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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Control of enzyme allosteric regulation is required to drive metabolic flux toward desired levels . Although the three-dimensional ( 3D ) structures of many enzyme-ligand complexes are available , it is still difficult to rationally engineer an allosterically regulatable enzyme without decreasing its catalytic activity...	Design of allosterically regulatable enzyme is essential to develop a highly efficient metabolite production . However , mutations on allosteric ligand binding sites often disrupt the catalytic activity of enzyme . To aid the design process of allosterically controllable enzymes , we develop an effective computational ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bioengineering", "biotechnology", "biological", "systems", "engineering", "genomics", "evolutionary", "biology", "evolutionary", "processes", "synthetic", "biology", "biology", "computational", "biology", "evolutionary", "selection", "structural", "genomics", "engineering" ]	2012	Rational Engineering of Enzyme Allosteric Regulation through Sequence Evolution Analysis
New microbial genomes are sequenced at a high pace , allowing insight into the genetics of not only cultured microbes , but a wide range of metagenomic collections such as the human microbiome . To understand the deluge of genomic data we face , computational approaches for gene functional annotation are invaluable . W...	While both the number and the diversity of sequenced prokaryotic genomes grow rapidly , the number of specific assignments of gene functions in the databases remains low and skewed toward the model prokaryote Escherichia coli . To aid in understanding the full set of newly sequenced genes , we created a computational m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "applications", "computer", "science", "web-based", "applications", "genomics", "functional", "genomics", "bio-ontologies", "genetics", "biology", "computational", "biology", "comparative", "genomics", "genetics", "and", "genomics", "gene", "function" ]	2013	Phyletic Profiling with Cliques of Orthologs Is Enhanced by Signatures of Paralogy Relationships
Canine hip dysplasia is a common , non-congenital , complex and hereditary disorder . It can inflict severe pain via secondary osteoarthritis and lead to euthanasia . An analogous disorder exists in humans . The genetic background of hip dysplasia in both species has remained ambiguous despite rigorous studies . We aim...	Hip dysplasia is a common orthopedic disorder in dogs and humans . It can pose a serious welfare problem with severe pain . The genetic background of this disorder remains inconclusive even after years of arduous research . We used the genotypes of 525 German Shepherds with carefully determined hip scores to identify g...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "dysplasia", "pathology", "and", "laboratory", "medicine", "statistics", "metaanalysis", "variant", "genotypes", "vertebrates", "dogs", "animals", "mammals", "genetic", "mapping", "mathemati...	2019	Novel protective and risk loci in hip dysplasia in German Shepherds
High-risk human papillomavirus ( HPV ) E6 proteins associate with the cellular ubiquitin ligase E6-Associated Protein ( E6AP ) , and then recruit both p53 and certain cellular PDZ proteins for ubiquitination and degradation by the proteasome . Low-risk HPV E6 proteins also associate with E6AP , yet fail to recruit p53 ...	Papillomaviruses cause benign squamous epithelial tumors through the action of virally encoded oncoproteins termed E6 and E7 , which are classified as either high or low-risk based upon the propensity of the tumor to evolve into cancer . E6 proteins from both high and low-risk HPVs interact with a cellular ubiquitin li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	E6 proteins from high-risk HPV, low-risk HPV, and animal papillomaviruses activate the Wnt/β-catenin pathway through E6AP-dependent degradation of NHERF1
In Taiwan , around 1 , 500 cases of dengue fever are reported annually and incidence has been increasing over time . A national web-based Notifiable Diseases Surveillance System ( NDSS ) has been in operation since 1997 to monitor incidence and trends and support case and outbreak management . We present the findings o...	In Taiwan , around 1 , 500 cases of dengue fever are reported annually . Surveillance and outbreak preparedness are important activities aimed at reducing the burden of dengue fever worldwide . A national web-based Notifiable Diseases Surveillance System ( NDSS ) for dengue fever has been established since 1997 in Taiw...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Evaluation of the National Notifiable Diseases Surveillance System for Dengue Fever in Taiwan, 2010–2012
By means of a computer search for upstream promoter elements ( distal sequence element and proximal sequence element ) typical of small nuclear RNA genes , we have identified in the human genome a number of previously unrecognized , putative transcription units whose predicted products are novel noncoding RNAs with hom...	After the sequence of the human genome was determined , it was immediately recognized that a large part of the regulation of the gene expression occurring in the cells under physiological , as well as under pathological conditions , is carried out by RNA molecules that do not code for proteins ( the “noncoding portion”...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "genetics", "and", "genomics", "homo", "(human)", "molecular", "biology" ]	2007	New Small Nuclear RNA Gene-Like Transcriptional Units as Sources of Regulatory Transcripts
Promoters are structurally and functionally diverse gene regulatory regions . The presence or absence of sequence motifs and the spacing between the motifs defines the properties of promoters . Recent alternative promoter usage analyses in Drosophila melanogaster revealed that transposable elements significantly contri...	The presence of several transposable element insertions in the promoter region of a Drosophila melanogaster gene has only been described in heat shock protein genes . In this work , we have discovered and characterized in detail several naturally occurring independent transposable element insertions in the promoter reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "gene", "regulation", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "genetic", "elements", "sequence", "motif", "analysis", "molecular", "biology", "techniques", ...	2016	Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila
4-anilino quinazolines have been identified as inhibitors of HCV replication . The target of this class of compounds was proposed to be the viral protein NS5A , although unequivocal proof has never been presented . A 4-anilino quinazoline moiety is often found in kinase inhibitors , leading us to formulate the hypothes...	It is estimated that 3% of the world's population are chronically infected by the hepatitis C virus ( HCV ) . Most infections become chronic and eventually evolve into cirrhosis and hepatocellular carcinoma . Host factors are interesting targets for anti-HCV therapies due to their inherent high genetic barrier to resis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2012	Metabolism of Phosphatidylinositol 4-Kinase IIIα-Dependent PI4P Is Subverted by HCV and Is Targeted by a 4-Anilino Quinazoline with Antiviral Activity
In acute Plasmodium falciparum ( P . falciparum ) malaria , the pro- and anti-inflammatory immune pathways must be delicately balanced so that the parasitemia is controlled without inducing immunopathology . An important mechanism to fine-tune T cell responses in the periphery is the induction of coinhibitory receptors...	In acute infections like malaria , our immune systems must achieve a careful balance between inflammatory and anti-inflammatory responses to successfully fight the infection without causing harm to the host . In this study , we examined the CD4+ T cell response and CD4+ T cell regulation in patients with acute malaria ...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "cells", "immune", "physiology", "cytokines", "plasmodium", "immunology", "tropical", "diseases", "parasitic", "diseases", "pa...	2016	Acute Malaria Induces PD1+CTLA4+ Effector T Cells with Cell-Extrinsic Suppressor Function
Previously , we identified an adolescent idiopathic scoliosis susceptibility locus near human ladybird homeobox 1 ( LBX1 ) and FLJ41350 by a genome-wide association study . Here , we characterized the associated non-coding variant and investigated the function of these genes . A chromosome conformation capture assay re...	Scoliosis is the most common type of spinal deformity with a lateral spinal curvature of at least 10 degrees , affecting 2–4% of the population . Scoliosis caused by a primary problem related to the spine itself is classified into congenital scoliosis ( CS ) and idiopathic scoliosis ( IS ) . Among these , adolescent id...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "classical", "mechanics", "vertebrates", "animals", "somites", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "organism", "development", "damage", "mechanics", "molecular", "biology", "techniques", "embryos", "research", "and", "anal...	2016	Functional Investigation of a Non-coding Variant Associated with Adolescent Idiopathic Scoliosis in Zebrafish: Elevated Expression of the Ladybird Homeobox Gene Causes Body Axis Deformation
Viruses and bacteria are critical components of the human microbiome and play important roles in health and disease . Most previous work has relied on studying bacteria and viruses independently , thereby reducing them to two separate communities . Such approaches are unable to capture how these microbial communities i...	The human microbiome , the collection of microbial communities that colonize the human body , is a crucial component to health and disease . Two major components of the human microbiome are the bacterial and viral communities . These communities have primarily been studied separately using metrics of community composit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "microbiome", "bacteriophages", "microbiology", "diet", "viruses", "nutrition", "network", "analysis", "bacteria", "microbial", "genomics", "research", "and", "analysis", "methods", "sequence", "analysis", "viral", "genomics", "c...	2018	Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome
