and thereby these two f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "in", "situ", "hybridization", "molecular", "probe", "techniques", "gene", "regulation", "animals", "animal", "models", "developmental", "biology", "model", "organisms", "experimental", "organism", "systems", "sequence", "motif", "analysis", "molecular", "biology", "tec...	2017	Differential gene expression along the animal-vegetal axis in the ascidian embryo is maintained by a dual functional protein Foxd
CD8+ cytotoxic T-lymphocytes ( CTLs ) perform a critical role in the immune control of viral infections , including those caused by human immunodeficiency virus type 1 ( HIV-1 ) and hepatitis C virus ( HCV ) . As a result , genetic variation at CTL epitopes is strongly influenced by host-specific selection for either e...	The rapid accumulation of genetic variation in human viruses , such as human immunodeficiency virus type 1 ( HIV-1 ) and hepatitis C virus ( HCV ) , enables these pathogens to elude the immune system and forestalls the development of effective vaccines . This variation may be shaped by selection due to host-specific im...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "infectious", "diseases", "immunology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2007	Adaptation to Human Populations Is Revealed by Within-Host Polymorphisms in HIV-1 and Hepatitis C Virus
Rabies is traditionally considered a uniformly fatal disease after onset of clinical manifestations . However , increasing evidence indicates that non-lethal infection as well as recovery from flaccid paralysis and encephalitis occurs in laboratory animals as well as humans . Non-lethal rabies infection in dogs experim...	Inexorable lethality is still commonly attributed to rabies infection , although there is increasing evidence for non-lethal infection and even recovery from clinical rabies in various animal species and humans . This paper reports non-lethal infection in dogs . The striking difference between dogs that survived a wt R...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Presence of Virus Neutralizing Antibodies in Cerebral Spinal Fluid Correlates with Non-Lethal Rabies in Dogs
Adaptation to ecologically complex environments can provide insights into the evolutionary dynamics and functional constraints encountered by organisms during natural selection . Adaptation to a new environment with abundant and varied resources can be difficult to achieve by small incremental changes if many mutations...	Changing environmental conditions are the norm in biology . However , understanding adaptation to complex environments presents many challenges . For example , adaptation to resource-rich environments can potentially have many successful evolutionary trajectories to increased fitness . Even in conditions of plenty , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "metabolic", "processes", "parallel", "evolution", "evolutionary", "adaptation", "catabolism", "microbial", "genetics", "microbial", "genomics", "amino", "acid", "metabolism", "proteins", "metabolic", "pathways", "proteomics", "genetic", "drift", ...	2014	Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments
Entamoeba histolytica causes intestinal disease in endemic settings throughout the world . Diagnosis of E . histolytica infection would be improved by the identification of biomarkers that are expressed by cysts of E . histolytica , but not by cysts of closely related commensal species of Entamoeba . Herein , we descri...	Entamoeba histolytica is a prevalent human parasite requiring sensitive and specific detection . Assays available for Entamoeba detection utilize antibodies to detect parasite protein in stool , and they distinguish E . histolytica from nonpathogenic commensal amoeba . However , these tests have exhibited suboptimal se...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "nuclear", "staining", "immune", "physiology", "immunology", "parasitic", "protozoans", "protozoans", "antibodies", "immunologic", "techniques", "research", "and", "analysis", "methods", "monoclonal",...	2016	Species-Specific Immunodetection of an Entamoeba histolytica Cyst Wall Protein
To better understand off-target effects of widely prescribed psychoactive drugs , we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a model system . Because the known human targets of these drugs do not exist in yeast , we could employ the yeast gene deletio...	Neuropsychiatric disorders such as depression and psychosis affect one-quarter of all individuals during their lifetime , and despite efforts to improve the selectivity of psychoactive drugs , all are associated with side effects . Drug efficacy and tolerance are known to be linked to an individual's genetic profile , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics", "genetics", "and", "genomics/functional", "genomics" ]	2008	Off-Target Effects of Psychoactive Drugs Revealed by Genome-Wide Assays in Yeast
Influenza virus particles are assembled at the plasma membrane in concert with incorporation of the virus genome , but the details of its spatio-temporal regulation are not understood . Here we showed that influenza virus infection induces the assembly of pericentrosomal endocytic recycling compartment ( ERC ) through ...	Influenza virus particles are assembled at the plasma membrane in concert with incorporation of the virus genome , but the details of its spatiotemporal regulation are unknown . We found that the virus genome is transported to the plasma membrane using cholesterol-enriched recycling endosomes through cell cycle-indepen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Influenza Virus Induces Cholesterol-Enriched Endocytic Recycling Compartments for Budozone Formation via Cell Cycle-Independent Centrosome Maturation
While the exopolysaccharide component of the biofilm matrix has been intensively studied , much less is known about matrix-associated proteins . To better understand the role of these proteins , we undertook a proteomic analysis of the V . cholerae biofilm matrix . Here we show that the two matrix-associated proteins ,...	The bacterial multilayer biofilm consists of matrix-enclosed cells attached to each other to form large aggregates . The base of these aggregates may be attached to a living or non-living surface . The biofilm matrix most often contains at least one exopolysaccharide component and may also contain protein and DNA . Whi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "bacterial", "biofilms", "gram", "negative", "microbial", "mutation", "ecology", "coastal", "ecology", "microbial", "pathogens", "marine", "and", "aquatic", "sciences", "biology", "microbiology", "marine", "biology", "bacterial", "pathogens", "microbial", ...	2011	A Communal Bacterial Adhesin Anchors Biofilm and Bystander Cells to Surfaces
Social animals may share information to obtain a more complete and accurate picture of their surroundings . However , physical constraints on communication limit the flow of information between interacting individuals in a way that can cause an accumulation of errors and deteriorated collective behaviors . Here , we th...	Cooperative groups are abundant on all scales of the biological world . Despite much empirical evidence on a wide variety of natural communication schemes , there is still a growing need for rigorous tools to quantify and understand the information flows involved . Here , we borrow techniques from information theory an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "collective", "animal", "behavior", "computer", "and", "information", "sciences", "animal", "behavior", "zoology", "cognition", "population", "modeling", "network", "analysis", "social", "networks", "information", "theory", "biology", "and", "life", "sciences", "computa...	2014	Confidence Sharing: An Economic Strategy for Efficient Information Flows in Animal Groups
In many immunological processes chemoattraction is thought to play a role in guiding cells to their sites of action . However , based on in vivo two-photon microscopy experiments in the absence of cognate antigen , T cell migration in lymph nodes ( LNs ) has been roughly described as a random walk . Although it has bee...	T lymphocytes are important actors of the immune system that find and kill infected cells . Before a T cell can mount such an immune response , it has to be activated through contact with a dendritic cell ( DC ) carrying antigen relevant to the specificity of the T cell receptor . This process typically takes place in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immunology", "biology", "computational", "biology" ]	2012	Chemotactic Migration of T Cells towards Dendritic Cells Promotes the Detection of Rare Antigens
