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A series of compounds based on the dipeptidyl nitrile scaffold were synthesized and assayed for their inhibitory activity against the T . cruzi cysteine protease cruzain . Structure activity relationships ( SARs ) were established using three , eleven and twelve variations respectively at the P1 , P2 and P3 positions ....	Chagas disease is a parasitic infection with high morbidity and mortality that is endemic in much of Latin America where it remains a serious public health problem . With increased migration , Chagas disease represents an emerging worldwide challenge and there is an urgent , unmet need for safe and effective medication...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2015	Molecular Design, Synthesis and Trypanocidal Activity of Dipeptidyl Nitriles as Cruzain Inhibitors
The bacterial H-NS protein silences expression from sequences with higher AT-content than the host genome and is believed to buffer the fitness consequences associated with foreign gene acquisition . Loss of H-NS results in severe growth defects in Salmonella , but the underlying reasons were unclear . An experimental ...	H-NS is an abundant DNA-binding protein found in enteric bacteria including the important pathogens Escherichia , Salmonella , Vibrio , and Yersinia , that plays a primary role in defending the bacterial genome by silencing AT-rich foreign genes . H-NS has been hypothesized to facilitate the evolution of bacterial spec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "horizontal", "gene", "transfer", "medicine", "and", "health", "sciences", "microbiology", "gene", "transfer", "bacterial", "diseases", "enterobacteriaceae", "bacteria", "bacterial", "pathogens", "foodborne", "diseases", "infectious", "diseases", "escherichia", "coli", "i...	2014	Silencing by H-NS Potentiated the Evolution of Salmonella
Successful prediction of the likely paths of tumor progression is valuable for diagnostic , prognostic , and treatment purposes . Cancer progression models ( CPMs ) use cross-sectional samples to identify restrictions in the order of accumulation of driver mutations and thus CPMs encode the paths of tumor progression ....	Knowing the likely paths of tumor progression is instrumental for cancer precision medicine as it would allow us to identify genetic targets that block disease progression and to improve therapeutic decisions . Direct information about paths of tumor progression is scarce , but cancer progression models ( CPMs ) , whic...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "infographics", "simulation", "and", "modeling", "epistasis", "mutation", "population", "biology", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "fitness", "epistasis", "evolutionary", "genetics", "population", "metrics", "birth",...	2019	Every which way? On predicting tumor evolution using cancer progression models
The human gut microbiota is an important metabolic organ , yet little is known about how its individual species interact , establish dominant positions , and respond to changes in environmental factors such as diet . In this study , gnotobiotic mice were colonized with an artificial microbiota comprising 12 sequenced h...	Our intestines are populated by an almost unimaginably large number of microbial cells , most of which are bacteria . This species assemblage operates as a microbial metabolic organ , performing myriad tasks that contribute to our well-being , including processing components of our diet . The way this incredible machin...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "microbial", "metabolism", "microbiology", "bacterial", "biochemistry", "animal", "models", "metagenomics", "model", "organisms", "microbial", "physiology", "medical", "microbiology", "biology", "proteomics", "mouse", "microbial", "ecology", "com...	2013	Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome
Emergomyces africanus is a thermally dimorphic fungus that causes a systemic mycosis in immunocompromised persons in South Africa . Infection is presumed to follow inhalation of airborne propagules . We developed a quantitative PCR protocol able to detect as few as 5 Es . africanus propagules per day . Samples were col...	Emergomyces africanus is a recently described dimorphic fungus that causes a serious and often fatal disease in immunocompromised patients in South Africa . Infection is presumed to occur via inhalation of infectious propagules; however , no attempts have yet been made to detect this fungus in the air . We developed a ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "condensed", "matter", "physics", "microbiology", "organisms", "fungi", "molecular", "biology", "techniques", "fungal", "diseases", "dna", "fungal", "pathogens", "extract...	2018	Molecular detection of airborne Emergomyces africanus, a thermally dimorphic fungal pathogen, in Cape Town, South Africa
Persistent infections are subject to constant surveillance by CD8+ cytotoxic T cells ( CTL ) . Their control should therefore depend on MHC class I-restricted epitope presentation . Many epitopes are described for γ-herpesviruses and form a basis for prospective immunotherapies and vaccines . However the quantitative r...	Chronic viral infections cause huge morbidity and mortality worldwide . γ-herpesviruses provide an example relevant to all human demographics , causing , inter alia , Hodgkin's disease , Burkitt's lymphoma , Kaposi's Sarcoma , and nasopharyngeal carcinoma . The proliferation of latently infected B cells and their contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "immune", "cells", "lymphocyte", "proliferation", "viral", "transmission", "and", "infection", "immunity", "to", "infections", "immunology", "microbiology", "lymphocyte", "activation", "herpesviruses", "viral", "load", "animal", "models", "of", "infect...	2014	Defining Immune Engagement Thresholds for In Vivo Control of Virus-Driven Lymphoproliferation
Aedes mediovittatus mosquitoes are found throughout the Greater Antilles in the Caribbean and often share the same larval habitats with Ae . Aegypti , the primary vector for dengue virus ( DENV ) . Implementation of vector control measures to control dengue that specifically target Ae . Aegypti may not control DENV tra...	Dengue is a potentially life-threatening tropical disease caused by four serotypes of virus , dengue virus 1 , -2 , -3 , and -4 . Worldwide , as many as 390 million people become infected with dengue virus each year after being bitten by infectious Aedes mosquitoes . Unfortunately , there is no commercially available v...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Comparison of Vector Competence of Aedes mediovittatus and Aedes aegypti for Dengue Virus: Implications for Dengue Control in the Caribbean
Seeds of flowering plants can be formed sexually or asexually through apomixis . Apomixis occurs in about 400 species and is of great interest for agriculture as it produces clonal offspring . It differs from sexual reproduction in three major aspects: ( 1 ) While the sexual megaspore mother cell ( MMC ) undergoes meio...	In flowering plants , asexual reproduction through seeds ( apomixis ) likely evolved from sexual ancestors several times independently . Only three key developmental steps differ between sexual reproduction and apomixis . In contrast to sexual reproduction , in apomicts the first cell of the female reproductive lineage...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "developmental", "biology", "plant", "science", "gene", "expression", "plant", "genomics", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "plant", "genetics", "genomics", "plant", "biotechnology" ]	2014	Apomictic and Sexual Germline Development Differ with Respect to Cell Cycle, Transcriptional, Hormonal and Epigenetic Regulation
Exome sequencing studies in complex diseases are challenged by the allelic heterogeneity , large number and modest effect sizes of associated variants on disease risk and the presence of large numbers of neutral variants , even in phenotypically relevant genes . Isolated populations with recent bottlenecks offer advant...	We explored the coding regions of 3 , 000 Finnish individuals with 3 , 000 non-Finnish Europeans ( NFEs ) using whole-exome sequence data , in order to understand how an individual from a bottlenecked population might differ from an individual from an out-bred population . We provide empirical evidence that there are m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genomics", "genetic", "disorders", "phenotypes", "genetic", "association", "studies", "genome", "analysis", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "quantitative", "traits", "computa...	2014	Distribution and Medical Impact of Loss-of-Function Variants in the Finnish Founder Population
The study of HIV-infected “controllers” who are able to maintain low levels of plasma HIV RNA in the absence of antiretroviral therapy ( ART ) may provide insights for HIV cure and vaccine strategies . Despite maintaining very low levels of plasma viremia , controllers have elevated immune activation and accelerated at...	HIV-infected “controllers” are rare individuals who are HIV-seropositive but are able to maintain low levels of plasma HIV RNA in the absence of antiretroviral therapy ( ART ) . There has been intense interest in characterizing these unique individuals because they have been considered as a potential model for a “funct...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Prospective Antiretroviral Treatment of Asymptomatic, HIV-1 Infected Controllers
Intracellular Salmonella enterica serovar Typhimurium ( STM ) deploy the Salmonella Pathogenicity Island 2-encoded type III secretion system ( SPI2-T3SS ) for the massive remodeling of the endosomal system for host cells . This activity results in formation of an extensive interconnected tubular network of Salmonella-i...	The facultative intracellular bacterium Salmonella enterica has evolved sophisticated mechanisms to adapt to life inside a pathogen-containing vacuole in mammalian host cells . Intracellular Salmonella manipulate the host cell endosomal system resulting in formation of a complex network of tubular vesicles , termed Sal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "protein", "metabolism", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "mu...	2019	Proteomics of intracellular Salmonella enterica reveals roles of Salmonella pathogenicity island 2 in metabolism and antioxidant defense
Manipulation of sex determination pathways in insects provides the basis for a wide spectrum of strategies to benefit agriculture and public health . Furthermore , insects display a remarkable diversity in the genetic pathways that lead to sex differentiation . The silkworm , Bombyx mori , has been cultivated by humans...	The sex determination system extremely diverse among organisms including insects in which even each order occupy a different manner of sex determination . The silkworm , Bombyx mori , is a lepidopteran model insect with economic importance . The mechanism of the silkworm sex determination has been in mystery for a long...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "invertebrates", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "silkworms", "experimental", "organism", "systems", "embryos", "morphogenesis", "drosophila", "genetic", "engineering", "research",...	2017	Bombyx mori P-element Somatic Inhibitor (BmPSI) Is a Key Auxiliary Factor for Silkworm Male Sex Determination