Following respiratory syncytial virus infection of adult CB6F1 hybrid mice , a predictable CD8+ T cell epitope hierarchy is established with a strongly dominant response to a Kd-restricted peptide ( SYIGSINNI ) from the M2 protein . The response to KdM282-90 is ∼5-fold higher than the response to a subdominant epitope ...	RSV causes yearly winter epidemics of respiratory disease with peak hospitalization rates at 2 . 5 months of age . Clearance of virus-infected cells depends on CD8 T-cells , and defining mechanisms of CD8 T-cell regulation is essential for understanding RSV disease pathogenesis and guiding therapeutic interventions . C...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "respiratory", "infections", "immunity", "to", "infections", "immunology", "microbiology", "pulmonology", "adaptive", "immunity", "immune", "defense", "immunoregulation", "lower", "respiratory", "tract", "infections", "asthma", "animal", "mo...	2011	Neonatal CD8 T-cell Hierarchy Is Distinct from Adults and Is Influenced by Intrinsic T cell Properties in Respiratory Syncytial Virus Infected Mice
At least six histone H1 variants exist in somatic mammalian cells that bind to the linker DNA and stabilize the nucleosome particle contributing to higher order chromatin compaction . In addition , H1 seems to be actively involved in the regulation of gene expression . However , it is not well known whether the differe...	Eukaryotic DNA is packaged into chromatin through its association with histone proteins . The linker histone H1 sits at the base of the nucleosome near the DNA entry and exit sites to stabilize two full turns of DNA . In particular , histone H1 participates in nucleosome spacing and formation of the higher-order chroma...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/chromatin", "structure", "molecular", "biology/transcription", "initiation", "and", "activation" ]	2008	Depletion of Human Histone H1 Variants Uncovers Specific Roles in Gene Expression and Cell Growth
A central challenge in host-pathogen systems biology is the elucidation of general , systems-level principles that distinguish host-pathogen interactions from within-host interactions . Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution , treat...	The goal of host-pathogen systems biology is to examine the complex interactions between species , such as those between a virus and its host . Analysis of protein-protein interaction ( PPI ) networks can identify general principles that distinguish between within-species and between-species interactions . However , PP...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Signatures of Pleiotropy, Economy and Convergent Evolution in a Domain-Resolved Map of Human–Virus Protein–Protein Interaction Networks
Alzheimer disease ( AD ) , Frontotemporal lobar degeneration ( FTD ) , Amyotrophic lateral sclerosis ( ALS ) and Parkinson disease ( PD ) have a certain degree of clinical , pathological and molecular overlap . Previous studies indicate that causative mutations in AD and FTD/ALS genes can be found in clinical familial ...	In this study we provide further genetic evidence of the clinical , pathological and molecular overlap between neurodegenerative diseases . We screened the known Mendelian genes in Alzheimer disease ( AD ) , Frontotemporal Dementia ( FTD ) , Parkinson disease ( PD ) and Amyotrophic Lateral Sclerosis ( ALS ) disease in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "neurodegenerative", "diseases", "pathogens", "amyotrophic", "lateral", "sclerosis", "alzheimer's", "disease", "motor", "neuron", "diseases", "dementia", "mental", "health", "and", "p...	2017	Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease
The Global Programme to Eliminate Lymphatic Filariasis ( GPELF ) , launched in 2000 , has the target of eliminating the disease as a public health problem by the year 2020 . The strategy adopted is mass drug administration ( MDA ) to all eligible individuals in endemic communities and the implementation of measures to ...	Mass drug administration ( MDA ) for the control of elephantiasis in the state of Kano in Nigeria , started in the year 2010 . It was estimated that by 2015 , the MDA programme will be extended to 11 remaining urban Local Government Areas ( LGAs ) . However , MDA in urban areas faces specific challenges , the most prom...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "animals", "filariasis", "neglected", "tropical", "diseases", "molecular", "biology", "techniques", "insect", "vectors", "lymphatic", "f...	2017	Is mass drug administration against lymphatic filariasis required in urban settings? The experience in Kano, Nigeria
The glycosylation of cell surface proteins plays a crucial role in a multitude of biological processes , such as cell adhesion and recognition . To understand the process of protein glycosylation , the reaction mechanisms of the participating enzymes need to be known . However , the reaction mechanism of retaining glyc...	Cell surface proteins are covered by a diverse array of glycan structures , important for mutual cell recognition and communication . These glycans are complex branched molecules assembled from monosaccharide units by a sophisticated cascade of enzymes from the group of glycosyltransferases . Disruptions in the synthes...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[]	2015	Stepwise Catalytic Mechanism via Short-Lived Intermediate Inferred from Combined QM/MM MERP and PES Calculations on Retaining Glycosyltransferase ppGalNAcT2
Plants have developed sophisticated systems to monitor and rapidly acclimate to environmental fluctuations . Light is an essential source of environmental information throughout the plant’s life cycle . The model plant Arabidopsis thaliana possesses five phytochromes ( phyA-phyE ) with important roles in germination , ...	As sessile organisms , plants respond to and integrate environmental information . An intriguing aspect is how plants integrate this information . We studied the interactions among members of the phytochrome family of photoreceptors , which detect the changes in light quality that occur upon shading by other plants , a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "plant", "growth", "and", "development", "plant", "embryo", "anatomy", "brassica", "social", "sciences", "plant", "physiology", "neuroscience", "developmental", "biology", "plant", "science", "model", "organisms", "plants", "flowering", "plants", "...	2016	Bottom-up Assembly of the Phytochrome Network
Despite the global threat caused by arthropod-borne viruses , there is not an efficient method for screening vector populations to detect novel viral sequences . Current viral detection and surveillance methods based on culture can be costly and time consuming and are predicated on prior knowledge of the etiologic agen...	Traditional methods for virus detection often rely on specific attributes , such as DNA sequences , of the viruses and therefore they not only require a priori knowledge of the agent in question , but they also are generally very specific in nature , capable of detecting viruses only from within a specific family , for...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology/emerging", "viral", "diseases", "genetics", "and", "genomics/gene", "expression" ]	2010	Arbovirus Detection in Insect Vectors by Rapid, High-Throughput Pyrosequencing
Trypanosoma cruzi is the obligate intracellular parasite that causes Chagas disease . The pathogenesis of this disease is a multifactorial complex process that involves a large number of molecules and particles , including the extracellular vesicles . The presence of EVs of T . cruzi was first described in 1979 and , s...	Extracellular vesicles ( EVs ) are a diverse group of nanoparticles involved in intercellular communication under physiological and pathological conditions . Trypanosoma cruzi , the protozoan that causes Chagas disease , releases EVs that facilitate parasite invasion of the host cell , immunomodulate the host response ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "vero", "cells", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "parasitic", "cell", "cycles", "biological", "cultures", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans", "parasitolo...	2019	Extracellular vesicles of Trypanosoma cruzi tissue-culture cell-derived trypomastigotes: Induction of physiological changes in non-parasitized culture cells
Ubiquitylation targets proteins for proteasome-mediated degradation and plays important roles in many biological processes including apoptosis . However , non-proteolytic functions of ubiquitylation are also known . In Drosophila , the inhibitor of apoptosis protein 1 ( DIAP1 ) is known to ubiquitylate the initiator ca...	The Drosophila inhibitor of apoptosis 1 ( DIAP1 ) readily promotes ubiquitylation of the CASPASE-9–like initiator caspase DRONC in vitro and in vivo . Because DRONC protein accumulates in diap1 mutant cells that are kept alive by effector caspase inhibition—producing so-called “undead” cells—it has been proposed that D...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "cell", "death", "developmental", "biology", "cell", "biology", "biology", "molecular", "cell", "biology" ]	2011	Drosophila IAP1-Mediated Ubiquitylation Controls Activation of the Initiator Caspase DRONC Independent of Protein Degradation