Identifying genetic factors responsible for serious adverse drug reaction ( SADR ) is of critical importance to personalized medicine . However , genome-wide association studies are hampered due to the lack of case-control samples , and the selection of candidate genes is limited by the lack of understanding of the und...	Why do tragedies caused by Vioxx or Avandia only happen to certain individuals ? The unexpected bindings among drugs and human proteins might play important roles in such serious adverse drug reactions ( SADRs ) . To mine these unexpected chemical-protein interactions , 162 drug molecules known to cause SADRs are ‘hybr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/pharmacogenomics", "computational", "biology/macromolecular", "structure", "analysis", "biochemistry/bioinformatics", "pharmacology/adverse", "reactions" ]	2009	Harvesting Candidate Genes Responsible for Serious Adverse Drug Reactions from a Chemical-Protein Interactome
In spite of the importance of hyaluronan in host protection against infectious organisms in the alveolar spaces , its role in mycobacterial infection is unknown . In a previous study , we found that mycobacteria interact with hyaluronan on lung epithelial cells . Here , we have analyzed the role of hyaluronan after myc...	Mycobacterium tuberculosis and Mycobacterium bovis are major bacterial pathogens that kill approximately 2 million people annually by causing tuberculosis . The M . tuberculosis complex has several strategies to parasitize the host . After infection is established , these pathogens are rarely eliminated from the host ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/medical", "microbiology" ]	2009	Mycobacteria Exploit Host Hyaluronan for Efficient Extracellular Replication
Functional magnetic resonance imaging ( fMRI ) measures brain activity by detecting the blood-oxygen-level dependent ( BOLD ) response to neural activity . The BOLD response depends on the neurovascular coupling , which connects cerebral blood flow , cerebral blood volume , and deoxyhemoglobin level to neuronal activit...	Functional magnetic resonance imaging ( fMRI ) is a widely used technique for measuring brain activity . However , the signal registered by fMRI is not a direct measurement of the neuronal activity in the brain , but it is influenced by the interplay between the metabolism , blood flow and blood volume in the active ar...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "body", "fluids", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "chemical", "compounds", "oxygen", "carbohydrates", "neuroscience", "glucose", "metabolism", "organic", "c...	2016	Mechanistic Mathematical Modeling Tests Hypotheses of the Neurovascular Coupling in fMRI
Mutations in dystrophin can lead to Duchenne muscular dystrophy or the more mild form of the disease , Becker muscular dystrophy . The hinge 3 region in the rod domain of dystrophin is particularly prone to deletion mutations . In-frame deletions of hinge 3 are predicted to lead to BMD , however the severity of disease...	Dystrophin functions like a large molecular spring between the muscle cytoskeleton and the extracellular matrix in order to protect the membrane from contraction-induced injury . Mutations in dystrophin can lead to a severe muscle wasting disease called Duchenne muscular dystrophy ( DMD ) in young boys . DMD patients a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/gene", "function", "genetics", "and",...	2010	The Polyproline Site in Hinge 2 Influences the Functional Capacity of Truncated Dystrophins
CellProfiler has enabled the scientific research community to create flexible , modular image analysis pipelines since its release in 2005 . Here , we describe CellProfiler 3 . 0 , a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional ( 3D ) image stacks , increasingly ...	The “big-data revolution” has struck biology: it is now common for robots to prepare cell samples and take thousands of microscopy images . Looking at the resulting images by eye would be extremely tedious , not to mention subjective . Thus , many biologists find they need software to analyze images easily and accurate...	[ "Abstract", "Introduction", "Results", "Future", "directions", "Materials", "and", "methods" ]	[ "open", "science", "blastocysts", "methods", "and", "resources", "engineering", "and", "technology", "signal", "processing", "applied", "mathematics", "biologists", "simulation", "and", "modeling", "algorithms", "developmental", "biology", "scientists", "mathematics", "sc...	2018	CellProfiler 3.0: Next-generation image processing for biology
The fungal pathogens Aspergillus fumigatus and Candida albicans are major health threats for immune-compromised patients . Normally , macrophages and neutrophil granulocytes phagocytose inhaled Aspergillus conidia in the two-dimensional ( 2-D ) environment of the alveolar lumen or Candida growing in tissue microabscess...	Aspergillus fumigatus and Candida albicans are the most common of all human pathogenic fungal germs . Normally , inhaled Aspergillus spores are destroyed by alveolar macrophages and polymorphonuclear neutrophils ( PMNs ) , both of which are lung phagocytes , i . e . , cells that kill inhaled microbes by ingestion . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "cell", "biology", "yeast", "and", "fungi", "in", "vitro", "immunology", "microbiology", "mus", "(mouse)" ]	2007	Environmental Dimensionality Controls the Interaction of Phagocytes with the Pathogenic Fungi Aspergillus fumigatus and Candida albicans
Activation-induced deaminase ( AID ) converts C to U and 5-methyl-C to T . These mutagenic activities are critical to immunoglobulin ( Ig ) gene diversification and epigenetic reprogramming , but they must be tightly controlled to prevent compromising cell fitness . AID acts in the nucleus but localizes predominately t...	Activation-induced deaminase ( AID ) is a mutagenic factor that plays a critical role in immunoglobulin gene diversification and also functions in early development to reprogram methylated regions of the genome . AID must be tightly regulated to prevent compromising cell fitness , but how this occurs is not thoroughly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "immune", "cells", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "metabolic", "processes", "cell", "processes", "immunology", "biological", "cultures", "in", "v...	2019	Activation-induced deaminase (AID) localizes to the nucleus in brief pulses
Bioluminescence techniques allow accurate monitoring of the circadian clock in single cells . We have analyzed bioluminescence data of Per gene expression in mouse SCN neurons and fibroblasts . From these data , we extracted parameters such as damping rate and noise intensity using two simple mathematical models , one ...	Earth's 24-h-rotation around its axis is mirrored in the circadian clock that resides within each of our cells , controlling expression of ∼10% of all genes . The circadian clock is constructed as a negative feedback loop , in which clock proteins inhibit their own synthesis . During the last decade , a picture has eme...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "biophysics/theory", "and", "simulation", "computational", "biology/systems", "biology", "cell", "biology/cell", "signaling" ]	2009	Quantification of Circadian Rhythms in Single Cells
Human fasciolosis is a re-emerging disease worldwide and is caused by species of the genus Fasciola ( F . hepatica and F . gigantica ) . Human fasciolosis can be diagnosed by classical coprological techniques , such as the Kato-Katz test , to reveal parasite eggs in faeces . However , although 100% specific , these met...	Fasciolosis is an important plant-borne trematode zoonosis . This disease is of both clinical and veterinary relevance and , according to the WHO , is considered a re-emerging disease that is spreading around the world . Fasciolosis has a serious impact on health because of the large size of the parasite and the effect...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "fascioliasis" ]	2011	Development and Evaluation of a New Lateral Flow Immunoassay for Serodiagnosis of Human Fasciolosis