The traditional view of cancer as a genetic disease that can successfully be treated with drugs targeting mutant onco-proteins has motivated whole-genome sequencing efforts in many human cancer types . However , only a subset of mutations found within the genomic landscape of cancer is likely to provide a fitness advan...	Evolutionary dynamic models have been intensively studied to elucidate the process of tumorigenesis . One key aspect of studying tumorigenesis is to distinguish the “driver” mutations providing a fitness advantage to cancer cells against neutral “passenger” or “hitchhiking” mutations . Many statistical models to addres...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer
Cancer genomes exhibit profound somatic copy number alterations ( SCNAs ) . Studying tumor SCNAs using massively parallel sequencing provides unprecedented resolution and meanwhile gives rise to new challenges in data analysis , complicated by tumor aneuploidy and heterogeneity as well as normal cell contamination . Wh...	Somatic copy number alterations ( SCNAs ) are essential in oncogensis and progression of a variety of cancers . Accurate identification and quatification of SCNAs are fundamental in the effort of cataloging different variants in cancer genome . This task has its own challenges due to complex nature of tumor SCNA profil...	[ "Abstract", "Introduction", "Methods", "and", "Materials", "Results", "Discussion" ]	[]	2015	SAAS-CNV: A Joint Segmentation Approach on Aggregated and Allele Specific Signals for the Identification of Somatic Copy Number Alterations with Next-Generation Sequencing Data
NKT cells play an important role in autoimmune diseases , tumor surveillance , and infectious diseases , providing in most cases protection against infection . NKT cells are reactive to CD1d presented glycolipid antigens . They can modulate immune responses by promoting the secretion of type 1 , type 2 , or immune regu...	Kala azar ( visceral leishmaniasis ) is a deadly disease caused by the parasitic protozoa Leishmania donovani . In absence of a suitable vaccine , the incidence of leishmaniasis has increased . The World Health Organization observes that , if the disease is not treated , the fatality rate in developing countries can be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "glycolipids", "immune", "cells", "protein", "interactions", "antigen-presenting", "cells", "immunology", "glycoproteins", "immunomodulation", "major", "histocompatibility", "complex", "t", "cells", "biology", "proteomics", "immune", "response", "immunopathology", "biochemist...	2012	TLR4 and NKT Cell Synergy in Immunotherapy against Visceral Leishmaniasis
Interpreting the impact of human genome variation on phenotype is challenging . The functional effect of protein-coding variants is often predicted using sequence conservation and population frequency data , however other factors are likely relevant . We hypothesized that variants in protein post-translational modifica...	Individual human genomes differ in numerous and infrequent small-scale changes such as single nucleotide variants . Understanding the biological role of variation and impact on phenotypes such as physical appearance or disease risk is an important challenge . We studied human variation of post-translational modificatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Evolutionary Constraint and Disease Associations of Post-Translational Modification Sites in Human Genomes
Pneumococcal neuraminidase is a key enzyme for sequential deglycosylation of host glycans , and plays an important role in host survival , colonization , and pathogenesis of infections caused by Streptococcus pneumoniae . One of the factors that can affect the activity of neuraminidase is the amount and position of ace...	Neuraminidase activity is critical for pneumococcal colonization and virulence as it is required for efficient cleavage of host glycans for nutritional requirements , attachment , and translocation of the microbe through biological membranes . Modifications , such as O-acetylation , in terminal sialic acid can affect t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "pneumococcus", "pathology", "and", "laboratory", "medicine", "sialic", "acids", "viral", "transmission", "and", "infection", "enzymes", "pathogens", "enzymology", "microbiology", "carbo...	2017	Deacetylation of sialic acid by esterases potentiates pneumococcal neuraminidase activity for mucin utilization, colonization and virulence
In non-alcoholic fatty liver disease ( NAFLD ) , lipid build-up and the resulting damage is known to occur more severely in pericentral cells . Due to the complexity of studying individual regions of the sinusoid , the causes of this zone specificity and its implications on treatment are largely ignored . In this study...	Fat build up in liver is known to increase the likelihood of developing numerous health problems around the body including cardiovascular problems , desensitisation to the hormone insulin leading to type 2 diabetes , and the development of fibrous tissue in liver ( fibrosis ) resulting in loss of liver function ( cirrh...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "steatosis", "anatomical", "pathology", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "diabetic", "endocrinology", "glucose", "metabolism", "cytopathology", "liver", "diseases", "hormones", "gastroentero...	2016	A Computational Model of Hepatic Energy Metabolism: Understanding Zonated Damage and Steatosis in NAFLD
Virulence functions of bacterial pathogens are often energetically costly and thus are subjected to intricate regulatory mechanisms . In Salmonella , invasion of the intestinal epithelium , an essential early step in virulence , requires the production of a multi-protein type III secretion apparatus . The pathogen miti...	Pathogenic bacteria tightly regulate the expression of their virulence functions to balance survival and proliferation within an animal host against the fitness costs that these functions engender . Salmonella has evolved an energetically favorable means to invade the intestinal epithelium , required for its virulence ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "messenger", "rna", "microbiology", "dna", "transcription", "bacterial", "diseases", "mutation", "regulator", "genes", "enterobacteriaceae", "gene", "types", "bacteria", ...	2019	Salmonella invasion is controlled through the secondary structure of the hilD transcript
Vascular cell adhesion molecule-1 ( VCAM-1 ) interacts with its major ligand very late antigen-4 ( VLA-4 ) to mediate cell adhesion and transendothelial migration of leukocytes . We report an important role for VCAM-1/VLA-4 interactions in the generation of immune responses during experimental visceral leishmaniasis ca...	VCAM-1 and its major ligand VLA-4 are adhesion molecules required for the recruitment and movement of leukocytes within tissue . In this study , we have investigated the role of these molecules during an experimental infection with Leishmania donovani , a protozoan parasite that causes a chronic disease called visceral...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections", "immunology/immune", "response", "pathology/immunology" ]	2008	VCAM-1 and VLA-4 Modulate Dendritic Cell IL-12p40 Production in Experimental Visceral Leishmaniasis
Diabetic kidney disease , or diabetic nephropathy ( DN ) , is a major complication of diabetes and the leading cause of end-stage renal disease ( ESRD ) that requires dialysis treatment or kidney transplantation . In addition to the decrease in the quality of life , DN accounts for a large proportion of the excess mort...	The global prevalence of diabetes has reached epidemic proportions , constituting a major health care problem worldwide . Diabetic kidney disease , or diabetic nephropathy ( DN ) —the major long term microvascular complication of diabetes—is associated with excess mortality among patients with type 1 diabetes . Even th...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "rna", "interference", "chronic", "kidney", "disease", "diabetic", "endocrinology", "gene", "expression", "endocrinology", "diabetes", "and", "endocrinology", "biology", "genetics", "diabetes", "mellitus", "type", "1", ...	2012	New Susceptibility Loci Associated with Kidney Disease in Type 1 Diabetes
FUS-proteinopathies , a group of heterogeneous disorders including ALS-FUS and FTLD-FUS , are characterized by the formation of inclusion bodies containing the nuclear protein FUS in the affected patients . However , the underlying molecular and cellular defects remain unclear . Here we provide evidence for mitochondri...	Amyotrophic lateral sclerosis ( ALS ) and frontotemporal lobar degeneration ( FTLD ) are two groups of common and devastating neurodegenerative diseases , characterized by losses of selected groups of neurons . Mutations in the FUS gene have been associated with ALS , whereas inclusion bodies containing the FUS protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	FUS Interacts with HSP60 to Promote Mitochondrial Damage
Aedes aegypti is the primary vector of dengue fever , a viral disease which has an estimated incidence of 390 million infections annually . Conventional vector control methods have been unable to curb the transmission of the disease . We have previously reported a novel method of vector control using a tetracycline rep...	Dengue fever is spread by the mosquito Aedes aegypti and the most effective method to limit the spread of dengue is to reduce the mosquito population . We have previously reported a transgenic strain of Ae . aegypti which results in >90% population suppression: males , which do not transmit disease , are released into ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Assessment of the Impact of Potential Tetracycline Exposure on the Phenotype of Aedes aegypti OX513A: Implications for Field Use
Modes of sexual reproduction in eukaryotic organisms are extremely diverse . The human fungal pathogen Candida albicans undergoes a phenotypic switch from the white to the opaque phase in order to become mating-competent . In this study , we report that functionally- and morphologically-differentiated white and opaque ...	In eukaryotic organisms , cells often undergo differentiation into distinct cell types in order to fulfill specialized roles . To achieve a certain function , different cell types may behave coordinately to complete a task that they may otherwise be incapable of completing independently . The human fungal pathogen Cand...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "organismal", "evolution", "mycology", "microbial", "physiology", "microbial", "evolution", "fungal", "genetics", "genetics", "fungal", "reproduction", "biology", "and", "life", "sciences", "microbiology", "evolutionary", "biology", "fungal", "structure" ]	2014	White Cells Facilitate Opposite- and Same-Sex Mating of Opaque Cells in Candida albicans
Antisense transcription is a pervasive phenomenon , but its source and functional significance is largely unknown . We took an expression-based approach to explore microRNA ( miRNA ) -related antisense transcription by computational analyses of published whole-genome tiling microarray transcriptome and deep sequencing ...	Antisense transcription is a pervasive but poorly understood phenomenon in a wide variety of organisms . We have found evidence for a novel source of antisense transcription in Arabidopsis thaliana associated with miRNA targets via computational analyses of published whole-genome tiling microarray data , deep sequencin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "growth", "and", "development", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "computational", "biology/transcriptional", "regulation" ]	2009	Evidence for Antisense Transcription Associated with MicroRNA Target mRNAs in Arabidopsis