West Nile virus ( WNV ) is an arbovirus maintained in nature in a bird-mosquito enzootic cycle which can also infect other vertebrates including humans . WNV is now endemic in the United States ( U . S . ) , causing yearly outbreaks that have resulted in an estimated total of 4–5 million human infections . Over 41 , 70...	West Nile virus ( WNV; family Flaviviridae , genus Flavivirus ) is a mosquito-borne virus maintained in a bird-mosquito enzootic cycle . WNV can occasionally infect other animals and humans , which are considered dead-end hosts because they produce too little virus in blood to re-infect mosquitoes . Most human infectio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "biogeography", "organismal", "evolution", "medicine", "and", "health", "sciences", "animal", "genetics", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "genetics", "micro...	2016	Genetic Variability of West Nile Virus in U.S. Blood Donors from the 2012 Epidemic Season
The most polymorphic gene family in P . falciparum is the ∼60 var genes distributed across parasite chromosomes , both in the subtelomeres and in internal regions . They encode hypervariable surface proteins known as P . falciparum erythrocyte membrane protein 1 ( PfEMP1 ) that are critical for pathogenesis and immune ...	Malaria kills >600 , 000 people each year , with most deaths caused by Plasmodium falciparum . A family of proteins known as P . falciparum erythrocyte membrane protein 1 , PfEMP1 , is expressed on the surface of infected erythrocytes and plays an important role in pathogenesis . Each P . falciparum genome contains app...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "immune", "system", "proteins", "apicomplexa", "parasite", "groups", "genomics", "proteins", "plasmodium", "antigens", "genetics", "biology", "and", "life", "sciences", "dna", "antigenic", "variation", "dna", "recombination", "immunology", "parasitology", ...	2014	Generation of Antigenic Diversity in Plasmodium falciparum by Structured Rearrangement of Var Genes During Mitosis
Autochthonous cutaneous and visceral leishmaniasis ( VL ) caused by Leishmania martiniquensis and Leishmania siamensis have been considered emerging infectious diseases in Thailand . The disease burden is significantly underestimated , especially the prevalence of Leishmania infection among HIV-positive patients . A cr...	Visceral leishmaniasis ( VL ) in Thailand is caused by two causative agents , Leishmania martiniquensis and Leishmania siamensis . A public health concern brought us to investigate the magnitude of Leishmania infection among individuals with HIV living in an affected area , Trang province , southern Thailand . The resu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "opportunistic", "infections", "parasitic", "diseases", "p...	2017	Prevalence and risk factors associated with Leishmania infection in Trang Province, southern Thailand
In Brazil , schistosomiasis is a parasitic disease of public health relevance , mainly in poor areas where Schistosoma mansoni is the only human species encountered and Biomphalaria straminea is one of the intermediate host snails . A nested-PCR based on a specific mitochondrial S . mansoni minisatellite DNA region has...	In Brazil , around 1 . 8 million people , mostly in the northeastern region of the country , are thought to be infected with Schistosoma mansoni . Snails of the genus Biomphalaria serve as intermediate hosts of the S . mansoni . A special program for schistosomiasis control was implemented more than 40 years ago in Bra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "biomphalaria", "helminths", "malacology", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "parasitology", "gastropods", "neglected", ...	2018	A field survey using LAMP assay for detection of Schistosoma mansoni in a low-transmission area of schistosomiasis in Umbuzeiro, Brazil: Assessment in human and snail samples
Polymerase basic protein 1 ( PB1 ) is the catalytic core of the influenza A virus ( IAV ) RNA polymerase complex essential for viral transcription and replication . Understanding the intrinsic mechanisms which block PB1 function could stimulate development of new anti-influenza therapeutics . Affinity purification coup...	Influenza A virus presents a continued threat to global health with considerable economic and social impact . Vaccinations against influenza are not always effective , and many influenza strains have developed resistance to current antiviral drugs . Thus , it is imperative to find new strategies for the prevention and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TRIM32 Senses and Restricts Influenza A Virus by Ubiquitination of PB1 Polymerase
Dynamin Guanosine Triphosphate hydrolases ( GTPases ) are best studied for their role in the terminal membrane fission process of clathrin-mediated endocytosis ( CME ) , but they have also been proposed to regulate earlier stages of CME . Although highly enriched in neurons , dynamin-1 ( Dyn1 ) is , in fact , widely ex...	Clathrin-mediated endocytosis ( CME ) , a major route for nutrient uptake , also controls signaling downstream of cell surface receptors . Recent studies have shown that signaling , in turn , can reciprocally regulate CME . CME is initiated by the assembly of clathrin-coated pits ( CCPs ) that mature to form deeply inv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "gene", "regulation", "enzymes", "cell", "processes", "enzymology", "light", "microscopy", "microscopy", "cellular", "structures", "and", "organelles", "optics", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "proteins", "fl...	2018	A noncanonical role for dynamin-1 in regulating early stages of clathrin-mediated endocytosis in non-neuronal cells
Aging is the major risk factor for neurodegenerative diseases such as Alzheimer's disease , but little is known about the processes that lead to age-related decline of brain structures and function . Here we use RNA-seq in combination with high resolution histological analyses to show that aging leads to a significant ...	Aging is frequently accompanied with frailty and cognitive decline . In recent years , increasing evidence has linked physical inactivity with the development of dementias such as Alzheimer’s disease . In fact , it is recognized that exercise combats frailty and cognitive decline in older adults , but the biological me...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction
Visceral leishmaniasis is a major neglected tropical disease , with an estimated 500 , 000 new cases and more than 50 , 000 deaths attributable to this disease every year . Drug therapy is available but costly and resistance against several drug classes has evolved . Despite all efforts , no commercial , let alone affo...	The leishmaniases are tropical diseases that affect the poorest of the poor . They are caused by Leishmania species , protozoan parasites transmitted by blood sucking insects and the visceral form of the disease is fatal . Vaccines that would tremendously boost disease control strategies need to be designed cost-effici...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunizations", "medicine", "infectious", "diseases", "immunity", "leishmaniasis", "neglected", "tropical", "diseases", "biology", "microbiology", "parasitic", "diseases" ]	2011	Single Dose Novel Salmonella Vaccine Enhances Resistance against Visceralizing L. major and L. donovani Infection in Susceptible BALB/c Mice
Deoxyribonuclease II ( DNase II ) is a well-known acidic endonuclease that catalyses the degradation of DNA into oligonucleotides . Only one or a few genes encoding DNase II have been observed in the genomes of many species . 125 DNase II-like protein family genes were predicted in the Trichinella spiralis ( T . spiral...	Deoxyribonuclease II ( DNase II ) is classified into a unique family of nucleases and mediates the degradation of DNA associated with apoptosis . Although DNase II activity was first observed in 1947 , and has been studied biochemically and enzymatically since the 1960s , only recently has genetic information on the en...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "trichinellosis", "parasitic", "diseases", "medicine", "and", "health", "sciences" ]	2014	Characterisation of a Plancitoxin-1-Like DNase II Gene in Trichinella spiralis
The disease severity of Entamoeba histolytica infection ranges from asymptomatic to life-threatening . Recent human and animal data implicate the gut microbiome as a modifier of E . histolytica virulence . Here we have explored the association of the microbiome with susceptibility to amebiasis in infants and in the mou...	Amebiasis , caused by intestinal infection of Entamoeba histolytica , is one of the leading causes of parasite infection-related mortality and morbidity around the world . However , pathogenesis , such as determinant factors of infection outcome , is still unclear although recent data indicate that the gut microbiome p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "antimicrobials", "children", "medicine", "and", "health", "sciences", "immune", "cells", "microbiome", "drugs", "immunology", "microbiology", "parasitic", "protozoans", "animal", "models", "colitis", "age", "groups", "model", "organisms", "protozoans"...	2017	Microbiome-mediated neutrophil recruitment via CXCR2 and protection from amebic colitis
Viral production from infected cells can occur continuously or in a burst that generally kills the cell . For HIV infection , both modes of production have been suggested . Standard viral dynamic models formulated as sets of ordinary differential equations can not distinguish between these two modes of viral production...	The dynamics of HIV infection and treatment has been extensively studied using ordinary differential equation models . Recent work on HIV transmission has suggested that most sexually transmitted infections are started by a single virus or infected cell . This observation coupled with the fact that successful HIV trans...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "mathematics/statistics", "biophysics", "immunology", "virology" ]	2011	Stochastic Theory of Early Viral Infection: Continuous versus Burst Production of Virions