Neonatal meningitis due to Escherichia coli K1 is a serious illness with unchanged morbidity and mortality rates for the last few decades . The lack of a comprehensive understanding of the mechanisms involved in the development of meningitis contributes to this poor outcome . Here , we demonstrate that depletion of mac...	Escherichia coli K1 is the most common cause of meningitis in premature infants; the mortality rate of this disease ranges from 5% to 30% . A better understanding of the pathogenesis of E . coli K1 meningitis is needed to develop new preventative strategies . We have shown that outer membrane protein A ( OmpA ) of E . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "microbiology/cellular", "microbiology", "and", "pathogenesis", "microbiology/innate", "immunity" ]	2010	Fcγ Receptor I Alpha Chain (CD64) Expression in Macrophages Is Critical for the Onset of Meningitis by Escherichia coli K1
Identifying the factors that determine microbial growth rate under various environmental and genetic conditions is a major challenge of systems biology . While current genome-scale metabolic modeling approaches enable us to successfully predict a variety of metabolic phenotypes , including maximal biomass yield , the p...	While current genome-scale metabolic modeling approaches enable us to successfully predict a variety of metabolic phenotypes , identifying the factors that determine microbial growth rate and the prediction of growth rates under various conditions is still an open challenge . Here we present a metabolic network-based a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "biology", "computational", "biology", "metabolic", "networks", "metabolism" ]	2012	Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
The success of Mycobacterium tuberculosis ( Mtb ) as a pathogen rests upon its ability to grow intracellularly in macrophages . Interferon-gamma ( IFN-γ ) is critical in host defense against Mtb and stimulates macrophage clearance of Mtb through an autophagy pathway . Here we show that the host protein ubiquilin 1 ( UB...	More people die from Mycobacterium tuberculosis ( Mtb ) , the causative agent of tuberculosis ( TB ) , than any other bacterial pathogen . It has long been appreciated that Mtb can survive and divide within macrophages , white blood cells that normally kill bacteria . Macrophages are able to partially control Mtb throu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Ubiquilin 1 Promotes IFN-γ-Induced Xenophagy of Mycobacterium tuberculosis
The burden of scrub typhus in endemic areas is poorly understood . This study aimed at estimating the proportion of hospitalisations and outpatient visits for undifferentiated fever in the community that may be attributable to scrub typhus . The study was a retrospective cohort with a nested case-control study conducte...	Scrub typhus is an important cause of fever in many Asian countries , including China , India , Vietnam and Japan . It is caused by the intra-cellular bacteria Orientia tsutsugamushi and is transmitted to humans by mite larvae ( chiggers ) which attach to the skin of the host . Scrub typhus is potentially life-threaten...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "typhus", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "immunology", "social", "sciences", "pulmonology", "social", "geography", "health", "care...	2019	Hospitalisations and outpatient visits for undifferentiated fever attributable to scrub typhus in rural South India: Retrospective cohort and nested case-control study
Studies in diverse organisms have revealed a surprising depth to the evolutionary conservation of genetic modules . For example , a systematic analysis of such conserved modules has recently shown that genes in yeast that maintain cell walls have been repurposed in vertebrates to regulate vein and artery growth . We re...	Yeast cells and vertebrate blood vessels would not seem to have much in common . However , we have discovered that during the course of evolution , a group of proteins whose function in yeast is to maintain cell walls has found an alternative use in vertebrates regulating angiogenesis . This remarkable repurposing of t...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "xenopus", "laevis", "microbiology", "animal", "models", "developmental", "biology", "model", "organisms", "morphogenesis", "biology", "mouse", "evolutionary", "genetics", "drug", "discovery", "systems", "biology", "yeast", "and", "fungal", "models", "s...	2012	Evolutionarily Repurposed Networks Reveal the Well-Known Antifungal Drug Thiabendazole to Be a Novel Vascular Disrupting Agent
The pseudohyphal growth response is a dramatic morphological transition and presumed foraging mechanism wherein yeast cells form invasive and surface-spread multicellular filaments . Pseudohyphal growth has been studied extensively as a model of conserved signaling pathways controlling stress responses , cell morphogen...	Cellular processes in eukaryotes are brought about through the contributions of large gene sets , and a continuing obstacle in studying these processes lies in the identification of critical constituent genes . The yeast pseudohyphal growth transition is an important example of a complex cellular growth transition . Du...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "fungal", "genomics", "functional", "genomics", "fungal", "genetics", "genetics", "biology", "and", "life", "sciences", "genomics" ]	2014	Pooled Segregant Sequencing Reveals Genetic Determinants of Yeast Pseudohyphal Growth
Sustained molecular oscillations are ubiquitous in biology . The obtained oscillatory patterns provide vital functions as timekeepers , pacemakers and spacemarkers . Models based on control theory have been introduced to explain how specific oscillatory behaviors stem from protein interaction feedbacks , whereas the en...	This paper presents a unique dissipation mode of converting biochemical free energy in ATP to regulatory function through the MinCDE bio-oscillator that marks the mid-cell position for symmetric bacterial cell division . Through assessing the oscillator’s performance-to-cost relation , we demonstrate that some dissipat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	An Optimal Free Energy Dissipation Strategy of the MinCDE Oscillator in Regulating Symmetric Bacterial Cell Division
When searching sequence databases for RNAs , it is desirable to score both primary sequence and RNA secondary structure similarity . Covariance models ( CMs ) are probabilistic models well-suited for RNA similarity search applications . However , the computational complexity of CM dynamic programming alignment algorith...	Database similarity searching is the sine qua non of computational molecular biology . Well-known and powerful methods exist for primary sequence searches , such as Blast and profile hidden Markov models . However , for RNA analysis , biologists rely not only on primary sequence but also on conserved RNA secondary stru...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "none", "computational", "biology" ]	2007	Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
Serratia marcescens is an entomopathogenic bacterium that opportunistically infects a wide range of hosts , including humans . In a model of septic injury , if directly introduced into the body cavity of Drosophila , this pathogen is insensitive to the host's systemic immune response and kills flies in a day . We find ...	The gut is a crucial interface of the host with its environment and represents an important portal of entry for pathogens . Here , we have developed a novel model of intestinal infections in the genetic model organism Drosophila melanogaster using the potent entomopathogen bacterium Serratia marcescens . In contrast to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "gastroenterology", "and", "hepatology", "immunology", "microbiology", "drosophila", "eubacteria" ]	2007	A Model of Bacterial Intestinal Infections in Drosophila melanogaster
Macrobrachium rosenbergii nodavirus ( MrNV ) is a pathogen of freshwater prawns that poses a threat to food security and causes significant economic losses in the aquaculture industries of many developing nations . A detailed understanding of the MrNV virion structure will inform the development of strategies to contro...	The freshwater prawn Macrobrachium rosenbergii is widely cultivated for food . Production is threatened by Macrobrachium rosenbergii nodavirus ( MrNV ) , the causative agent of white-tail disease . Outbreaks in hatcheries often result in mortality rates of up to 100% in larvae and post-larvae , leading to devastating e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "microbiology", "viral", "structure", "signs", "and", "symptoms", "aquatic", "environments", "microscopy", "fresh", "water", "centrifuga...	2018	Structure of the Macrobrachium rosenbergii nodavirus: A new genus within the Nodaviridae?