Tungiasis is a neglected tropical disease caused by female sand fleas ( Tunga penetrans ) embedded in the skin . The disease is associated with important morbidity . Tungiasis is endemic along the Coast of Kenya with a prevalence ranging from 11% to 50% in school-age children . Hitherto , studies on epidemiological cha...	Tungiasis ( sand flea disease ) is an ectoparasitic skin disease and belongs to the group of NTDs ( Neglected Tropical Diseases ) . It is caused by sand fleas penetrating into the skin of the feet , causing an inflammatory reaction with pain and itching . Attempts to remove the flea with inappropriate sharp tools are p...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "education", "sociology", "geographical", "locations", "social", "sciences", "bivariate", "analysis", "animals", "health", "care", "multivariate", "analysis", "mathemat...	2017	Prevalence, intensity and risk factors of tungiasis in Kilifi County, Kenya: I. Results from a community-based study
The diagnosis of human African trypanosomiasis ( HAT ) caused by Trypanosoma brucei gambiense relies mainly on the Card Agglutination Test for Trypanosomiasis ( CATT ) . There is no immunodiagnostic for HAT caused by T . b . rhodesiense . Our principle aim was to develop a prototype lateral flow test that might be an i...	Human African Trypanosomiasis ( HAT ) is caused by infection with Trypanosoma brucei gambiense or T . b . rhodesiense . The diagnosis of T . b . gambiense infections currently relies primarily on a Card Agglutination Test for Trypanosomiasis ( CATT ) , which has acknowledged limitations , and there is no simple test fo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "biology", "and", "life", "sciences", "immunology", "microbiology" ]	2014	Identification of sVSG117 as an Immunodiagnostic Antigen and Evaluation of a Dual-Antigen Lateral Flow Test for the Diagnosis of Human African Trypanosomiasis
Neisseria meningitis remains a leading cause of sepsis and meningitis , and vaccines are required to prevent infections by this important human pathogen . Factor H binding protein ( fHbp ) is a key antigen that elicits protective immunity against the meningococcus and recruits the host complement regulator , fH . As th...	Vaccines are currently available against several serogroups of Neisseria meningitidis . However broadly effective serogroup B vaccines are still required as capsule-based approaches cannot be implemented with this serogroup because of the risks of auto-immunity . As a result , vaccines based on proteins in the bacteria...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meningococcal", "infections", "medicine", "bacterial", "diseases", "infectious", "diseases", "meningococcal", "disease", "immunity", "innate", "immunity", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "meningoccal", "septi...	2012	Design and Evaluation of Meningococcal Vaccines through Structure-Based Modification of Host and Pathogen Molecules
C-type lectins ( CTLs ) are characterized by the presence of a C-type carbohydrate recognition domain ( CTLD ) that by recognizing microbial glycans , is responsible for their roles as pattern recognition receptors in the immune response to bacterial infection . In addition to the CTLD , however , some CTLs display add...	The JAK/STAT pathway mediates the effects of a large number of cytokines and growth factors . It is activated following binding of a cytokine or growth factor to its respective receptor . To date , over 50 cytokines and growth factors have been shown to utilize the pathway to regulate cell growth , survival differentia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "phosphorylation", "shrimp", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "rna", "interference", "immunology", "animals", "crustaceans", "epigenetics", "stat", "proteins", "digestive", "system", "white", "blood", "cells"...	2017	Binding of a C-type lectin’s coiled-coil domain to the Domeless receptor directly activates the JAK/STAT pathway in the shrimp immune response to bacterial infection
Onchocerciasis causes a considerable disease burden in Africa , mainly through skin and eye disease . Since 1995 , the African Programme for Onchocerciasis Control ( APOC ) has coordinated annual mass treatment with ivermectin in 16 countries . In this study , we estimate the health impact of APOC and the associated co...	In 1995 , the World Health Organization launched the African Programme for Onchocerciasis Control ( APOC ) with the aim to control morbidity due to the parasitic infectious disease onchocerciasis ( river blindness ) . APOC aims to set up sustainable national control programs against onchocerciasis in 16 countries in su...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "applied", "mathematics", "parasitic", "diseases", "mathematics", "neglected", "tropical", "diseases", "onchocerciasis", "infectious", "disease", "control", "complex", "systems",...	2013	African Programme for Onchocerciasis Control 1995–2015: Model-Estimated Health Impact and Cost
During development , neurons extend axons to different brain areas and produce stereotypical patterns of connections . The mechanisms underlying this process have been intensively studied in the visual system , where retinal neurons form retinotopic maps in the thalamus and superior colliculus . The mechanisms active i...	Neural development is a process that involves a wide range of behaviors . As a result of these behaviors , neurons are able to extend axons to different brain areas and produce stereotypical patterns of innervation . One of the most commonly studied of these projections is in the visual system , where retinal axons pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience/theoretical", "neuroscience" ]	2009	A Multi-Component Model of the Developing Retinocollicular Pathway Incorporating Axonal and Synaptic Growth
Pneumococcal bacteriocins ( pneumocins ) are antibacterial toxins that mediate intra-species competition within the human host . However , the triggers of pneumocin expression are poorly understood . Using RNA-sequencing , we mapped the regulon of the pneumocin cluster ( blp ) of Streptococcus pneumoniae D39 . Furtherm...	Streptococcus pneumoniae is an opportunistic pathogen with high carriage rates in children . Pneumococci express pneumocins that kill competing bacteria . Pneumocin expression is controlled by a pheromone-induced two-component system ( BlpR/H ) but the triggers for the system are poorly understood . We show that the ph...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "antimicrobials", "medicine", "and", "health", "sciences", "luciferase", "toxins", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "enzymes", "drugs", "microbiology", "enzymology", "toxicology", "toxic", "agents", "plasmid", "constructi...	2016	Expression of Streptococcus pneumoniae Bacteriocins Is Induced by Antibiotics via Regulatory Interplay with the Competence System
Albendazole and mebendazole are increasingly deployed for preventive chemotherapy targeting soil-transmitted helminth ( STH ) infections . We assessed the efficacy of single oral doses of albendazole ( 400 mg ) and mebendazole ( 500 mg ) for the treatment of hookworm infection in school-aged children in Lao PDR . Since...	Parasitic worms remain a public health problem in developing countries . Regular deworming with the drugs albendazole and mebendazole is the current global control strategy . We assessed the efficacies of a single tablet of albendazole ( 400 mg ) and mebendazole ( 500 mg ) against hookworm in children of southern Lao P...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "parasitic", "diseases", "food-borne", "trematodes", "helminth", "infection", "clinical", "epidemiology", "hookworm", "infection", "neglected", "tropical", "diseases", "infectious", "disease", "control", "ascariasis", ...	2012	Low Efficacy of Single-Dose Albendazole and Mebendazole against Hookworm and Effect on Concomitant Helminth Infection in Lao PDR
Systemic upregulation of inflammatory cytokines is characteristic of critical severe hand , foot , and mouth disease ( HFMD ) with pulmonary edema . Thus , immunomodulatory medicines such as steroids , including methylprednisolone , have been proposed to treat patients with severe HFMD in China , because it is postulat...	Systemic inflammation is characteristic of severe hand , foot , and mouth disease ( HFMD ) . Steroids are considered immunomodulators and have been officially recommended to treat the severe HFMD patients with CNS complications in China . So far , it is uncertain whether steroid treatment has an immunomodulatory role i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	The Cytokine and Chemokine Profiles in Patients with Hand, Foot and Mouth Disease of Different Severities in Shanghai, China, 2010
Plasmacytoid dendritic cells ( pDCs ) are innate sensors of viral infections and important mediators of antiviral innate immunity through their ability to produce large amounts of IFN-α . Moreover , Toll-like receptor 7 ( TLR7 ) and 9 ( TLR9 ) ligands , such as HIV and CpG respectively , turn pDCs into TRAIL-expressing...	Plasmacytoid dendritic cells ( pDC ) are the most potent IFN-α-producing cells and serve as an essential link between innate and adaptive immunity . Exposure of pDCs to HIV-1 triggers IFN-α production , which in turn upregulates TNF-related apoptosis-inducing ligand ( TRAIL ) , turning pDCs into killer pDCs , able to k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "enzyme-linked", "immunoassays", "pa...	2016	HMGB1 Is Involved in IFN-α Production and TRAIL Expression by HIV-1-Exposed Plasmacytoid Dendritic Cells: Impact of the Crosstalk with NK Cells
Upon the ligand-dependent dimerization of the epidermal growth factor receptor ( EGFR ) , the intrinsic protein tyrosine kinase ( PTK ) activity of one receptor monomer is activated , and the dimeric receptor undergoes self-phosphorylation at any of eight candidate phosphorylation sites ( P-sites ) in either of the two...	The epidermal growth factor receptor ( EGFR ) is one of a large group of cell surface receptors that allow cells to respond to growth-stimulating signals in their environment . Upon sensing of growth factor , the EGFR is activated , which triggers a signaling cascade leading to the cell nucleus and ultimately initiatin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemistry", "biology" ]	2014	Coarse-Grained Molecular Simulation of Epidermal Growth Factor Receptor Protein Tyrosine Kinase Multi-Site Self-Phosphorylation
Infection by Zika virus ( ZIKV ) is linked to microcephaly and other neurological disorders , posing a significant health threat . Innate immunity is the first line of defense against invading pathogens , but relatively little is understood regarding host intrinsic mechanisms that guard against ZIKV . Here , we show th...	The E3 ligase TRIM56 was previously shown to inhibit the replication of several viruses in the family Flaviviridae , including dengue virus serotype 2 , yellow fever virus and bovine viral diarrhea virus , but had not demonstrable antiviral effect against hepatitis C virus , a hepatotropic virus in the same family . No...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "natural", "antisense", "transcripts", "gene", "regulation", "enzymes", "pathogens", "microbiology", "immunoblotting", "enzymology", "neuroscience", ...	2019	The E3 ligase TRIM56 is a host restriction factor of Zika virus and depends on its RNA-binding activity but not miRNA regulation, for antiviral function