Primary microcephaly is a congenital neurodevelopmental disorder of reduced head circumference and brain volume , with fewer neurons in the cortex of the developing brain due to premature transition between symmetrical and asymmetrical cellular division of the neuronal stem cell layer during neurogenesis . We now show ...	One of the major events in human evolution is the significant increase in brain volume in the transition from primates to humans . The molecular pathways determining the larger size of the human brain are not fully understood . Hereditary primary microcephaly , a neurodevelopmental disorder in which infants are born wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "invertebrates", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "luciferase", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "neuronal", "differentiation", "enzymology", "animals", "cell", "differe...	2016	ALFY-Controlled DVL3 Autophagy Regulates Wnt Signaling, Determining Human Brain Size
The IκB kinase ( IKK ) complex is a key regulator of signal transduction pathways leading to the induction of NF-κB-dependent gene expression and production of pro-inflammatory cytokines . It therefore represents a major target for the development of anti-inflammatory therapeutic drugs and may be targeted by pathogens ...	Vaccinia virus ( VACV ) is the live vaccine used to eradicate smallpox and is also the most intensively studied poxvirus . Like many poxviruses , VACV produces a wide variety of proteins that inhibit parts of the host response to infection . Consequently , the virus can escape destruction by the immune system and be pa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "immunology", "virology" ]	2008	Inhibition of IκB Kinase by Vaccinia Virus Virulence Factor B14
Most of the somatic cells of adult metazoans , including mammals , do not undergo continuous cycles of replication . Instead , they are quiescent and devote most of their metabolic activity to gene expression . The mutagenic consequences of exposure to DNA–damaging agents are well documented , but less is known about t...	The DNA molecule is used as a template for duplication , to transmit genetic information to the progeny of a given cell , but also as a template for the transcription machinery . This machinery converts genetic information from the DNA form to the RNA form used for protein synthesis . Chemical alterations of the DNA mo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/translation", "mechanisms", "genetics", "and", "genomics/genetics", "of", "disease", "molecular", "biology/dna", "repair" ]	2009	Transcriptional Mutagenesis Induced by 8-Oxoguanine in Mammalian Cells
Understanding tumor invasion and metastasis is of crucial importance for both fundamental cancer research and clinical practice . In vitro experiments have established that the invasive growth of malignant tumors is characterized by the dendritic invasive branches composed of chains of tumor cells emanating from the pr...	The goal of the present work is to develop an efficient single-cell based cellular automaton ( CA ) model that enables one to investigate the growth dynamics and morphology of invasive solid tumors . Recent experiments have shown that highly malignant tumors develop dendritic branches composed of tumor cells that follo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physics", "mathematics", "materials", "science", "biology" ]	2011	Emergent Behaviors from a Cellular Automaton Model for Invasive Tumor Growth in Heterogeneous Microenvironments
Interactions among genes and the environment are a common source of phenotypic variation . To characterize the interplay between genetics and the environment at single nucleotide resolution , we quantified the genetic and environmental interactions of four quantitative trait nucleotides ( QTN ) that govern yeast sporul...	Phenotypic variation among individuals is caused by naturally occurring genetic differences , or alleles . The relationship between an allele and the phenotype is extremely complex; for example , the effect of an allele often depends upon both the environment and the individual's genetic background . To better understa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits" ]	2010	Gene–Environment Interactions at Nucleotide Resolution
Malaria control relies heavily on pyrethroid insecticides , to which susceptibility is declining in Anopheles mosquitoes . To combat pyrethroid resistance , application of alternative insecticides is advocated for indoor residual spraying ( IRS ) , and carbamates are increasingly important . Emergence of a very strong ...	Malaria control depends heavily on only four classes of insecticide to which Anopheles mosquitoes are increasingly resistant . It is important to manage insecticide application carefully to minimise increases in resistance , for example by using different compounds in combination or rotation . Recently , mosquitoes res...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "genetic", "mutation", "gene", "expression", "genetics", "biology", "evolutionary", "biology" ]	2014	CYP6 P450 Enzymes and ACE-1 Duplication Produce Extreme and Multiple Insecticide Resistance in the Malaria Mosquito Anopheles gambiae
Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths . Because such paths are curves in a high-dimensional space , it has been difficult to quantitatively compare...	Many proteins are nanomachines that perform mechanical or chemical work by changing their three-dimensional shape and cycle between multiple conformational states . Computer simulations of such conformational transitions provide mechanistic insights into protein function but such simulations have been challenging . In ...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "distance", "measurement", "crystal", "structure", "molecular", "dynamics", "engineering", "and", "technology", "applied", "mathematics", "condensed", "matter", "physics", "simulation", "and", "modeling", "algorithms", "interpolation", "mathematics", "network", "analysis", ...	2015	Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways
Effectors of the bacterial type III secretion system provide invaluable molecular probes to elucidate the molecular mechanisms of plant immunity and pathogen virulence . In this report , we focus on the AvrBs2 effector protein from the bacterial pathogen Xanthomonas euvesicatoria ( Xe ) , the causal agent of bacterial ...	The bacterial pathogen Xanthomonas euvesicatoria ( Xe ) is the causal agent of bacterial leaf spot disease of pepper and tomato . This pathogen is capable of delivering more than 28 effector proteins to plant cells via the type three secretion and translocation system ( TTSS ) . The AvrBs2 protein is a TTSS effector of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "agriculture", "biology" ]	2011	Computational and Biochemical Analysis of the Xanthomonas Effector AvrBs2 and Its Role in the Modulation of Xanthomonas Type Three Effector Delivery
Developmental programming links growth in early life with health status in adulthood . Although environmental factors such as maternal diet can influence the growth and adult health status of offspring , the genetic influences on this process are poorly understood . Using the mouse as a model , we identify the imprinte...	Experiences during early life can impact on health status in adulthood; low birth weight , for example , is linked to an increased risk of diabetes and obesity in later life . Such developmental programming can be influenced by environmental factors such as diet , but the importance of genetics in this process is not w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "histology", "animal", "genetics", "model", "organisms", "organism", "development", "genomic", "imprinting", "genetics", "epigenetics", "molecular", "genetics", "biology", "anatomy", "and", "physiology", "molecular", "cell",...	2014	Developmental Programming Mediated by Complementary Roles of Imprinted Grb10 in Mother and Pup
Snakebites are a major Collective Health problem worldwide . In Brazil , Bothrops jararaca snake venom ( BjV ) evokes hemostatic disturbances , bleeding manifestations , and redox status imbalance . Specific antivenom therapy , although efficacious to revert most snakebite-induced manifestations , is incapable of treat...	Snakebite is a neglected disease and a major health issue in tropical countries . Bites by Bothrops snakes ( jararacas ) are frequent throughout South and Central Americas and usually lead to inflammatory and bleeding manifestations in patients , which may be highly severe in some cases . Antivenom therapy is highly ef...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "toxins", "pathology", "and", "laboratory", "medicine", "platelet", "aggregation", "tropical", "diseases", "vertebrates", "animals", "toxicology", "toxic", "agents", "protein", "expression", ...	2018	Rutin (quercetin-3-rutinoside) modulates the hemostatic disturbances and redox imbalance induced by Bothrops jararaca snake venom in mice
NKG2D plays a major role in controlling immune responses through the regulation of natural killer ( NK ) cells , αβ and γδ T-cell function . This activating receptor recognizes eight distinct ligands ( the MHC Class I polypeptide-related sequences ( MIC ) A andB , and UL16-binding proteins ( ULBP ) 1–6 ) induced by cel...	Human cytomegalovirus ( HCMV ) is a herpesvirus that infects most people in the world , usually without producing symptoms . However , infection is life-long and must be kept in check by the immune system . When the immune system is weakened , the outcome of HCMV infection can be very serious . Thus , HCMV is the major...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "virology", "biology", "and", "life", "sciences", "microbiology", "viral", "diseases" ]	2014	Two Novel Human Cytomegalovirus NK Cell Evasion Functions Target MICA for Lysosomal Degradation