To validate and update a prediction rule for estimating the risk of leprosy-related nerve function impairment ( NFI ) . Prospective cohort using routinely collected data , in which we determined the discriminative ability of a previously published rule and an updated rule with a concordance statistic ( c ) . Additional...	Leprosy is caused by a bacterium that attacks the peripheral nerves . This may cause nerve function impairment ( NFI ) , resulting in handicaps and disabilities . Therefore , prediction and prevention of NFI is extremely important in the management of leprosy . In 2000 , a prediction rule for NFI was published , but ci...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evidence-based", "healthcare/clinical", "decision-making", "pathology/neuropathology", "infectious", "diseases/neglected", "tropical", "diseases", "neurological", "disorders/infectious", "diseases", "of", "the", "nervous", "system", "immunology/immune", "response", "dermatology/sk...	2008	Preventing Nerve Function Impairment in Leprosy: Validation and Updating of a Prediction Rule
Aging is a complex phenotype responsive to a plethora of environmental inputs; yet only a limited number of transcriptional regulators are known to influence life span . How the downstream expression programs mediated by these factors ( or others ) are coordinated into common or distinct set of aging effectors is an ad...	Animal life span is regulated in response to developmental and environmental inputs through coordinate changes in gene expression . Thus , longevity determinants include DNA-binding proteins that regulate gene expression by controlling transcription . Here , we explored the physiological role of the transcriptional reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "developmental...	2010	ETS-4 Is a Transcriptional Regulator of Life Span in Caenorhabditis elegans
Eradication of HIV infection will require the identification of all cellular reservoirs that harbor latent infection . Despite low or lack of CD4 receptor expression on Vδ2 T cells , infection of these cells has previously been reported . We found that upregulation of the CD4 receptor may render primary Vδ2 cells targe...	Antiretroviral therapy ( ART ) has led to a decreased HIV-related morbidity and mortality across the world . While successful ART restores health , it does not cure infection as latent HIV-1 remains integrated within different cell populations , unaffected by ART . To date resting memory CD4+ T cells are the best-chara...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Peripheral Vγ9Vδ2 T Cells Are a Novel Reservoir of Latent HIV Infection
Systemic lupus erythematosus ( SLE ) is an autoimmune disease with known genetic , epigenetic , and environmental risk factors . To assess the role of DNA methylation in SLE , we collected CD4+ T-cells , CD19+ B-cells , and CD14+ monocytes from 49 SLE patients and 58 controls , and performed genome-wide DNA methylation...	We have analyzed DNA methylation , an epigenetic modification that influences gene expression , in lupus patients and control subjects . Our analysis was run in three different immune cell types , T-cells , B-cells , and monocytes , to discern common epigenetic effects in lupus from cell type-specific effects . We have...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systemic", "lupus", "erythematosus", "medicine", "rheumatology", "genome", "analysis", "tools", "genomics", "x", "chromosome", "inactivation", "immune", "cells", "b", "cells", "chromosome", "biology", "genome", "scans", "monocytes", "genetics", "t", "cells", "epigene...	2013	Genome-Wide DNA Methylation Analysis of Systemic Lupus Erythematosus Reveals Persistent Hypomethylation of Interferon Genes and Compositional Changes to CD4+ T-cell Populations
Short interspersed nuclear elements ( SINEs ) are highly abundant , RNA polymerase III-transcribed noncoding retrotransposons that are silenced in somatic cells but activated during certain stresses including viral infection . How these induced SINE RNAs impact the host-pathogen interaction is unknown . Here we reveal ...	Short interspersed nuclear elements ( SINEs ) are noncoding mobile genetic elements that are present at ~106 copies per mammalian genome , roughly comprising 10% of mammalian genomic real estate . SINEs are typically transcriptionally silenced , though in some cases viral infection can promote their expression , yet to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Infection-Induced Retrotransposon-Derived Noncoding RNAs Enhance Herpesviral Gene Expression via the NF-κB Pathway
The var genes of the human malaria parasite Plasmodium falciparum present a challenge to population geneticists due to their extreme diversity , which is generated by high rates of recombination . These genes encode a primary antigen protein called PfEMP1 , which is expressed on the surface of infected red blood cells ...	The human malaria parasite kills nearly 1 million people each year globally . Frequent genetic exchange between malaria parasites creates enormous genetic diversity that largely explains the lack of an effective vaccine for the disease . Traditional phylogenetic tools cannot accommodate this type of diversity , however...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2013	A Network Approach to Analyzing Highly Recombinant Malaria Parasite Genes
Circadian clocks control many self-sustained rhythms in physiology and behavior with approximately 24-hour periodicity . In many organisms , oxidative stress and aging negatively impact the circadian system and sleep . Conversely , loss of the clock decreases resistance to oxidative stress , and may reduce lifespan and...	Circadian clocks are highly conserved from flies to humans . They control rhythms in most physiological functions , with free-running periods close to 24 h . Clock disruption , as occurs in shift-work or jet lag , is increasingly suspected to reduce healthspan . Aging and neurodegenerative disorders , like Parkinson’s ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "neurochemistry", "sleep", "dopaminergics", "neuroscience", "animals", "biomechanics", "biological", "locomotion", "animal", "models", "physiological", "processes", "drosophila", "melanogaster", "model", "organisms", ...	2017	Drosophila Clock Is Required in Brain Pacemaker Neurons to Prevent Premature Locomotor Aging Independently of Its Circadian Function
The benefits of ever-growing numbers of sequenced eukaryotic genomes will not be fully realized until we learn to decipher vast stretches of noncoding DNA , largely composed of transposable elements . Transposable elements persist through self-replication , but some genes once encoded by transposable elements have , th...	The genomes of complex organisms are mostly made up not of ordinary genes but of transposable elements . Transposable elements have been called “selfish DNA” because they normally persist by copying themselves , not by helping the organism to survive or reproduce . Yet transposable elements can help organisms to evolve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	A Gene Family Derived from Transposable Elements during Early Angiosperm Evolution Has Reproductive Fitness Benefits in Arabidopsis thaliana