Parasite loads were quantified in repeated skin biopsies from lesions of 2 patients with Old-World cutaneous leishmaniasis ( CL ) caused by Leishmania major and L . infantum during and after treatment with miltefosine . Miltefosine induced a rapid therapeutic effect on both infections with an initial decline of parasit...	The clinical evaluation of the ulcerated lesions in cutaneous leishmaniasis ( CL ) is both difficult and subjective . As a result , the evaluation of therapeutic efficacy of drugs for CL remains complicated . The relationship between dose and effect of antileishmanial drugs in CL is unclear and a good quantitative desc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "dermatology", "infectious", "diseases", "skin", "infections", "pharmacodynamics", "drugs", "and", "devices", "leishmaniasis", "neglected", "tropical", "diseases", "pharmacology", "parasitic", "diseases", "pharmacokinetics" ]	2011	Dynamics of Parasite Clearance in Cutaneous Leishmaniasis Patients Treated with Miltefosine
Mutations that result in amino acid changes can affect both pre-mRNA splicing and protein function . Understanding the combined effect is essential for correct diagnosis and for establishing the most appropriate therapeutic strategy at the molecular level . We have identified a series of disease-causing splicing mutati...	Clarification of if an exonic variant has an effect on splicing and/or on protein function is an important aspect in clinical genetics and in development of appropriate therapeutic strategies , and most of published evidence consider splicing and protein function separately . In exons , the presence of dense splicing r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "physiological", "processes", "substitution", "mutation", "mutation", "nonsense", "mutation", "forms", "of", "dna", "dna", "small", "interfering", "rnas", "gene", "expression", "rna", "splicing", "compleme...	2016	Molecular Basis and Therapeutic Strategies to Rescue Factor IX Variants That Affect Splicing and Protein Function
Most cell surface receptors for growth factors and cytokines dimerize in order to mediate signal transduction . For many such receptors , the Janus kinase ( Jak ) family of non-receptor protein tyrosine kinases are recruited in pairs and juxtaposed by dimerized receptor complexes in order to activate one another by tra...	Janus kinases ( Jaks ) interact with and activate receptors on the cell surface that mediate changes in gene expression . How these interactions are promoted and regulated is of central interest in fields such as cellular endocrinology and immunology . Here , detailed computational models of Jak activation are offered ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/signaling", "networks", "biophysics/cell", "signaling", "and", "trafficking", "structures", "cell", "biology/cell", "signaling" ]	2009	A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases
Aquaporins of the TIP subfamily ( Tonoplast Intrinsic Proteins ) have been suggested to facilitate permeation of water and ammonia across the vacuolar membrane of plants , allowing the vacuole to efficiently sequester ammonium ions and counteract cytosolic fluctuations of ammonia . Here , we report the structure determ...	Ammonia is a central molecule in nitrogen metabolism . Aquaporins are integral membrane proteins that form channels that accelerate the passive permeation of small polar uncharged molecules , like water and ammonia , across lipid membranes of the cell . Structural information of ammonia-permeable aquaporins has been la...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "bonding", "crystal", "structure", "chemical", "compounds", "permeability", "condensed", "matter", "physics", "organic", "compounds", "membrane", "proteins", "materials", "science", "basic", "amino", "acids", "amino", "acids", "crystallography", "cellular", ...	2016	Crystal Structure of an Ammonia-Permeable Aquaporin
Constraint-based modeling ( CBM ) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology , biomedicine , and various biotechnological processes . While CBM is an established framework for studying the metabolism of single species with linear stoichiometric models , CBM of co...	Microbial communities are involved in many fundamental processes in nature , health and biotechnology . The elucidation of interdependencies between the involved players of microbial communities and how the interactions shape the composition , behavior and characteristic features of the consortium has become an importa...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "chemical", "compounds", "enrichment", "culture", "engineering", "and", "technology", "atmospheric", "science", "bioenergy", "biological", "cultures", "metabolic", "networks", "organic", "compounds", "biogas", "metabolites", ...	2019	RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion
What is the relationship between the complexity and the fitness of evolved organisms , whether natural or artificial ? It has been asserted , primarily based on empirical data , that the complexity of plants and animals increases as their fitness within a particular environment increases via evolution by natural select...	It has often been asserted that as organisms adapt to natural environments with many independent forces and actors acting over a variety of different time scales , they become more complex . We investigate this question from the point of view of information theory as applied to the nervous systems of simple creatures e...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology", "biology", "computational", "biology" ]	2013	The Minimal Complexity of Adapting Agents Increases with Fitness
The growth plate mediates bone growth where SOX9 and GLI factors control chondrocyte proliferation , differentiation and entry into hypertrophy . FOXA factors regulate hypertrophic chondrocyte maturation . How these factors integrate into a Gene Regulatory Network ( GRN ) controlling these differentiation transitions i...	In the development of the mammalian growth plate , while several transcription factors are individually well known for their key roles in regulating phases of chondrocyte differentiation , there is little information on how they interact and cooperate with each other . We took an unbiased genome wide approach to identi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "growth", "plate", "dimers", "(chemical", "physics)", "medicine", "and", "health", "sciences", "chondrocytes", "gene", "regulation", "bone", "connective", "tissue", "cells", "sequence", "motif", "analysis", "cartilage", "research", "and", "analysis", "methods", "seque...	2018	Synergistic co-regulation and competition by a SOX9-GLI-FOXA phasic transcriptional network coordinate chondrocyte differentiation transitions
Heritable microbial symbionts have profound impacts upon the biology of their arthropod hosts . Whilst our current understanding of the dynamics of these symbionts is typically cast within a framework of vertical transmission only , horizontal transmission has been observed in a number of cases . For instance , several...	Most insects house heritable symbionts and these represent an important component of their biology , both as partners conveying beneficial traits such as defence against natural enemies , or as antagonists manipulating their hosts’ reproduction . Work on these bacteria mostly assumes that such phenotypes have evolved p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "insect", "metamorphosis", "pathology", "and", "laboratory", "medicine", "parasite", "evolution", "parasitic", "diseases", "parasitology", "reproductive", "physiology", "developmental", ...	2016	Superparasitism Drives Heritable Symbiont Epidemiology and Host Sex Ratio in a Wasp
Retinal ganglion cells receive inputs from multiple bipolar cells which must be integrated before a decision to fire is made . Theoretical studies have provided clues about how this integration is accomplished but have not directly determined the rules regulating summation of closely timed inputs along single or multip...	Visual information is coded by the output of retinal ganglion cells . Through evolution retinal ganglion cells acquired unique properties that allowed them to transmit to the brain such signals as direction of movement . The quest for the cellular mechanism of the detection of movement by retinal ganglion cells has bee...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "visual", "system", "biology", "sensory", "systems", "neuroscience" ]	2013	Directional Summation in Non-direction Selective Retinal Ganglion Cells
Grid cells in the rat entorhinal cortex display strikingly regular firing responses to the animal's position in 2-D space and have been hypothesized to form the neural substrate for dead-reckoning . However , errors accumulate rapidly when velocity inputs are integrated in existing models of grid cell activity . To pro...	Even in the absence of external sensory cues , foraging rodents maintain an estimate of their position , allowing them to return home in a roughly straight line . This computation is known as dead reckoning or path integration . A discovery made three years ago in rats focused attention on the dorsolateral medial entor...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neuroscience/animal", "cognition", "neuroscience/theoretical", "neuroscience" ]	2009	Accurate Path Integration in Continuous Attractor Network Models of Grid Cells
Japanese encephalitis ( JE ) is very prevalent in China , but the incidence of JE among children has been greatly reduced by extensive promotion of vaccinations . The incidence of JE among adults , however , has increased in some parts of China . Data on JE in mainland China , in terms of incidence , gender , and age ,...	It is well known that children are the population most susceptible to Japanese encephalitis ( JE ) , and the incidence of JE among children in China has been greatly reduced by extensive promotion of vaccinations aiming at children . The incidence of JE among adults , however , has increased in some parts of China . Du...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "death", "rates", "invertebrates", "medicine", "and", "health", "sciences", "demography", "china", "immunology", "geographical", "locations", "animals", "vaccines", "preventive", "medicine", "age", "groups", "adults", "population", "biology", "vaccination", "and", "immu...	2016	The Spatio-temporal Distribution of Japanese Encephalitis Cases in Different Age Groups in Mainland China, 2004 – 2014
As the development of new classes of antibiotics slows , bacterial resistance to existing antibiotics is becoming an increasing problem . A potential solution is to develop treatment strategies with an alternative mode of action . We consider one such strategy: anti-adhesion therapy . Whereas antibiotics act directly u...	Humankind is engaged in an arms race; one we are in danger of losing . Since the development and application of the first antibiotics , resistant strains of bacteria have steadily emerged . As the rate of discovery of new antibiotics slows , the threat increases . At present , 700 , 000 individuals globally die each ye...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "binding", "antimicrobials", "cell", "physiology", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "dose", "prediction", "methods", "drugs", "microbiology", "mathematical", "models", "bacterial", "diseases", "antibiotic", "r...	2018	Predictive modelling of a novel anti-adhesion therapy to combat bacterial colonisation of burn wounds
Correct chromosome segregation is essential in order to prevent aneuploidy . To segregate sister chromatids equally to daughter cells , the sisters must attach to microtubules emanating from opposite spindle poles . This so-called biorientation manifests itself by increased tension and conformational changes across kin...	Accurate chromosome segregation is required for the equal distribution of genetic information to progeny . Failure to equally segregate chromosomes leads to aneuploidy , cell death or cancer . Proteins of the conserved shugoshin family contribute to accurate chromosome segregation in both meiosis and mitosis . The role...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "molecular", "cell", "biology" ]	2014	Sgo1 Regulates Both Condensin and Ipl1/Aurora B to Promote Chromosome Biorientation