In everyday life , we have to decide whether it is worth exerting effort to obtain rewards . Effort can be experienced in different domains , with some tasks requiring significant cognitive demand and others being more physically effortful . The motivation to exert effort for reward is highly subjective and varies cons...	Rewards are rarely obtained without the motivation to exert effort . In humans , effort can be perceived in both the cognitive and physical domains , yet little is known about how the brain evaluates whether it is worth exerting different types of effort in return for rewards . In this study , we used functional magnet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "decision", "making", "prefrontal", "cortex", "brain", "social", "sciences", "neuroscience", "magnetic", "resonance", "imaging", "cognitive", "psychology"...	2017	Neurocomputational mechanisms underlying subjective valuation of effort costs
One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution . We studied the evolution of genetic networks in Saccharomyces cerevisiae ( budding yeast ) populations propagated for more than 200 generations in different nitrogen-limiting conditions . We find that ...	We studied adaptive evolution in different nitrogen-limited environments using long-term selection of asexually reproducing Saccharomyces cerevisiae populations in chemostats . Using next generation sequencing and DNA microarrays , we identified all acquired genetic variation associated with increased fitness , in both...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "mutation", "model", "organisms", "microbial", "evolution", "genetics", "yeast", "and", "fungal", "models", "biology", "microbiology", "evolutionary", "biology", "genomic", "evolution", "gene", "networks", "evolutionary", "genetics", "saccharomyces", "cerevis...	2014	Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments
Koolen-de Vries syndrome ( KdVS ) is a multi-system disorder characterized by intellectual disability , friendly behavior , and congenital malformations . The syndrome is caused either by microdeletions in the 17q21 . 31 chromosomal region or by variants in the KANSL1 gene . The reciprocal 17q21 . 31 microduplication s...	The 17q21 . 31 deletion syndrome , also named Koolen-de Vries syndrome ( KdVS ) , is a rare copy number variants associated in humans with intellectual disability , friendly behavior , congenital malformations . The syndrome is caused either by microdeletions in the 17q21 . 31 region or by variants in the KANSL1 gene i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "sociology", "brain", "vertebrates", "social", "sciences", "mice", "neuroscience", "animals", "mammals", "biological", "locomotion", "animal", "models", "model", "organisms", "animal", "behavior", "experimental", "organism", "sys...	2017	Mouse models of 17q21.31 microdeletion and microduplication syndromes highlight the importance of Kansl1 for cognition
Myocyte enhancer factor 2 protein ( Mef2 ) is an evolutionarily conserved activator of transcription that is critical to induce and control complex processes in myogenesis and neurogenesis in vertebrates and insects , and osteogenesis in vertebrates . In Drosophila , Mef2 null mutants are unable to produce differentiat...	Schistosome parasites infect more than 200 million people worldwide and cause human schistosomiasis . Free-swimming schistosome larvae are highly mobile and invade and penetrate the host's skin to perpetuate their lifecycle in their human host , growing from 90–215 micrometers in length as a schistosomulum to a 7–20 mi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "biotechnology", "medicine", "biochemistry", "developmental", "biology", "infectious", "diseases", "zoology", "global", "health", "genetics", "biology", "genomics", "microbiology", "genetics", "and", "genomics", "parasitology" ]	2012	Identification and Characterization of a Mef2 Transcriptional Activator in Schistosome Parasites
The stress-activated protein kinase Gcn2 regulates protein synthesis by phosphorylation of translation initiation factor eIF2α . Gcn2 is activated in amino acid-deprived cells by binding of uncharged tRNA to the regulatory domain related to histidyl-tRNA synthetase , but the molecular mechanism of activation is unclear...	The survival of all living organisms depends on their capacity to adapt their gene expression program to variations in the environment . When subjected to various stresses , eukaryotic cells modulate general and gene-specific protein synthesis by phosphorylating the α-subunit of eukaryotic translation initiation factor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Interaction between the tRNA-Binding and C-Terminal Domains of Yeast Gcn2 Regulates Kinase Activity In Vivo
Many pathogens are equipped with factors providing resistance against the bactericidal action of complement . Yersinia enterocolitica , a Gram-negative enteric pathogen with invasive properties , efficiently resists the deleterious action of human complement . The major Y . enterocolitica serum resistance determinants ...	To cause disease in humans , pathogenic bacteria have to evade the versatile immune system of the host . An important part of innate immunity is the complement system that is composed of over 30 proteins on host cells and in blood able to detect and destroy foreign material . To survive , bacteria can bind complement r...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/immunity", "to", "infections", "microbiology/innate", "immunity", "immunology/innate", "immunity", "infectious", "diseases/bacterial", "infections", "immunology/immunity", "to", "infections", "infectious", "diseases/gastrointestinal", "infections" ]	2008	Yersinia enterocolitica Serum Resistance Proteins YadA and Ail Bind the Complement Regulator C4b-Binding Protein
The non-virulent Wolbachia strain wMel and the life-shortening strain wMelPop-CLA , both originally from Drosophila melanogaster , have been stably introduced into the mosquito vector of dengue fever , Aedes aegypti . Each of these Wolbachia strains interferes with viral pathogenicity and/or dissemination in both their...	Wolbachia pipientis is an inherited intracellular bacterium that is widespread in insects . Because of its ability to interfere with various pathogens such as dengue viruses , nematodes and Plasmodium in insects , it has been proposed as a possible tool to control insect-transmitted disease . Recently , two strains of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	The Relative Importance of Innate Immune Priming in Wolbachia-Mediated Dengue Interference
State transitions allow for the balancing of the light excitation energy between photosystem I and photosystem II and for optimal photosynthetic activity when photosynthetic organisms are subjected to changing light conditions . This process is regulated by the redox state of the plastoquinone pool through the Stt7/STN...	To grow optimally , photosynthetic organisms need to constantly adjust to changing light conditions . One of these adjustments , called state transitions , allows light energy to be redistributed between the two photosynthetic reaction center complexes in a cell's chloroplasts . These complexes act in concert with othe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology" ]	2009	Analysis of the Chloroplast Protein Kinase Stt7 during State Transitions
The corneal micropocket angiogenesis assay is an experimental protocol for studying vessel network formation , or neovascularization , in vivo . The assay is attractive due to the ease with which the developing vessel network can be observed in the same animal over time . Measurements from the assay have been used in c...	Neovascularization , or the formation of new blood vessels , is an important process in development , wound healing and cancer . The corneal micropocket assay is used to better understand the process and , in the case of cancer , how it can be controlled with drug therapies for improved patient outcomes . In the assay ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "physiology", "endothelial", "cells", "applied", "mathematics", "ocular", "anatomy", "radii", "mathematical", "models", "geometry", "finite", "element", "analysis", "epithelial", "cells", "angiogenesis", "developm...	2018	The importance of geometry in the corneal micropocket angiogenesis assay
We present a novel surrogate modeling method that can be used to accelerate the solution of uncertainty quantification ( UQ ) problems arising in nonlinear and non-smooth models of biological systems . In particular , we focus on dynamic flux balance analysis ( DFBA ) models that couple intracellular fluxes , found fro...	Construction and validation of mathematical models in biological systems involving genome-scale biomolecular networks is a challenging problem . This article presents a novel surrogate modeling method that can accelerate parameter inference from experimental data and the quantification of uncertainty in the predictions...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "carbohydrate", "metabolism", "chemical", "compounds", "metabolic", "networks", "experimental", "design", "carbohydrates", "glucose", "metabolism", "organic", "compounds", "glucose", "simulation", "and", "modeling", "xylose", "research", "design", "mathematics", "algebra", ...	2019	Fast uncertainty quantification for dynamic flux balance analysis using non-smooth polynomial chaos expansions
DNA viruses , retroviruses and hepadnaviruses , such as hepatitis B virus ( HBV ) , are vulnerable to genetic editing of single stranded DNA by host cell APOBEC3 ( A3 ) cytidine deaminases . At least three A3 genes are up regulated by interferon-α in human hepatocytes while ectopic expression of activation induced deam...	Retroviruses and hepadnaviruses such as hepatitis B virus ( HBV ) are vulnerable to mutation by host cell single stranded DNA cytidine deaminases . The result is hypermutated viral peppered with uracil residues . While there are potentially 11 such human enzymes , the major players belong to the 7 gene APOBEC3 cluster ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/viral", "infections", "pathology/histopathology", "virology/viruses", "and", "cancer", "virology" ]	2010	Massive APOBEC3 Editing of Hepatitis B Viral DNA in Cirrhosis