All positive-strand RNA viruses induce the biogenesis of cytoplasmic membrane-bound virus factories for viral genome multiplication . We have previously demonstrated that upon plant potyvirus infection , the potyviral 6K2 integral membrane protein induces the formation of ER-derived replication vesicles that subsequent...	Potyviruses constitute the largest group of known plant viruses which includes many agriculturally important viruses . Like all other positive-strand RNA viruses , potyviruses induce the cytoplasmic membranous-bound virus factory for viral genome multiplication . But the mechanism by which such a factory is formed and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "virology", "plant", "pathogens", "plant", "pathology", "viral", "replication", "complex", "biology", "microbiology", "viral", "replication" ]	2013	The SNARE Protein Syp71 Is Essential for Turnip Mosaic Virus Infection by Mediating Fusion of Virus-Induced Vesicles with Chloroplasts
In human cytomegalovirus ( HCMV ) , tropism to epithelial and endothelial cells is dependent upon a pentameric complex ( PC ) . Given the structure of the placenta , the PC is potentially an important neutralizing antibody target antigen against congenital infection . The guinea pig is the only small animal model for c...	Congenital CMV is a leading cause of mental retardation and deafness in newborns . An effective vaccine against congenital CMV remains an elusive goal . HCMV encodes a pentameric glycoprotein complex ( PC ) necessary for tropism to epithelial , endothelial and myeloid cells . Given the structure of the placenta , the v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "microbiology", "vertebrates", "animals", "mammals", "fibroblasts", "epithelial", "cells", "animal", "models", "developmental", "biology", "model", "organisms", "immunoprecipitation", "connective", "tissue",...	2016	A Homolog Pentameric Complex Dictates Viral Epithelial Tropism, Pathogenicity and Congenital Infection Rate in Guinea Pig Cytomegalovirus
Correlated changes of nucleic or amino acids have provided strong information about the structures and interactions of molecules . Despite the rich literature in coevolutionary sequence analysis , previous methods often have to trade off between generality , simplicity , phylogenetic information , and specific knowledg...	The sequences of different components within and across genes often undergo coordinated changes in order to maintain the structures or functions of the genes . Identifying the coordinated changes—the “coevolution”—of those components in the context of evolution is important in predicting the structures , interactions ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Accession", "Numbers" ]	[ "eubacteria", "eukaryotes", "computational", "biology" ]	2007	Detecting Coevolution in and among Protein Domains
There is considerable variability in the susceptibility of smokers to develop chronic obstructive pulmonary disease ( COPD ) . The only known genetic risk factor is severe deficiency of α1-antitrypsin , which is present in 1–2% of individuals with COPD . We conducted a genome-wide association study ( GWAS ) in a homoge...	There is considerable variability in the susceptibility of smokers to develop chronic obstructive pulmonary disease ( COPD ) , which is a heritable multi-factorial trait . Identifying the genetic determinants of COPD risk will have tremendous public health importance . This study describes the first genome-wide associa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "respiratory", "medicine/copd", "and", "allied", "disorders", "genetics", "and", "genomics/gene", "discovery", "respiratory", "medicine/lung", "cancer" ]	2009	A Genome-Wide Association Study in Chronic Obstructive Pulmonary Disease (COPD): Identification of Two Major Susceptibility Loci
Interactions between antigen-presenting dendritic cells ( DCs ) and T cells are essential for the induction of an immune response . However , during malaria infection , DC function is compromised and immune responses against parasite and heterologous antigens are reduced . Here , we demonstrate that malaria infection o...	Malaria is a major infectious disease , affecting 500 million people and causing 2 . 7 million deaths each year . The severity of malaria is , in part , due to the failure of the host immune system to effectively clear an infection and generate protective immunity . Dendritic cells ( DCs ) are central to the immune sys...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "mus", "(mouse)", "immunology", "plasmodium" ]	2007	Malaria Impairs T Cell Clustering and Immune Priming despite Normal Signal 1 from Dendritic Cells
During meiosis , chromosomes align with their homologous pairing partners and stabilize this alignment through assembly of the synaptonemal complex ( SC ) . Since the SC assembles cooperatively yet is indifferent to homology , pairing and SC assembly must be tightly coordinated . We identify HAL-2 as a key mediator in ...	For successful segregation of homologous chromosomes during sexual reproduction , homologs must first identify and pair with their correct partners . Further , many organisms stabilize and maintain alignment between paired homologs through assembly of a highly ordered structure known as the synaptonemal complex ( SC ) ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosomal", "inheritance", "phenotypes", "heredity", "gene", "identification", "and", "analysis", "genetics", "molecular", "genetics", "biology", "genetics", "and", "genomics", "gene", "function" ]	2012	HAL-2 Promotes Homologous Pairing during Caenorhabditis elegans Meiosis by Antagonizing Inhibitory Effects of Synaptonemal Complex Precursors
Fatal outcomes of Ebola virus ( EBOV ) infections are typically preceded by a ‘sepsis-like’ syndrome and lymphopenia despite T cells being resistant to Ebola infection . The mechanisms that lead to T lymphocytes death remain largely unknown; however , the degree of lymphopenia is highly correlative with fatalities . He...	The latest outbreak of Ebola virus ( EBOV ) in West Africa resulted in more than 28 , 000 human infections including more than 11 , 000 deaths thus highlighting the necessity for the development of countermeasures . Monocytes and dendritic cells are among the primary targets of EBOV infection; infection of these critic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "immunology", "cell", "processes", "cell", "differentiation", "immune", "receptor", "signaling", "developmental", "biology", "membrane", "receptor", "si...	2017	Ebola virus glycoprotein directly triggers T lymphocyte death despite of the lack of infection
Visceral leishmaniasis ( VL ) is a vector-borne disease whose factors involved in transmission are poorly understood , especially in more urban and densely populated counties . In Brazil , the VL urbanization is a challenge for the control program . The goals were to identify the greater risk areas for human VL and the...	Visceral leishmaniasis ( VL ) is a vector-borne disease whose factors involved in transmission are poorly understood , especially in more urban and densely populated counties . In Brazil , the increasing occurrence of human VL cases in urban centers is a challenge for the control program . We aimed to identify the risk...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Relative Risk of Visceral Leishmaniasis in Brazil: A Spatial Analysis in Urban Area
Developing embryos exhibit a robust capability to reduce phenotypic variations that occur naturally or as a result of experimental manipulation . This reduction in variation occurs by an epigenetic mechanism called canalization , a phenomenon which has resisted understanding because of a lack of necessary molecular dat...	Animals have an astonishing ability to develop reliably in spite of variable conditions during embryogenesis . More than 60 years ago , it was proposed that this property of development , called canalization , results from genetic interactions that adjust biochemical reactions so as to bring about reliable outcomes . S...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "mathematics", "computational", "biology", "evolutionary", "biology", "biophysics", "genetics", "and", "genomics" ]	2009	Canalization of Gene Expression in the Drosophila Blastoderm by Gap Gene Cross Regulation