Bat echolocation is an ability consisting of many subtasks such as navigation , prey detection and object recognition . Understanding the echolocation capabilities of bats comes down to isolating the minimal set of acoustic cues needed to complete each task . For some tasks , the minimal cues have already been identifi...	Echolocating bats can fly through complex environments in complete darkness . Swift and apparently effortless obstacle avoidance is the most fundamental function supported by biosonar . Despite this , we still do not know which acoustic cues , from among the many possible cues , bats actually exploit while avoiding obs...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Sensorimotor Model of Obstacle Avoidance in Echolocating Bats
Because coevolution takes place across a broad scale of time and space , it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time . Comparing populations across a range of an interaction , especially for long-lived species , can provide insi...	Arms races between natural enemies can lead to the rapid evolution of extreme traits , high degrees of specialization , and the formation of new species . They also serve as the ecological model for the evolution of drug resistance by diseases and for host–pathogen interactions in general . Revealing who wins these arm...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology", "ecology" ]	2008	Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution
Primary open angle glaucoma ( POAG ) is a leading cause of blindness worldwide , with elevated intraocular pressure as an important risk factor . Increased resistance to outflow of aqueous humor through the trabecular meshwork causes elevated intraocular pressure , but the specific mechanisms are unknown . In this stud...	Primary open angle glaucoma ( POAG ) is a leading cause of vision loss and blindness affecting tens of millions of people . Ocular hypertension is a strong risk factor for the disease and the only effective target of treatment . Ocular hypertension results from increased resistance to outflow of aqueous humor through t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/gene", "expression", "ophthalmology/inherited", "eye", "disorders", "genetics", "and", "genomics/disease", "models", "ophthalmology", "genetics", ...	2011	Mapping of the Disease Locus and Identification of ADAMTS10 As a Candidate Gene in a Canine Model of Primary Open Angle Glaucoma
Three closely related thermally dimorphic pathogens are causal agents of major fungal diseases affecting humans in the Americas: blastomycosis , histoplasmosis and paracoccidioidomycosis . Here we report the genome sequence and analysis of four strains of the etiological agent of blastomycosis , Blastomyces , and two s...	Dimorphic fungal pathogens including Blastomyces are the cause of major fungal diseases in North and South America . The genus Emmonsia includes species infecting small mammals as well as a newly emerging pathogenic species recently reported in HIV-positive patients in South Africa . Here , we synthesize both genome se...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Dynamic Genome and Transcriptome of the Human Fungal Pathogen Blastomyces and Close Relative Emmonsia
Recent discoveries on the origins of modern humans from multiple archaic hominin populations and the diversity of human papillomaviruses ( HPVs ) suggest a complex scenario of virus-host evolution . To evaluate the origin of HPV pathogenesis , we estimated the phylogeny , timing , and dispersal of HPV16 variants using ...	Epidemiologic studies have demonstrated that persistent infection of select oncogenic human papillomaviruses ( HPVs ) is the main cause of cervix precancer and cancer . Nevertheless , our knowledge of the underlying evolutionary mechanisms driving the divergence and emergence of viral oncogenicity in specific types of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "organismal", "evolution", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "social", "sciences", "anthropology", "animals", "mammals", "viruses", "primates", "neanderthals", "ph...	2018	Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans
During its developmental cycle within the sand fly vector , Leishmania must survive an early proteolytic attack , escape the peritrophic matrix , and then adhere to the midgut epithelia in order to prevent excretion with remnants of the blood meal . These three steps are critical for the establishment of an infection w...	For a successful development within the midgut of the sand fly vector , Leishmania must overcome several barriers which are imposed by the vector . The ability to overcome these barriers has been associated with species specificity , and interference with the sand fly vector-parasite balance can change the outcome of t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "molecular", "biology/mrna", "stability", "biochemistry/transcription", "and", "translation", "molecular", "biology" ]	2010	Targeting the Midgut Secreted PpChit1 Reduces Leishmania major Development in Its Natural Vector, the Sand Fly Phlebotomus papatasi
Genome-wide somatic mutation profiles of tumours can now be assessed efficiently and promise to move precision medicine forward . Statistical analysis of mutation profiles is however challenging due to the low frequency of most mutations , the varying mutation rates across tumours , and the presence of a majority of pa...	The transition from a normal cell to a cancer cell is driven by genetic alterations , such as mutations , that induce uncontrolled cell proliferation . With the advent of next-generation sequencing technologies ( NGS ) in the last decade , thousands of tumours have been sequenced and their mutation profiles determined ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "genetic", "networks", "basic", "cancer", "research", "oncology", "mutation", "network", "analysis", "silent", "mutation", "mutation", "databases", "research", "and", "analysis", "methods", "computer", "an...	2017	NetNorM: Capturing cancer-relevant information in somatic exome mutation data with gene networks for cancer stratification and prognosis
Solute carrier family 7 member 2 ( SLC7A2 ) is an inducible transporter of the semi-essential amino acid L-arginine ( L-Arg ) , which has been implicated in immune responses to pathogens . We assessed the role of SLC7A2 in murine infection with Citrobacter rodentium , an attaching and effacing enteric pathogen that cau...	Intestinal infections by attaching and effacing ( A/E ) bacteria widely impact human health , with major social and economic repercussions . Mucosal immunity plays a critical role in determining the outcome of these infections . The amino acid L-arginine regulates inflammatory responses to bacterial pathogens . We stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "immunology", "microbiology", "epithelial", "cells", "colitis", "histology", "dev...	2016	The L-Arginine Transporter Solute Carrier Family 7 Member 2 Mediates the Immunopathogenesis of Attaching and Effacing Bacteria
The tsetse fly Glossina fuscipes s . l . is responsible for the transmission of approximately 90% of cases of human African trypanosomiasis ( HAT ) or sleeping sickness . Three G . fuscipes subspecies have been described , primarily based upon subtle differences in the morphology of their genitalia . Here we describe a...	Glossina fuscipes s . l . tsetse flies are responsible for transmission of approximately 90% of the cases of Human African Typanosomiasis in Sub Saharan Africa . It was previously proposed on the basis of morphology that G . fuscipes is composed of three sub-species . Using genetic evidence from G . fuscipes nuclear , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "taxonomy", "medicine", "infectious", "diseases", "african", "trypanosomiasis", "molecular", "systematics", "neglected", "tropical", "diseases", "biology", "evolutionary", "biology", "infectious", "disease", "control", "evolutionary", "systematics" ]	2011	Cryptic Diversity within the Major Trypanosomiasis Vector Glossina fuscipes Revealed by Molecular Markers
Aspergillus fumigatus is responsible for a disproportionate number of invasive mycosis cases relative to other common filamentous fungi . While many fungal factors critical for infection establishment are known , genes essential for disease persistence and progression are ill defined . We propose that fungal factors th...	Medical treatment advances such as organ transplants and chemotherapies that suppress the immune system have increased the number of patients susceptible to invasive fungal diseases . The most common filamentous fungus isolated from these infections is the environmental mold , Aspergillus fumigatus , the causative agen...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "aspergillus", "fumigatus", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "aspergillus", "fungal", "genetics", "pathogens", "microbiology", "carbohydrates", "glucose", "metabolis...	2017	Filamentous fungal carbon catabolite repression supports metabolic plasticity and stress responses essential for disease progression
Hookworm-related cutaneous larva migrans ( CLM ) is a common but neglected tropical skin disease caused by the migration of animal hookworm larvae in the epidermis . The disease causes intense pruritus and is associated with important morbidity . The extent to which CLM impairs skin disease-associated life quality has ...	Hookworm-related cutaneous larva migrans ( CLM ) is a parasitic skin disease common in developing countries with hot climates . In resource-poor settings , CLM is associated with considerable morbidity . The disease is caused by animal hookworm larvae that penetrate the skin and migrate aimlessly in the epidermis as th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "soil-transmitted", "helminths", "cutaneous", "larva", "migrans", "neglected", "tropical", "diseases", "hookworm", "parasitic", "diseases" ]	2011	Life Quality Impairment Caused by Hookworm-Related Cutaneous Larva Migrans in Resource-Poor Communities in Manaus, Brazil
Sensitivity to pain varies considerably between individuals and is known to be heritable . Increased sensitivity to experimental pain is a risk factor for developing chronic pain , a common and debilitating but poorly understood symptom . To understand mechanisms underlying pain sensitivity and to search for rare gene ...	Chronic widespread pain is a complex clinical problem . Identification of underlying genetic factors would shed light on the biology of pain and offer targets for novel therapies . We aimed to identify rare genetic variants in the normal population associated with pain sensation by performing exome sequencing on indivi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "genetic", "epidemiology" ]	2012	Genes Contributing to Pain Sensitivity in the Normal Population: An Exome Sequencing Study
Perfusion bioreactors regulate flow conditions in order to provide cells with oxygen , nutrients and flow-associated mechanical stimuli . Locally , these flow conditions can vary depending on the scaffold geometry , cellular confluency and amount of extra cellular matrix deposition . In this study , a novel application...	Tissue Engineering involves the combination of cells , growth factors and biomaterials into artificial constructs which , upon implantation , can improve the healing capacity of the human body . A remaining challenge involves providing physical stimuli to individual cells , thereby guiding them towards the properties o...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "stiffness", "mechanical", "properties", "classical", "mechanics", "fluid", "mechanics", "mechanical", "stress", "materials", "science", "damage", "mechanics", "cellular", "structures", "and", "organelles", "cytoskeleton", "bending", "mechanical", "tension", "deformation", ...	2016	Immersed Boundary Models for Quantifying Flow-Induced Mechanical Stimuli on Stem Cells Seeded on 3D Scaffolds in Perfusion Bioreactors