Protein kinase B ( PKB/Akt ) is a pivotal regulator of diverse metabolic , phenotypic , and antiapoptotic cellular controls and has been shown to be a key player in cancer progression . Here , using fluorescent reporters , we shown in cells that , contrary to in vitro analyses , 3-phosphoinositide–dependent protein kin...	Regulation of intracellular signaling depends on the precise operation of molecular switches such as kinases and phosphatases . Disruption of their activities leads to inappropriate cellular proliferation , growth , and survival . Protein kinase B ( PKB ) is a critical kinase that regulates events downstream of growth ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "cell", "biology", "computational", "biology", "biophysics", "homo", "(human)" ]	2007	Intramolecular and Intermolecular Interactions of Protein Kinase B Define Its Activation In Vivo
The intraerythrocytic parasite Plasmodium—the causative agent of malaria—produces an inorganic crystal called hemozoin ( Hz ) during the heme detoxification process , which is released into the circulation during erythrocyte lysis . Hz is rapidly ingested by phagocytes and induces the production of several pro-inflamma...	Malaria is widespread in the tropical and sub-tropical regions of the world , and is responsible for 2–3 million deaths annually . This disease is caused by parasites of the Plasmodium genus . The parasite feeds on the hemoglobin of red blood cells and generates a metabolic waste called hemozoin ( Hz ) . Hz is released...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "infectious", "diseases/protozoal", "infections", "immunology/leukocyte", "signaling", "and", "gene", "expression", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "immunology/leukocyte", "activation" ]	2009	Malarial Hemozoin Activates the NLRP3 Inflammasome through Lyn and Syk Kinases
The emergent human pathogen Mycoplasma genitalium , with one of the smallest genomes among cells capable of growing in axenic cultures , presents a flask-shaped morphology due to a protrusion of the cell membrane , known as the terminal organelle , that is involved in cell adhesion and motility and is an important viru...	Mycoplasma genitalium is one of the smallest bacteria known and a common human pathogen . M . genitalium cells present a flask-shaped morphology due to the presence of a characteristic protrusion , known as the terminal organelle , that has several key biological roles . The terminal organelle allows mycoplasmas to mov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "condensed", "matter", "physics", "microbiology", "mutation", "crystals", "materials", "science", "mycoplasma", "mycoplasma", ...	2016	Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium
The readily releasable pool ( RRP ) of vesicles is a core concept in studies of presynaptic function . However , operating principles lack consensus definition and the utility for quantitative analysis has been questioned . Here we confirm that RRPs at calyces of Held from 14 to 21 day old mice have a fixed capacity fo...	Short-term plasticity has a dramatic impact on the connection strength of almost every type of synapse during normal use . Some synapses enhance , some depress , and many enhance or depress depending on the recent history of use . A better understanding is needed for modeling information processing in biological circui...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "anatomy", "action", "potentials", "medicine", "and", "health", "sciences", "vesicles", "nervous", "system", "membrane", "potential", "cell", "processes", "electrophysiology", "neuroscience", "plant", "science", "synaptic", "plasticity", "nerve", "fibers", "cel...	2016	A Well-Defined Readily Releasable Pool with Fixed Capacity for Storing Vesicles at Calyx of Held
Global deworming programs aim to reach 75% of at-risk preschool-age children ( pre-SAC ) by 2020 . The 2013 global pre-SAC deworming coverage initially published by the World Health Organization ( WHO ) was 23 . 9% , but this estimate inadequately captured deworming delivered through Child Health Day ( CHD ) platforms ...	Soil-transmitted helminthiases are a group of parasitic diseases caused by intestinal worms that are linked to poor physical and cognitive development among preschool aged children . The administration of deworming drugs designed to reduce the intensity of the worm infection in the child is effective and efficient inte...	[ "Abstract", "Introduction", "Method", "Results", "Discussion" ]	[]	2015	The Role of Child Health Days in the Attainment of Global Deworming Coverage Targets among Preschool-Age Children
The biological pacemaker approach is an alternative to cardiac electronic pacemakers . Its main objective is to create pacemaking activity from added or modified distribution of spontaneous cells in the myocardium . This paper aims to assess how automaticity strength of pacemaker cells ( i . e . their ability to mainta...	Implantation of electronic pacemakers is a standard treatment to pathologically slow heart rhythm . Despite improving quality of life , those devices display many shortcomings . Bioengineered tissue pacemakers may be a therapeutic alternative , but associated design methods usually lack control of the way cells with sp...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "microstructure", "cardiovascular", "anatomy", "electricity", "condensed", "matter", "physics", "anisotropy", "materials", "science", "pacemakers", "materials", "physics", "ionic", "current", "bioenergetics", "myocar...	2018	In silico study of multicellular automaticity of heterogeneous cardiac cell monolayers: Effects of automaticity strength and structural linear anisotropy
Among the several challenges faced by bloodsucking arthropods , the vertebrate hemostatic response against blood loss represents an important barrier to efficient blood feeding . Here we report the first inhibitor of collagen-induced platelet aggregation derived from the salivary glands of a black fly ( Simulium nigrim...	Blood feeding arthropods—like mosquitoes and black flies—have evolved salivary secretions rich in molecules that affect hemostasis , including vasodilators and inhibitors of blood clotting and platelet aggregation . Among the platelet inhibitors , antagonists of collagen-induced platelet aggregation and adhesion have b...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "proteins", "epidemiology", "biology", "and", "life", "sciences", "evolutionary", "biology", "disease", "vectors" ]	2014	Simplagrin, a Platelet Aggregation Inhibitor from Simulium nigrimanum Salivary Glands Specifically Binds to the Von Willebrand Factor Receptor in Collagen and Inhibits Carotid Thrombus Formation In Vivo
Subjects typically choose to be presented with stimuli that predict the existence of future reinforcements . This so-called ‘observing behavior’ is evident in many species under various experimental conditions , including if the choice is expensive , or if there is nothing that subjects can do to improve their lot with...	The theory of Reinforcement Learning ( RL ) has been influential in explaining basic learning and behavior in humans and other animals , and in accounting for key features of the activity of dopamine neurons . However , perhaps due to this very success , paradigms that challenge RL are at a premium . One case concerns ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/animal", "cognition", "neuroscience/theoretical", "neuroscience", "neuroscience/cognitive", "neuroscience" ]	2010	Pavlovian-Instrumental Interaction in ‘Observing Behavior’
Response to antidepressant treatment in major depressive disorder ( MDD ) cannot be predicted currently , leading to uncertainty in medication selection , increasing costs , and prolonged suffering for many patients . Despite tremendous efforts in identifying response-associated genes in large genome-wide association s...	Major depression is the second leading cause of disability worldwide . However , only one-third of patients with depression benefit from the first antidepressant compound they are prescribed . It is a fundamental problem that the outcomes of individual antidepressant treatments are still highly unpredictable . In clini...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "antidepressants", "gene", "regulation", "drugs", "biomarkers", "bioassays", "and", "physiological", "analysis", "pharmacology", "mood", "disorders", "research", "and", "analysis", "methods", "gene", "expression...	2017	Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity
The ability to generalize over naturally occurring variation in cues indicating food or predation risk is highly useful for efficient decision-making in many animals . Honeybees have remarkable visual cognitive abilities , allowing them to classify visual patterns by common features despite having a relatively miniatur...	We present two very simple neural network models based directly on the neural circuitry of honeybees . These models , using just four large-field visual input neurons from each eye that sparsely connect to a single layer of interneurons within the bee brain learning centres , are able to discriminate complex achromatic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "invertebrates", "medicine", "and", "health", "sciences", "honey", "bees", "nervous", "system", "social", "sciences", "electrophysiology", "neuroscience", "animals", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "psychology", "vi...	2017	Insect Bio-inspired Neural Network Provides New Evidence on How Simple Feature Detectors Can Enable Complex Visual Generalization and Stimulus Location Invariance in the Miniature Brain of Honeybees
For the past five years , genome-wide association studies ( GWAS ) have identified hundreds of common variants associated with human diseases and traits , including high-density lipoprotein cholesterol ( HDL-C ) , low-density lipoprotein cholesterol ( LDL-C ) , and triglyceride ( TG ) levels . Approximately 95 loci ass...	Low-density lipoprotein cholesterol ( LDL-C ) , high-density lipoprotein cholesterol ( HDL-C ) , and triglyceride ( TG ) levels are well known independent risk factors for cardiovascular disease . Lipid-associated genetic variants are being discovered in genome-wide association studies ( GWAS ) in samples of European d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genetic", "polymorphism", "genetic", "association", "studies", "genetics", "population", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2011	Genetic Determinants of Lipid Traits in Diverse Populations from the Population Architecture using Genomics and Epidemiology (PAGE) Study