Comparative genomics usually involves managing the functional aspects of genomes , by simply comparing gene-by-gene functions . Following this approach , Mushegian and Koonin proposed a hypothetical minimal genome , Minimal Gene Set ( MGS ) , aiming for a possible oldest ancestor genome . They obtained MGS by comparing...	The origins of life represent a fascinating problem that has been addressed using different approaches and a wide variety of technologies . A theoretical approach consists of inferring a possible oldest ancestor genome from a well-defined comparison of current ones . A crucial problem concerns the validation of the pro...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "none", "computational", "biology" ]	2007	A Computational Approach to the Functional Screening of Genomes
Of all the age-related declines , memory loss is one of the most devastating . While conditions that increase longevity have been identified , the effects of these longevity-promoting factors on learning and memory are unknown . Here we show that the C . elegans Insulin/IGF-1 receptor mutant daf-2 improves memory perfo...	In humans , aging is often associated with a decline in cognitive function . Progress toward an understanding of the molecular mechanisms underlying the initiation and progression of age-related neuronal decline could be hastened by the development of experimental systems that quickly test early and true symptoms ( rat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "developmental", "biology/aging", "neurological", "disorders/cognitive", "neurology", "and", "dementia" ]	2010	Insulin Signaling and Dietary Restriction Differentially Influence the Decline of Learning and Memory with Age
TPL-2 ( COT , MAP3K8 ) kinase activates the MEK1/2-ERK1/2 MAPK signaling pathway in innate immune responses following TLR , TNFR1 and IL-1R stimulation . TPL-2 contributes to type-1/Th17-mediated autoimmunity and control of intracellular pathogens . We recently demonstrated TPL-2 reduces severe airway allergy to house ...	Helminth infections remain a huge global burden , causing significant morbidity in both animals and humans . Morbidity and recurring infections are associated with limited access to anthelmintic drugs . While vaccination remains the best available solution to treat helminthiasis , mechanisms of natural or vaccine-media...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "t", "helper", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "microbiome", "immunology", "cell-mediated", "immunity", "microbiology", "parasitic", "diseases", "microbial", "genomics", "digestive", "system", "white", "blood", "c...	2017	TPL-2 restricts Ccl24-dependent immunity to Heligmosomoides polygyrus
Cutaneous Leishmaniasis ( CL ) is a parasitic infection classified by the WHO as one of the most uncontrolled spreading neglected diseases . Syria is endemic for Leishmania tropica and Leishmania major , causing CL in the Eastern Mediterranean . The large-scale displacement of Syrian refugees exacerbated the spread of ...	Cutaneous Leishmaniasis ( CL ) is a parasitic infection caused by Leishmania ( L . ) parasites . In the Old World and the Near East , CL is mainly caused by L . major and L . tropica . The ongoing Syrian war and the resulting massive population displacement led to an alarming increase in the incidence of CL , in Syria ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "tropical", "diseases", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", ...	2018	EAPB0503: An Imiquimod analog with potent in vitro activity against cutaneous leishmaniasis caused by Leishmania major and Leishmania tropica
Successful execution of the meiotic program depends on the timely establishment and removal of sister chromatid cohesion . LAB-1 has been proposed to act in the latter by preventing the premature removal of the meiosis-specific cohesin REC-8 at metaphase I in C . elegans , yet the mechanism and scope of LAB-1 function ...	A critical step for achieving successful cell division is the regulation of how the cohesin complexes that bind sister chromatids are initially deposited , then maintained , and finally removed to allow the chromatids to separate into daughter cells . This is particularly challenging during meiosis , when the sister ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	LAB-1 Targets PP1 and Restricts Aurora B Kinase upon Entrance into Meiosis to Promote Sister Chromatid Cohesion
To understand how excitable tissues give rise to arrhythmias , it is crucially necessary to understand the electrical dynamics of cells in the context of their environment . Multicellular monolayer cultures have proven useful for investigating arrhythmias and other conduction anomalies , and because of their relatively...	One of the major challenges in trying to understand how arrhythmias can form in cardiac tissue is studying how the electrical activity of cardiac cells is affected by their surroundings . Current approaches have focused on studying cardiac cells in vitro and using computational models to elucidate the mechanisms behind...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "chemical", "compounds", "applied", "mathematics", "membrane", "potential", "fibrosis", "electrophysiology", "genetic", "algorithms", "neuroscience", "simulation", "and", "modeling", "algorithms", "development...	2017	Modeling an Excitable Biosynthetic Tissue with Inherent Variability for Paired Computational-Experimental Studies
Bacterial uptake by phagocytic cells is a vital event in the clearance of invading pathogens such as Streptococcus pneumoniae . A major role of the P-selectin glycoprotein ligand-1 ( PSGL-1 ) on leukocytes against invasive pneumococcal disease is described in this study . Phagocytosis experiments using different seroty...	S . pneumoniae is one of the most important and devastating human pathogens worldwide , mainly affecting young children , elderly people and immunocompromised patients . In terms of host immune defense against invasive pneumococcal isolates , professional phagocytes require receptor-mediated recognition of certain liga...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "enzyme-linked", "immunoassays", "pathogens", "cell", "processes", "immunology", "microbiology", "pulmonology", "pneumonia", "se...	2016	PSGL-1 on Leukocytes is a Critical Component of the Host Immune Response against Invasive Pneumococcal Disease
Odors are initially represented in the olfactory bulb ( OB ) by patterns of sensory input across the array of glomeruli . Although activated glomeruli are often widely distributed , glomeruli responding to stimuli sharing molecular features tend to be loosely clustered and thus establish a fractured chemotopic map . Ne...	Many sensory brain areas contain topographic maps where the physical location of neuronal activity contains information about a stimulus feature . In the first central processing center of the olfactory pathway , the olfactory bulb , chemically distinct odors often elicit spatially segregated input activity so that gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "danio", "(zebrafish)", "computational", "biology", "neuroscience" ]	2007	Topological Reorganization of Odor Representations in the Olfactory Bulb