Understanding the mechanism of infection control in elite controllers ( EC ) may shed light on the correlates of control of disease progression in HIV infection . However , limitations have prevented a clear understanding of the mechanisms of elite controlled infection , as these studies can only be performed at random...	A small proportion of HIV-infected patients control viral replication and disease progression in the absence of any antiretroviral treatment . Understanding the mechanisms of viral control in these elite controllers may help to identify new therapeutic approaches in order to control HIV infection . However , elite cont...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "retrovirology", "and", "hiv", "immunopathogenesis", "immunity", "to", "infections", "immunology", "immune", "defense", "infectious", "diseases", "hiv", "t", "cells", "immune", "response", "immunopathology", "clinical", "immunology", "immu...	2011	Functional Cure of SIVagm Infection in Rhesus Macaques Results in Complete Recovery of CD4+ T Cells and Is Reverted by CD8+ Cell Depletion
Latently-infected CD4+ T cells are widely considered to be the major barrier to a cure for HIV . Much of our understanding of HIV latency comes from latency models and blood cells , but most HIV-infected cells reside in lymphoid tissues such as the gut . We hypothesized that tissue-specific environments may impact the ...	Available antiretroviral drugs significantly prolong life expectancy and reduce morbidity in people living with HIV . However , HIV can escape host immune responses and drug treatment by establishing a reversibly silent ( "latent" ) infection in CD4+ T cells . This latent infection represents the major barrier to a cur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "pathology", "and", "laboratory", "medicine", "biopsy", "enzymes", "pathogens", "immunology", "rna", "extraction", "microbiology", "enzymology", "surgical", "and", "invasiv...	2018	Gut and blood differ in constitutive blocks to HIV transcription, suggesting tissue-specific differences in the mechanisms that govern HIV latency
Elimination of Plasmodium vivax malaria would be greatly facilitated by the development of an effective vaccine . A comprehensive and systematic characterization of antibodies to P . vivax antigens in exposed populations is useful in guiding rational vaccine design . In this study , we investigated antibodies to a larg...	Plasmodium vivax is now the predominant malaria parasite outside Africa . Because P . vivax can remain dormant in the liver for months , identifying and treating P . vivax in asymptomatic individuals is difficult . Additionally , current widely-used vector control measures are less efficient against mosquitoes that tra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "vaccines", "preventive", "medicin...	2016	An Antibody Screen of a Plasmodium vivax Antigen Library Identifies Novel Merozoite Proteins Associated with Clinical Protection
Buruli ulcer , caused by infection with Mycobacterium ulcerans , is a chronic ulcerative neglected tropical disease of the skin and subcutaneous tissue that is most prevalent in West African countries . M . ulcerans produces a cytotoxic macrolide exotoxin called mycolactone , which causes extensive necrosis of infected...	Buruli ulcer is a slow progressing ulcerative disease of the skin and subcutaneous tissue that is most prevalent in West African rural communities . Mycobacterium ulcerans , the causative agent of the disease , produces a toxin called mycolactone , which is held responsible for the extensive tissue damage seen in advan...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "animal", "models", "of", "disease", "immunology", "microbiology", "animal", "models", "preventive", "medicine", "model", "organisms", "immunologic", "adjuvants", "antibodies...	2016	Vaccination with the Surface Proteins MUL_2232 and MUL_3720 of Mycobacterium ulcerans Induces Antibodies but Fails to Provide Protection against Buruli Ulcer
Intrinsic immunity describes the set of recently discovered but poorly understood cellular mechanisms that specifically target viral pathogens . Their discovery derives in large part from intensive studies of HIV and SIV that revealed restriction factors acting at various stages of the retroviral life cycle . Recent st...	Retrotransposons are mobile DNA elements that duplicate themselves by a "copy and paste" mechanism using an RNA intermediate . They are insertional mutagens that have had profound effects on genome evolution , fostering DNA deletions , insertions and rearrangements , and altering gene expression . LINE-1 retrotransposo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Broad-Spectrum Antiviral Protein ZAP Restricts Human Retrotransposition
Cell intercalation is a highly directed cell rearrangement that is essential for animal morphogenesis . As such , intercalation requires orchestration of cell polarity across the plane of the tissue . CDC-42 is a Rho family GTPase with key functions in cell polarity , yet its role during epithelial intercalation has no...	As embryos develop , tissues must change shape to establish an animal’s form . One key form-shaping movement , cell intercalation , often occurs when a tissue elongates in a preferred direction . How cells in epithelial sheets can intercalate while maintaining tissue integrity is not well understood . Here we use the d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "biosensors", "cell", "physiology", "invertebrates", "cell", "motility", "medicine", "and", "health", "sciences", "integumentary", "system", "engineering", "and", "technology", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", ...	2016	CDC-42 Orients Cell Migration during Epithelial Intercalation in the Caenorhabditis elegans Epidermis
Rapid and selective ion transport is essential for the generation and regulation of electrical signaling pathways in living organisms . Here , we use molecular dynamics ( MD ) simulations with an applied membrane potential to investigate the ion flux of bacterial sodium channel NaVMs . 5 . 9 µs simulations with 500 mM ...	Voltage gated sodium channels are essential components of living cell membranes . They regulate the cell potential by facilitating permeation of ions across the membrane . In the past decades , studies revealed that the bacterial selectivity filter ( SF ) exhibits a constricted architecture lined with electronegative c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry", "biochemical", "simulations", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Different Inward and Outward Conduction Mechanisms in NaVMs Suggested by Molecular Dynamics Simulations
Group B coxsackieviruses ( CVB ) are associated with viral-induced heart disease and are among the leading causes of aseptic meningitis worldwide . Here we show that CVB entry into polarized brain microvasculature and aortic endothelial cells triggers a depletion of intracellular calcium stores initiated through viral ...	Enteroviruses are associated with a number of diverse syndromes such as myocarditis , febrile illness , and are the main causative agents of aseptic meningitis . No effective therapeutics exist to combat non-poliovirus enterovirus infections . A better understanding of the mechanisms by which these viruses infect host ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "cell", "biology/cell", "signaling" ]	2010	Release of Intracellular Calcium Stores Facilitates Coxsackievirus Entry into Polarized Endothelial Cells
Carriage of the genetic combination encoding a high expression inhibitory Killer Immunoglobulin-like Receptor ( KIR ) 3DL1 with its ligand , HLA-B57 ( h/y+B57 ) is associated with slower time to AIDS and better HIV viral load control than being a Bw6 homozygote ( Bw6hmz ) . Natural Killer ( NK ) cells from h/y+B*...	Natural Killer ( NK ) cells function in anti-tumor and anti-viral defenses , including those directed against HIV . HIV infected cells can activate NK cells , which , once activated , inhibit HIV replication in infected targets . NK cell activation levels depend on the interaction of cell surface receptors on NK cells ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "cytokines", "viral", "classification", "immunity", "to", "infections", "population", "genetics", "microbiology", "retroviruses", "immunodeficiency", "viruses", "mechanisms", "of", "resistance", "and", "susceptibility", "sexually", "transmitte...	2014	HIV Protective KIR3DL1/S1-HLA-B Genotypes Influence NK Cell-Mediated Inhibition of HIV Replication in Autologous CD4 Targets
A universal feature of metazoan sexual development is the generation of oocyte P granules that withhold certain mRNA species from translation to provide coding potential for proteins during early post-fertilization development . Stabilisation of translationally quiescent mRNA pools in female Plasmodium gametocytes depe...	Transmission of malaria relies on ingestion of male and female sexual precursor cells ( gametocytes ) from the human host by the mosquito vector . Fertilization results in the formation of a diploid zygote that transforms into the ookinete , the motile form of the parasite that is capable of escaping the hostile mosqui...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "molecular", "biology/rna-protein", "interactions", "genetics", "and", "genomics/gene", "expression", "molecular", "biology/mrna", "stability", "cell", "biology/microbial", "growth", "and", "...	2010	Universal Features of Post-Transcriptional Gene Regulation Are Critical for Plasmodium Zygote Development
The transcriptome in a cell is finely regulated by a large number of molecular mechanisms able to control the balance between mRNA production and degradation . Recent experimental findings have evidenced that fine and specific regulation of degradation is needed for proper orchestration of a global cell response to env...	The amount of a given transcript in a cell is determined by a fine tuned balance of production and degradation in a complex regulatory network . Regulation of transcription controls when transcription occurs and how much mRNA is created , whereas regulation of degradation controls the rate at which messengers are destr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "computational", "biology" ]	2012	Stochastic Modeling of Expression Kinetics Identifies Messenger Half-Lives and Reveals Sequential Waves of Co-ordinated Transcription and Decay
Early warning systems ( EWS ) are management tools to predict the occurrence of epidemics of infectious diseases . While climate-based EWS have been developed for malaria , no standard protocol to evaluate and compare EWS has been proposed . Additionally , there are several neglected tropical diseases whose transmissio...	Early Warning Systems ( EWS ) are management tools to predict the occurrence of epidemics . They are based on the dependence of a given infectious disease on environmental variables . Although several neglected tropical diseases are sensitive to the effect of climate , our ability to predict their dynamics has been bar...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ecology/theoretical", "ecology", "ecology/population", "ecology", "science", "policy", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2007	Comparing Models for Early Warning Systems of Neglected Tropical Diseases
Almost every animal lineage is characterized by unique sex-specific traits , implying that such traits are gained and lost frequently in evolution . However , the genetic mechanisms responsible for these changes are not understood . In Drosophila , the activity of the sex determination pathway is restricted to sexually...	Most animals are sexually dimorphic , yet each species has a different set of sex-specific traits . Much of evolutionary biology since Darwin has focused on explaining these differences . In contrast to the well-developed theories of sexual selection ( how and why males compete for females ) we are still far from under...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2011	Evolution of Sex-Specific Traits through Changes in HOX-Dependent doublesex Expression
The rymv1-2 and rymv1-3 alleles of the RYMV1 resistance to Rice yellow mottle virus ( RYMV ) , coded by an eIF ( iso ) 4G1 gene , occur in a few cultivars of the Asiatic ( Oryza sativa ) and African ( O . glaberrima ) rice species , respectively . The most salient feature of the resistance breaking ( RB ) process is th...	A fundamental question in virus evolution is whether emergence into a new host species/cultivar requires adaptation of the virus during the early stages of infection or whether it is largely via a chance transmission of a viral strain with the requisite characteristics . Our studies of the breakdown of RYMV1 resistance...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "virology", "plant", "biology", "plant", "pathology", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2012	Historical Contingencies Modulate the Adaptability of Rice Yellow Mottle Virus
Echinococcosis is a complex zoonosis that has domestic and sylvatic lifecycles , and a range of different intermediate and definitive host species . The complexities of its transmission and the sparse evidence on the effectiveness of control strategies in diverse settings provide significant challenges for the design o...	Echinococcosis is a complex zoonosis for which there is sparse evidence on the effectiveness of control strategies in diverse settings . This presents significant challenges for the design of effective public health policy against this disease . Mathematical modelling is a useful tool for simulating control packages un...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "population", "modeling", "infectious", "disease", "modeling", "biology", "computational", "biology" ]	2013	Synthesising 30 Years of Mathematical Modelling of Echinococcus Transmission
Influenza A virus ( IAV ) polymerase complexes function in the nucleus of infected cells , generating mRNAs that bear 5′ caps and poly ( A ) tails , and which are exported to the cytoplasm and translated by host machinery . Host antiviral defences include mechanisms that detect the stress of virus infection and arrest ...	Like all viruses , Influenza A virus ( IAV ) is absolutely dependent on host-cell protein synthesis machinery . This dependence makes the virus vulnerable to the innate ability of cells to inhibit protein synthesis in response to various types of stress . This inhibition , termed translation arrest , helps cells surviv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "protein", "translation", "gene", "expression", "genetics", "influenza", "biology", "and", "life", "sciences", "viral", "diseases", "molecular", "cell", "biology" ]	2014	Influenza A Virus Host Shutoff Disables Antiviral Stress-Induced Translation Arrest
Mitochondrial DNA ( mtDNA ) encodes for proteins required for oxidative phosphorylation , and mutations affecting the genome have been linked to a number of diseases as well as the natural ageing process in mammals . Human mtDNA is replicated by a molecular machinery that is distinct from the nuclear replisome , but th...	Mitochondria are cytoplasmatic organelles that produce most of the adenosine triphosphate ( ATP ) used by the cell as a source of chemical energy . A subset of proteins required for ATP production is encoded by a distinct mitochondrial DNA genome ( mtDNA ) . Proper maintenance of mtDNA is essential , since mutations or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "medicine", "and", "health", "sciences", "mitochondrial", "dna", "forms", "of", "dna", "mitochondria", "biology", "and", "life", "sciences", "bioenergetics", "dna", "energy-producing", "organelles" ]	2014	In Vivo Occupancy of Mitochondrial Single-Stranded DNA Binding Protein Supports the Strand Displacement Mode of DNA Replication
The organismal roles of the ubiquitously expressed class I PI3K isoform p110β remain largely unknown . Using a new kinase-dead knockin mouse model that mimics constitutive pharmacological inactivation of p110β , we document that full inactivation of p110β leads to embryonic lethality in a substantial fraction of mice ....	Class I PI3Ks are important signalling enzymes and drug targets in cancer and inflammation . We report that p110α and p110β , the two ubiquitously expressed class I PI3K isoforms , control fertility , with no evidence for such a role for p110δ , a PI3K highly expressed in leukocytes . Infertility is therefore a possibl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Novel Role for p110β PI 3-Kinase in Male Fertility through Regulation of Androgen Receptor Activity in Sertoli Cells
Tomato ( Solanum lycopersicum ) is one of the highest-value vegetable crops worldwide . Understanding the genetic regulation of primary metabolite levels can inform efforts aimed toward improving the nutrition of commercial tomato cultivars , while maintaining key traits such as yield and stress tolerance . We identifi...	Deciphering the diverse , interconnected plant metabolome can facilitate crop improvement . In this study , the use of a combination of multiple technologies has allowed us to obtain novel functional and genetic insights into our GWAS investigating variation in ascorbate accumulation in tomato . The InDel_8 in the prom...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "chemical", "compounds", "organic", "compounds", "metabolites", "genome", "analysis", "crops", "plants", "vitamin", "c", "crop", "science", "gene", "expression", "chemistry", "vitamins", "tomatoes", "genetic", "loci", "fruits", ...	2019	Genome-wide association analysis identifies a natural variation in basic helix-loop-helix transcription factor regulating ascorbate biosynthesis via D-mannose/L-galactose pathway in tomato
Fluorescent proteins have been widely used as genetically encodable fusion tags for biological imaging . Recently , a new class of fluorescent proteins was discovered that can be reversibly light-switched between a fluorescent and a non-fluorescent state . Such proteins can not only provide nanoscale resolution in far-...	Proteins whose fluorescence can be reversibly switched on and off hold great promise for applications in high-resolution optical microscopy and nanotechnology . To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements of their properties requires a detailed understand...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biophysics/theory", "and", "simulation", "biochemistry/theory", "and", "simulation", "computational", "biology", "biophysics", "computational", "biology/molecular", "dynamics" ]	2008	Chromophore Protonation State Controls Photoswitching of the Fluoroprotein asFP595
Neurons utilize bursts of action potentials as an efficient and reliable way to encode information . It is likely that the intrinsic membrane properties of neurons involved in burst generation may also participate in preserving its temporal features . Here we examined the contribution of the persistent and resurgent co...	The nervous system extracts meaningful information from natural environments to guide precise behaviors . Sensory neurons encode and relay such complex peripheral information as electrical events , known as action potentials or spikes . The timing intervals between the spikes carry stimulus-relevant information . There...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "depolarization", "signal", "processing", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "research", "and", "analysis", "me...	2019	Resurgent Na+ Current Offers Noise Modulation in Bursting Neurons
We previously reported that autosomal recessive demyelinating Charcot-Marie-Tooth ( CMT ) type 4B1 neuropathy with myelin outfoldings is caused by loss of MTMR2 ( Myotubularin-related 2 ) in humans , and we created a faithful mouse model of the disease . MTMR2 dephosphorylates both PtdIns3P and PtdIns ( 3 , 5 ) P2 , th...	Charcot-Marie-Tooth type 4B1 ( CMT4B1 ) and Charcot-Marie-Tooth type 4J ( CMT4J ) are severe autosomal recessive demyelinating neuropathies with childhood onset . We previously demonstrated that loss of the phospholipid phosphatase MTMR2 causes CMT4B1 with myelin outfoldings in human and mouse and that loss of the phos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "neurological", "disorders", "neurology", "genetics", "biology", "molecular", "cell", "biology", "neuroscience", "genetics", "and", "genomics" ]	2011	Genetic Interaction between MTMR2 and FIG4 Phospholipid Phosphatases Involved in Charcot-Marie-Tooth Neuropathies
In some Pacific Island countries , such as Solomon Islands and Fiji , active trachoma is common , but ocular Chlamydia trachomatis ( Ct ) infection and trachomatous trichiasis ( TT ) are rare . On Tarawa , the most populous Kiribati island , both the active trachoma sign “trachomatous inflammation—follicular” ( TF ) an...	Ocular infection with Chlamydia trachomatis causes trachoma . It is the leading infectious cause of blindness , and the target of an international campaign for elimination as a public health problem . Trachoma is endemic to Tarawa , the most populated island of Kiribati , housing approximately half the national populat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "geomorphology", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "landforms", "chlamydia", "trachomatis", "pathogens", "topography", "tropical", "diseases", "geographical", "loca...	2017	Prevalence of signs of trachoma, ocular Chlamydia trachomatis infection and antibodies to Pgp3 in residents of Kiritimati Island, Kiribati
Salmonella enterica infections are a significant global health issue , and development of vaccines against these bacteria requires an improved understanding of how vaccination affects the growth and spread of the bacteria within the host . We have combined in vivo tracking of molecularly tagged bacterial subpopulations...	The bacterium Salmonella enterica causes gastroenteritis and the severe systemic diseases typhoid , paratyphoid fever and non-typhoidal septicaemia ( NTS ) . Treatment of systemic disease with antibiotics is becoming increasingly difficult due to the acquisition of resistance . Licensed vaccines are available for the p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "disease", "immunology", "cell-mediated", "immunity", "microbiology", "vaccines", "infectious", "disease", "immunology", "antibacterial", "therapy", "mathematics", "statistics", "(mathematics)", "population", "modeling", "population", "biology", "v...	2014	The Effects of Vaccination and Immunity on Bacterial Infection Dynamics In Vivo