In countries with a high prevalence of tuberculosis there is high coincident of helminth infections that might worsen disease outcome . While Mycobacterium tuberculosis ( Mtb ) gives rise to a pro-inflammatory Th1 response , a Th2 response is typical of helminth infections . A strong Th2 response has been associated wi...	The innate immune system is the first response against invading pathogens like the bacterium Mycobacterium tuberculosis ( Mtb ) or parasitic worms ( helminths ) . The adaptive immune response takes over after being primed by the innate immune response . Infection with Mycobacterium tuberculosis typically gives rise to ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "schistosoma", "invertebrates", "schistosoma", "mansoni", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "helminths", "immunology", "parasitic", "diseases", "animals", "dev...	2017	Species dependent impact of helminth-derived antigens on human macrophages infected with Mycobacterium tuberculosis: Direct effect on the innate anti-mycobacterial response
Bioactive peptides ( i . e . , neuropeptides or peptide hormones ) represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function . In vertebrates , peptide hormones play an integral role in endocrine signaling between the brain and the gonads th...	Flatworms cause diseases affecting hundreds of millions of people , so understanding what influences their reproductive activity is of fundamental importance . Neurally derived signals have been suggested to coordinate sexual reproduction in free-living flatworms , yet the neuroendocrine signaling repertoire has not be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "chemical", "biology/protein", "chemistry", "and", "proteomics", "neuroscience", "genetics", "and", "genomics/functional", "genomics" ]	2010	Genome-Wide Analyses Reveal a Role for Peptide Hormones in Planarian Germline Development
Assessment of the response to the 2014–15 Ebola outbreak indicates the need for innovations in data collection , sharing , and use to improve case detection and treatment . Here we introduce a Machine Learning pipeline for Ebola Virus Disease ( EVD ) prognosis prediction , which packages the best models into a mobile a...	We introduce a machine-learning framework and field-deployable app to predict outcome of Ebola patients from their initial clinical symptoms . Recent work from other authors also points out to the clinical factors that can be used to better understand patient prognosis , but there is currently no predictive model that ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "clinical", "laboratory", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "neuroscience", "artificial", "neural", "networks", "viruses", "diarrhea"...	2016	Transforming Clinical Data into Actionable Prognosis Models: Machine-Learning Framework and Field-Deployable App to Predict Outcome of Ebola Patients
Many bacteria have complex cell shapes , but the mechanisms producing their distinctive morphologies are still poorly understood . Caulobacter crescentus , for instance , exhibits a stalk-like extension that carries an adhesive holdfast mediating surface attachment . This structure forms through zonal peptidoglycan bio...	Bacteria show a variety of different cell shapes that are critical for survival in the environmental niche they inhabit . While the mechanisms generating the prototypic rod-shaped and coccoid morphologies have been studied intensively , only little is known about the processes that underlie the formation of more comple...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cell", "walls", "chemical", "compounds", "phosphates", "caulobacter", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cell", "polarity", "materials", "science", "cellular", "structures", "and", "organelles", "bacteria", "macrom...	2019	A specialized MreB-dependent cell wall biosynthetic complex mediates the formation of stalk-specific peptidoglycan in Caulobacter crescentus
Much effort is being devoted for developing new indicators to evaluate the human exposure to Aedes mosquito bites and the risk of arbovirus transmission . Human antibody ( Ab ) responses to mosquito salivary components could represent a promising tool for evaluating the human-vector contact . To develop a specific biom...	Aedes aegypti mosquito is the primary vector of major ( re ) -emerging human arboviruses , such as Dengue and Chikungunya . In absence of effective treatment and vaccine , the evaluation of human exposure to vector bites is crucial to estimate the risk of the viruses' transmission . Currently , exposure to Aedes aegypt...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "antigen", "processing", "and", "recognition", "entomology", "dengue", "fever", "neglected", "tropical", "diseases", "immunology", "biology", "arboviral", "infections", "zoology", "infectious", "disease", "control", "immune", "respons...	2012	First Attempt To Validate Human IgG Antibody Response to Nterm-34kDa Salivary Peptide as Biomarker for Evaluating Exposure to Aedes aegypti Bites
In checkpoint-deficient cells , DNA double-strand breaks ( DSBs ) are produced during replication by the structure-specific endonuclease MUS81 . The mechanism underlying MUS81-dependent cleavage , and the effect on chromosome integrity and viability of checkpoint deficient cells is only partly understood , especially i...	The replication checkpoint ensures a smooth duplication of the genome . It counteracts the replication stress , which can cause chromosome rearrangements as found in most tumours . Given the importance of dealing with perturbed replication , and since in tumours secondary mutations or epigenetic changes may hamper effi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Survival of the Replication Checkpoint Deficient Cells Requires MUS81-RAD52 Function
In the olfactory bulb , lateral inhibition mediated by granule cells has been suggested to modulate the timing of mitral cell firing , thereby shaping the representation of input odorants . Current experimental techniques , however , do not enable a clear study of how the mitral-granule cell network sculpts odor inputs...	In the paper we address the role of lateral inhibition in a neuronal network . It is an essential and widespread mechanism of neural processing that has been demonstrated in many brain systems . A key finding that would reveal how and to what extent it can modulate input signals and give rise to some form of perception...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "circuit", "models", "computational", "neuroscience", "olfactory", "system", "biology", "sensory", "systems", "neuroscience", "coding", "mechanisms" ]	2013	Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit
Salmonella enterica serotype Typhimurium ( S . Typhimurium ) is one of the most frequent causes of food-borne illness in humans and usually associated with acute self-limiting gastroenteritis . However , in immunocompromised patients , the pathogen can disseminate and lead to severe systemic diseases . S . Typhimurium ...	Salmonella Typhimurium is one of the most common causes of gastroenteritis in humans . In immunocompromised patients , the pathogen can cause systemic infections . Crucial virulence factors are encoded on two Salmonella pathogenicity islands SPI-1 and SPI-2 . While SPI-1 encodes virulence factors essential for host cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "immunology", "microbiology", "directed", "cell", "migration", "salmonellosis...	2018	Salmonella Typhimurium effector SseI inhibits chemotaxis and increases host cell survival by deamidation of heterotrimeric Gi proteins