Arboviruses have overlapping geographical distributions and can cause symptoms that coincide with more common infections . Therefore , arbovirus infections are often neglected by travel diagnostics . Here , we assessed the potential of syndrome-based approaches for diagnosis and surveillance of neglected arboviral dise...	Physicians attending travelers with particular symptoms often neglect those infections that are transmitted by arthropods like ticks and mosquitoes ( arboviruses ) or don’t test for the appropriate arboviruses . This is because arboviruses cause symptoms that are similar to more common infections and because there is a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Syndromic Approach to Arboviral Diagnostics for Global Travelers as a Basis for Infectious Disease Surveillance
Topological , chemical and immunological barriers are thought to limit infection by enteropathogenic bacteria . However , in many cases these barriers and their consequences for the infection process remain incompletely understood . Here , we employed a mouse model for Salmonella colitis and a mixed inoculum approach t...	Salmonella Typhimurium can colonize the human intestine and cause severe diarrhea . In recent years , it has become clear that this pathogen profits from inflammatory changes in the intestinal lumen , as the inflamed gut helps Salmonella to out-compete the resident microbiota . Granulocytes transmigrating into the gut ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "of", "infection", "infectious", "disease", "immunology", "clinical", "immunology", "population", "modeling", "medical", "microbiology", "microbial", "pathogens", "immunology", "biology", "and", "life", "sciences", "infectious", "disease", "modeling", ...	2014	Granulocytes Impose a Tight Bottleneck upon the Gut Luminal Pathogen Population during Salmonella Typhimurium Colitis
Sex-biased demographic events ( “sex-bias” ) involve unequal numbers of females and males . These events are typically inferred from the relative amount of X-chromosomal to autosomal genetic variation and have led to conflicting conclusions about human demographic history . Though population size changes alter the rela...	Sex-biased demographic events involve unequal numbers of females and males , and is referred to as “sex-bias” . In humans , short-range migrations ( e . g . , due to marriage practices ) are known to be sex-biased , and some long-range migrations , such as the one out of Africa , are hypothesized to be sex-biased . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "evolutionary", "biology", "statistics", "population", "genetics", "geographical", "locations", "simulation", "and", "modeling", "mathematics", "test", "statistics", "population", "biology", "research", "and", "analysis", "methods", "sex", "chromosomes", "chromosome", "bi...	2019	The inference of sex-biased human demography from whole-genome data
FLAGELLIN-SENSING 2 ( FLS2 ) is a leucine-rich repeat/transmembrane domain/protein kinase ( LRR-RLK ) that is the plant receptor for bacterial flagellin or the flagellin-derived flg22 peptide . Previous work has shown that after flg22 binding , FLS2 releases BIK1 kinase and homologs and associates with BAK1 kinase , an...	As a Pattern-Recognition Receptor ( PRR ) that detects conserved microbial molecules , FLS2 mediates the plant innate immunity responses triggered by bacterial flagellin or the flagellin epitope flg22 . Even though several protein kinases including BAK1 , BKK1 , BIK1 are known to play early roles in FLS2-mediated signa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "model", "organisms", "plant", "and", "algal", "models", "plant", "microbiology", "plant", "biology", "plant", "pathology", "biology", "microbiology", "host-pathogen", "interaction", "arabidopsis", "thaliana" ]	2013	Mutations in FLS2 Ser-938 Dissect Signaling Activation in FLS2-Mediated Arabidopsis Immunity
Genomic mapping of DNA replication origins ( ORIs ) in mammals provides a powerful means for understanding the regulatory complexity of our genome . Here we combine a genome-wide approach to identify preferential sites of DNA replication initiation at 0 . 4% of the mouse genome with detailed molecular analysis at disti...	The duplication of the genetic information of a cell starts from specific sites on the chromosomes called DNA replication origins . Their number varies from a few hundred in yeast cells to several thousands in human cells , distributed along the genome at comparable distances in both systems . An important question in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/dna", "replication", "molecular", "biology/chromatin", "structure", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "gen...	2009	Transcription Initiation Activity Sets Replication Origin Efficiency in Mammalian Cells
Methane produced by methanogenic archaea in ruminants contributes significantly to anthropogenic greenhouse gas emissions . The host genetic link controlling microbial methane production is unknown and appropriate genetic selection strategies are not developed . We used sire progeny group differences to estimate the ho...	Methane is a highly potent greenhouse gas and ruminants are the major source of methane emissions from anthropogenic activities . Here we show in an experiment with cattle that genetic selection of low-emitting animals is a viable option based on a newly developed selection criterion . The experimental data provided a ...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "livestock", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "microbiome", "chemical", "compounds", "ruminants", "microbiology", "diet", "vertebrates", "animals", "mammals", "metagenomics", "nutrition", "microbial", "genetics", "met...	2016	Bovine Host Genetic Variation Influences Rumen Microbial Methane Production with Best Selection Criterion for Low Methane Emitting and Efficiently Feed Converting Hosts Based on Metagenomic Gene Abundance
Bacillus anthracis , the etiological agent of anthrax , is a spore-forming Gram-positive bacterium . Infection with this pathogen results in multisystem dysfunction and death . The pathogenicity of B . anthracis is due to the production of virulence factors , including edema toxin ( ET ) . Recently , we established the...	All mammals are susceptible to infection by Bacillus anthracis , the etiological agent of anthrax . Infection can occur either accidentally or as a potential consequence of a terrorism threat . Pulmonary infection is the most life-threatening form of the disease , causing a near 100% mortality . Despite appropriate the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology", "in", "vitro", "eukaryotes", "eubacteria" ]	2007	Edema Toxin Impairs Anthracidal Phospholipase A2 Expression by Alveolar Macrophages
The intestinal ecosystem is formed by a complex , yet highly characteristic microbial community . The parameters defining whether this community permits invasion of a new bacterial species are unclear . In particular , inhibition of enteropathogen infection by the gut microbiota ( = colonization resistance ) is poorly ...	The commensal microbiota , populating the intestinal tract to high levels , is fundamental to human health . It exerts beneficial effects on the immune system and contributes to protection against gastrointestinal infections ( = colonization resistance ) by largely unknown mechanisms . Here , we reveal characteristics ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections", "microbiology/microbial", "evolution", "and", "genomics", "microbiology/innate", "immunity", "ecology/environmental", "microbiology", "microbiology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/gastrointestinal"...	2010	Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria
During development , neural competence is conferred and maintained by integrating spatial and temporal regulations . The Drosophila sensory bristles that detect mechanical and chemical stimulations are arranged in stereotypical positions . The anterior wing margin ( AWM ) is arrayed with neuron-innervated sensory brist...	A critical step in building a functional nervous system is to generate neurons at the appropriate locations . Neural competence is acquired at the precursor stage with the expression of specific transcription factors . One such critical factor is Senseless ( Sens ) , as precursors lacking Sens fail to develop to neuron...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	The COP9 Signalosome Converts Temporal Hormone Signaling to Spatial Restriction on Neural Competence
We present a network framework for analyzing multi-level regulation in higher eukaryotes based on systematic integration of various high-throughput datasets . The network , namely the integrated regulatory network , consists of three major types of regulation: TF→gene , TF→miRNA and miRNA→gene . We identified the targe...	The precise control of gene expression lies at the heart of many biological processes . In eukaryotes , the regulation is performed at multiple levels , mediated by different regulators such as transcription factors and miRNAs , each distinguished by different spatial and temporal characteristics . These regulators are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "genomics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2011	Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data
A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste . Pseudomonas putida is an archetype of such microbes due to its metabolic versatility , stress resistance , amenability to genetic modifications , and vast potential for environmen...	The pseudomonads include a diverse set of bacteria whose metabolic versatility and genetic plasticity have enabled their survival in a broad range of environments . Many members of this family are able to either degrade toxic compounds or to efficiently produce high value compounds and are therefore of interest for bot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology/biocatalysis", "biotechnology/applied", "microbiology", "computational", "biology/metabolic", "networks", "biotechnology/bioengineering", "computational", "biology/systems", "biology" ]	2008	Genome-Scale Reconstruction and Analysis of the Pseudomonas putida KT2440 Metabolic Network Facilitates Applications in Biotechnology
Protein arginine methyltransferase 4 ( PRMT4 ) –dependent methylation of arginine residues in histones and other chromatin-associated proteins plays an important role in the regulation of gene expression . However , the exact mechanism of how PRMT4 activates transcription remains elusive . Here , we identify the chroma...	Our manuscript deals with the Protein arginine methyltransferase 4 ( PRMT4 ) , which modifies arginine residues in histones and other chromatin-associated proteins and plays an important role in the regulation of gene expression . We addressed the question of how the transcriptional function of PRMT4 might contribute t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "biochemistry", "developmental", "biology", "biology", "proteomics", "molecular", "cell", "biology", "hematology" ]	2013	PRMT4 Is a Novel Coactivator of c-Myb-Dependent Transcription in Haematopoietic Cell Lines
Genomic imprinting causes the expression of an allele depending on its parental origin . In plants , most imprinted genes have been identified in Arabidopsis endosperm , a transient structure consumed by the embryo during seed formation . We identified imprinted genes in rice seed where both the endosperm and embryo ar...	The expression of maternal or paternal alleles in either a preferentially or exclusively uniparental manner , termed imprinting , is prevalent in the transient endosperm of seeds in the model plant Arabidopsis . Cereals form seeds where both the embryo and endosperm are present at seed maturity . They are an important ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2011	A Genome-Wide Survey of Imprinted Genes in Rice Seeds Reveals Imprinting Primarily Occurs in the Endosperm

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