The type I interferon ( IFN ) response is a crucial innate immune signalling pathway required for defense against viral infection . Accordingly , the great majority of mammalian viruses possess means to inhibit this important host immune response . Here we show that vaccinia virus ( VACV ) strain Western Reserve protei...	In response to a viral infection , infected host cells mount an early , innate immune response to limit viral replication and spread . Type I interferons ( IFNs ) are produced by a cell when a viral infection is detected and are a crucial aspect of this early immune response . IFNs are released from the infected cell a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "luciferase", "molecular", "probe", "techniques", "enzymes", "enzymology", "immunoblotting", "plasmid", "construction", "signal", "inhibition", "immunoprecipitation", "dna", "construction", "molecular", "biology", "techniques", "research", "and", "analysis"...	2016	Vaccinia Virus Protein C6 Inhibits Type I IFN Signalling in the Nucleus and Binds to the Transactivation Domain of STAT2
Soil-transmitted helminth ( STH ) infections are endemic in Honduras and efforts are underway to decrease their transmission . However , current evidence is lacking in regards to their prevalence , intensity and their impact on children's health . To evaluate the prevalence and intensity of STH infections and their ass...	Soil-transmitted helminth ( STH ) infections are endemic in Honduras but their impact on children's health is not well studied . With the purpose of determining the prevalence and intensity of STH infections and their association with nutritional status in a sample of Honduran children , a cross-sectional study was und...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "epidemiology", "biology", "microbiology", "parasitology" ]	2013	Soil-Transmitted Helminth Infections and Nutritional Status in School-age Children from Rural Communities in Honduras
Cryptococcus neoformans is a leading cause of invasive fungal infections among immunocompromised patients . However , the cellular constituents of the innate immune response that promote clearance versus progression of infection upon respiratory acquisition of C . neoformans remain poorly defined . In this study , we f...	Cryptococcus neoformans is a fungus that is prevalent throughout the environment and can cause a fatal infection of the central nervous system when inhaled into the lungs by patients with impaired immune systems . Our understanding of the immune responses that either help clear C . neoformans from the lungs or permit d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "cryptococcosis", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "immune", "cells", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "pathogens", "immunology", "microbiology", "pulmonology",...	2019	Inflammatory monocytes are detrimental to the host immune response during acute infection with Cryptococcus neoformans
Membrane proteins are frequently present in crowded environments , which favour lateral association and , on occasions , two-dimensional crystallization . To better understand the non-specific lateral association of a membrane protein we have characterized the free energy landscape for the dimerization of a bacterial o...	Cells are surrounded by selectively-permeable bilayer membranes , enabling the cell to control its internal environment . Embedded within these membranes are a variety of membrane proteins , many of which facilitate this environmental control and are integral to numerous metabolic processes . Their location within the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "properties", "physics", "biochemistry", "lipids", "computational", "chemistry", "transmembrane", "proteins", "protein", "interactions", "molecular", "dynamics", "biochemistry", "simulations", "proteins", "biophysic", "al", "simulations", "dimerization", "statisti...	2014	The Free Energy Landscape of Dimerization of a Membrane Protein, NanC
Thioester-containing protein 1 ( TEP1 ) is a central component in the innate immune response of Anopheles gambiae to Plasmodium infection . Two classes of TEP1 alleles , TEP1S and TEP1R , are found in both laboratory strains and wild isolates , related by a greater or lesser susceptibility , respectively to both P . ...	Anopheles mosquitoes transmit malaria , the world's most devastating parasitic disease , of which Anopheles gambiae is the principal vector for malaria in Sub-Saharan Africa . Different populations of mosquitoes vary widely in how readily they become infected with malaria parasites , while some strains do not transmit ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "immune", "system", "proteins", "proteins", "immunity", "innate", "immunity", "protein", "structure", "vector", "biology", "immunology", "biology", "microbiology", "anopheles", "host-pathogen", "interaction" ]	2012	Molecular Basis for Genetic Resistance of Anopheles gambiae to Plasmodium: Structural Analysis of TEP1 Susceptible and Resistant Alleles
Many types of large cells have multiple nuclei . In skeletal muscle fibers , the nuclei are distributed along the cell to maximize their internuclear distances . This myonuclear positioning is crucial for cell function . Although microtubules , microtubule associated proteins , and motors have been implicated , mechani...	How the cell organizes its interior is one of the fundamental biological questions , but the principles of organelles’ positioning remains largely unclear . In this study we use computational modeling and image analysis to elucidate mechanisms of positioning of multiple nuclei in muscle cells . We start with the genera...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "kinesins", "microtubules", "muscle", "tissue", "geometry", "animals", "aspect", "ratio", "simulation", "and", "modeling", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "systems", "scien...	2018	Mechanical positioning of multiple nuclei in muscle cells
Notch receptors act as ligand-dependent membrane-tethered transcription factors with a prominent role in binary cell fate decisions during development , which is conserved across species . In addition there is increasing evidence for other functions of Notch , particularly in connection with Wnt signalling: Notch is ab...	Establishment of the correct shape and pattern of tissues within an organism requires the integration of molecular information present in signalling and transcriptional networks and demands delicate exchanges and balances of their activities . A large body of experimental work has revealed close correlations in the act...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "cell", "biology", "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling" ]	2009	Ligand-Independent Traffic of Notch Buffers Activated Armadillo in Drosophila
Accurate diagnosis of infection with the parasite Strongyloides stercoralis is hampered by the low concentration of larvae in stool , rendering parasitological diagnosis insensitive . Even if the more sensitive agar plate culture method is used repeated stool sampling is necessary to achieve satisfactory sensitivity . ...	Strongyloides stercoralis is almost unique among human nematode infections in its ability to replicate within a patient's body , potentially leading to life-long infections if left untreated . Given the potential for severe life threatening Strongyloides infections and the unsatisfactory results of current parasitologi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "infectious", "diseases/neglected", "tropical", "diseases" ]	2011	A Coproantigen Diagnostic Test for Strongyloides Infection

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