We describe the development and application of a suite of modular tools for high-resolution detection of proteins and intracellular protein complexes by electron microscopy ( EM ) . Conditionally stable GFP- and mCherry-binding nanobodies ( termed csGBP and csChBP , respectively ) are characterized using a cell-free ex...	The use of enzymatic tags such as the ascorbate peroxidase ( APEX ) for electron microscopic detection of proteins is changing electron microscopy ( EM ) in the same way that the use of GFP and related proteins caused a revolution in light microscopy . We previously developed expression plasmids encoding GFP-binding pe...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "methods", "and", "resources", "protein", "interactions", "condensed", "matter", "physics", "cytoplasmic", "staining", "membrane", "proteins", "microscopy", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "specimen", "preparation",...	2018	Ultrastructural localisation of protein interactions using conditionally stable nanobodies
In simple organisms like E . coli , the metabolic response to an external perturbation passes through a transient phase in which the activation of a number of latent pathways can guarantee survival at the expenses of growth . Growth is gradually recovered as the organism adapts to the new condition . This adaptation ca...	In modeling metabolic networks , concepts like biomass optimization are often used to determine flux distributions of simple organisms such as E . coli . Although they often give good results in practice , they normally rely on heuristic considerations like “evolution has tuned metabolic fluxes to optimize growth , hen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Metabolic Adaptation Processes That Converge to Optimal Biomass Flux Distributions
The m-AAA protease preserves proteostasis of the inner mitochondrial membrane . It ensures a functional respiratory chain , by controlling the turnover of respiratory complex subunits and allowing mitochondrial translation , but other functions in mitochondria are conceivable . Mutations in genes encoding subunits of t...	Oligodendrocytes are cells of the central nervous system that produce the myelin sheath . Myelin production is extremely costly from the energetic point of view , and oligodendrocytes that are synthesizing myelin are particularly susceptible to mitochondrial dysfunction . However , the function of mitochondria in matur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "enzymes", "enzymology", "brain", "neuroscience", "epithelial", "cells", "nerve", "fibers", "mitochondria", "chromatophores", "bioenergetics", "cellular", "structures", "and", "organelles", "spinal", "cord", ...	2016	The Mitochondrial m-AAA Protease Prevents Demyelination and Hair Greying
There is renewed interest in effective measures to control Zika and dengue vectors . A synthesis of published literature with a focus on the quality of evidence is warranted to determine the effectiveness of vector control strategies . We conducted a meta-review assessing the effectiveness of any Aedes control measure ...	Various strategies for the control of mosquito-borne diseases exist and have been used for decades . The effectiveness of these control measures has been evaluated in several systematic reviews , however , their conclusions were contradicting . The current Zika outbreak in the Americas renewed the global health communi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "larvicides", "invertebrates", "medicine", "and", "health", "sciences", "animals", "copepods", "developmental", "biology", "pest", "control", "crustaceans", "infectious", "disease", "control", "insect", "vectors", "zoology", "research", "and", "analysis", "methods", "in...	2016	Public Health Interventions for Aedes Control in the Time of Zikavirus– A Meta-Review on Effectiveness of Vector Control Strategies
Specific intestinal microbiota has been shown to induce Foxp3+ regulatory T cell development . However , it remains unclear how development of another regulatory T cell subset , Tr1 cells , is regulated in the intestine . Here , we analyzed the role of two probiotic strains of intestinal bacteria , Lactobacillus casei ...	Unlike induction of Foxp3+ regulatory T cell development , it remains unclear how intestinal environmental factors regulate development of another regulatory T cell subset , Tr1 cells that produce IL-10 . In this study , we reveal that a probiotic strain , Bifidobacterium breve induces IL-10-producing Tr1 cells that ex...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "gastroenterology", "and", "hepatology" ]	2012	Probiotic Bifidobacterium breve Induces IL-10-Producing Tr1 Cells in the Colon
Many types of epigenetic profiling have been used to classify stem cells , stages of cellular differentiation , and cancer subtypes . Existing methods focus on local chromatin features such as DNA methylation and histone modifications that require extensive analysis for genome-wide coverage . Replication timing has eme...	While continued advances in stem cell and cancer biology have uncovered a growing list of clinical applications for stem cell technology , errors in indentifying cell lines have undermined a number of recent studies , highlighting a growing need for improvements in cell typing methods for both basic biological and clin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "differentiation", "algorithms", "developmental", "biology", "stem", "cells", "induced", "pluripotent", "stem", "cells", "dna", "replication", "dna", "cell", "potency", "embryonic", "stem", "cells", "biology", "molecular", "biology", "microarrays", "computer", ...	2011	Replication Timing: A Fingerprint for Cell Identity and Pluripotency
The use of mutagenic drugs to drive HIV-1 past its error threshold presents a novel intervention strategy , as suggested by the quasispecies theory , that may be less susceptible to failure via viral mutation-induced emergence of drug resistance than current strategies . The error threshold of HIV-1 , , however , is no...	Currently available antiretroviral drugs curtail HIV infection but fail to eradicate the virus . A strategy of intervention radically different from that employed by current drugs has been proposed by the molecular quasispecies theory . The theory predicts that increasing the viral mutation rate beyond a critical value...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "theoretical", "biology", "evolutionary", "biology", "hiv", "population", "genetics", "biology", "computational", "biology", "viral", "diseases", "infectious", "disease", "modeling", "evolutionary", "theory" ]	2012	Stochastic Simulations Suggest that HIV-1 Survives Close to Its Error Threshold
Representational models specify how activity patterns in populations of neurons ( or , more generally , in multivariate brain-activity measurements ) relate to sensory stimuli , motor responses , or cognitive processes . In an experimental context , representational models can be defined as hypotheses about the distrib...	Modern neuroscience can measure activity of many neurons or the local blood oxygenation of many brain locations simultaneously . As the number of simultaneous measurements grows , we can better investigate how the brain represents and transforms information , to enable perception , cognition , and behavior . Recent stu...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "statistical", "noise", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "engineering", "and", "technology", "signal", "processing", "neuroscience", "simulation", "and", "modeling", "magnetic", "resonanc...	2017	Representational models: A common framework for understanding encoding, pattern-component, and representational-similarity analysis
The histone H2A variant H2A . Z is essential for embryonic development and for proper control of developmental gene expression programs in embryonic stem cells ( ESCs ) . Divergent regions of amino acid sequence of H2A . Z likely determine its functional specialization compared to core histone H2A . For example , H2A ....	Elucidating how regulation of chromatin structure modulates gene expression patterns is fundamental for understanding mammalian development . Replacement of core histones with histone variants has recently emerged as a key mechanism for regulating chromatin states . The histone H2A variant H2A . Z is of particular inte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "biochemistry", "developmental", "biology", "biology" ]	2013	H2A.Z Acidic Patch Couples Chromatin Dynamics to Regulation of Gene Expression Programs during ESC Differentiation
Cellular senescence involves epigenetic alteration , e . g . loss of H3K27me3 in Ink4a-Arf locus . Using mouse embryonic fibroblast ( MEF ) , we here analyzed transcription and epigenetic alteration during Ras-induced senescence on genome-wide scale by chromatin immunoprecipitation ( ChIP ) -sequencing and microarray ....	To avoid becoming cancer cells , cells have a barrier system to block cellular proliferation by falling into irreversible growth arrest , so-called cellular senescence . For future strategy of cancer treatment , it is important to understand how cancer occurs , and investigation of underlying mechanism in senescence ca...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "sequencing", "genome", "analysis", "tools", "cancer", "genetics", "genome", "scans", "genetics", "epigenetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	Activation of Bmp2-Smad1 Signal and Its Regulation by Coordinated Alteration of H3K27 Trimethylation in Ras-Induced Senescence
Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon . Here , we report on the capability and key enabling metabolic machinery of Geobacter m...	The ability of microorganisms to exchange electrons directly with their environment has large implications for our knowledge of industrial and environmental processes . For decades , it has been known that microbes can use electrodes as electron acceptors in microbial fuel cell settings . Geobacter metallireducens has ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "biotechnology", "applied", "microbiology", "bioengineering", "systems", "biology", "biological", "systems", "engineering", "microbial", "metabolism", "microbial", "physiology", "industrial", "microbiology", "engineering", "and", "technology", "biology", "and", "life", "sci...	2014	Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens
Dysregulation of AMPK signaling has been implicated in many human diseases , which emphasizes the importance of characterizing AMPK regulators . The tumor suppressor FLCN , responsible for the Birt-Hogg Dubé renal neoplasia syndrome ( BHD ) , is an AMPK-binding partner but the genetic and functional links between FLCN ...	The FLCN gene is responsible for the hereditary human tumor disease called Birt-Hogg-Dube syndrome ( BHD ) . Patients that inherit an inactivating mutation in the FLCN gene develop lung collapse as well as tumors in the kidney , colon , and skin . It is not clear yet what the exact function of this protein is in the ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "genetics", "of", "disease", "biochemistry", "signal", "transduction", "cellular", "stress", "responses", "animal", "genetics", "cancer", "genetics", "model", "organisms", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "bioene...	2014	Folliculin Regulates Ampk-Dependent Autophagy and Metabolic Stress Survival
Buruli ulcer ( BU ) , caused by Mycobacterium ulcerans , is a neglected tropical disease frequently leading to permanent disabilities . The ulcers are treated with rifampicin and streptomycin , wound care and , if necessary surgical intervention . Professionals have exclusively shaped the research agenda concerning man...	Buruli ulcer ( BU ) is a skin and soft tissue infection possibly leading to deformities and long term consequences with severe impact on patients’ lives . It is one of the neglected tropical diseases . The current research agenda is created solely by health professionals , whereas patients might indicate different prio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "health", "services", "research", "disabilities", "tropical", "diseases", "health", "care", "bacterial", "diseases", "research", "design", "signs", "and", "symptoms", "pharmaceutics",...	2016	Former Buruli Ulcer Patients’ Experiences and Wishes May Serve as a Guide to Further Improve Buruli Ulcer Management
Tsetse are vectors of pathogenic trypanosomes , agents of human and animal trypanosomiasis in Africa . Components of tsetse saliva ( sialome ) are introduced into the mammalian host bite site during the blood feeding process and are important for tsetse’s ability to feed efficiently , but can also influence disease tra...	Insect saliva contains many proteins that are injected into the mammalian host during the blood feeding process . Saliva proteins enhance the blood feeding ability of insects , but they can also induce mammalian immune responses that inhibit successful feeding , or modulate the bite site to benefit pathogen transmissio...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	Immunogenicity and Serological Cross-Reactivity of Saliva Proteins among Different Tsetse Species
The modeling of large-scale communicable epidemics has greatly benefited in the last years from the increasing availability of highly detailed data . Particullarly , in order to achieve quantitative descriptions of the evolution of epidemics , contact networks and mixing patterns are key . These heterogeneous patterns ...	Large scale epidemic outbreaks represent an ever increasing threat to humankind . In order to anticipate eventual pandemics , mathematical modeling should not only have the capacity to model in real time an ongoing disease , but also to predict the evolution of potential outbreaks in different locations and times . To ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "people", "and", "places", "poland", "infectious", "diseases", "age", "groups", "medicine", "and", "health", "sciences", "zimbabwe", "european", "union", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "epidemiology", "pathogens", ...	2018	Projecting social contact matrices to different demographic structures
The lysin motif ( LysM ) containing proteins can bind chitin and are ubiquitous in various organisms including fungi . In plant pathogenic fungi , a few LysM proteins have been characterized as effectors to suppress chitin-induced immunity in plant hosts and therefore contribute to fungal virulence . The effector mecha...	Insect pathogenic fungi are of importance for both applied and basic research . Relative to the advances in understanding fungus-plant interactions , the mechanisms of the molecular pathogenesis of entomopathogenic fungi are rather limitedly understood . In particular , the machinery of effector-mediated inhibition of ...	[ "Abstract", "Introduction", "Results", "Discussions", "Materials", "and", "methods" ]	[ "chitin", "invertebrates", "fungal", "genetics", "animals", "fungi", "plant", "science", "materials", "science", "plant", "pathology", "macromolecules", "materials", "by", "structure", "polymers", "polymer", "chemistry", "mycology", "proteins", "chemistry", "insects", "...	2017	Divergent LysM effectors contribute to the virulence of Beauveria bassiana by evasion of insect immune defenses
Enzymes of the M32 family are Zn-dependent metallocarboxypeptidases ( MCPs ) widely distributed among prokaryotic organisms and just a few eukaryotes including Trypanosoma brucei and Trypanosoma cruzi , the causative agents of sleeping sickness and Chagas disease , respectively . These enzymes are absent in humans and ...	In recent years , the pharmaceutical company GlaxoSmithKline announced the disclosure of small collections of antiparasitic compounds to facilitate research and drug development for three of the main Tropical Neglected Diseases- i . e . Human African Trypanosomiasis , Leishmaniasis and Chagas Disease . These collection...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "bonding", "medicine", "and", "health", "sciences", "enzymes", "tropical", "diseases", "enzymology", "parasitic", "diseases", "parasitic", "protozoans", "fluorophotometry", "trypanosoma", "brucei", "protozoans", "neglected", "tropical", "diseases", "enzyme", "...	2019	Potent and selective inhibitors for M32 metallocarboxypeptidases identified from high-throughput screening of anti-kinetoplastid chemical boxes
Delineating the strategies by which cells contend with combinatorial changing environments is crucial for understanding cellular regulatory organization . When presented with two carbon sources , microorganisms first consume the carbon substrate that supports the highest growth rate ( e . g . , glucose ) and then switc...	To survive in resource-limited and dynamic environments , microbial populations implement a diverse repertoire of regulatory strategies . These strategies often rely on anticipating impending environmental shifts , enabling the population to be prepared for a future change in conditions . It has long been known that ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts
Advancing age is the dominant risk factor for most of the major killer diseases in developed countries . Hence , ameliorating the effects of ageing may prevent multiple diseases simultaneously . Drugs licensed for human use against specific diseases have proved to be effective in extending lifespan and healthspan in an...	Human life expectancy is continuing to increase worldwide , as a result of successive improvements in living conditions and medical care . Although this trend is to be celebrated , advancing age is the major risk factor for multiple impairments and chronic diseases . As a result , the later years of life are often spen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "caenorhabditis", "animals", "drug", "screening", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems", "genome", "analysis", "pharmacology", "research", "and...	2019	Using the drug-protein interactome to identify anti-ageing compounds for humans
Dengue viruses ( DENV ) cause debilitating and potentially life-threatening acute disease throughout the tropical world . While drug development efforts are underway , there are concerns that resistant strains will emerge rapidly . Indeed , antiviral drugs that target even conserved regions in other RNA viruses lose ef...	Dengue viruses cause debilitating and potentially life-threatening acute disease throughout the tropical world . While drug development efforts are underway , there are concerns that drug-resistant strains will emerge rapidly . Indeed , many antiviral drugs for other RNA viruses lose efficacy over time as the virus mut...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints
Recently , a novel approach has been developed to study gene expression in single cells with high time resolution using RNA Fluorescent In Situ Hybridization ( FISH ) . The technique allows individual mRNAs to be counted with high accuracy in wild-type cells , but requires cells to be fixed; thus , each cell provides o...	Programs of gene expression lie at the heart of how cells regulate their internal processes . Some dynamical gene-expression programs , such as the cell cycle , are well known and studied , others , such as metabolic cycles , have only recently been recognized , and many other dynamical programs including switches are ...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "computational", "biology/transcriptional", "regulation", "biophysics/theory", "and", "simulation", "computational", "biology" ]	2010	Evaluating Gene Expression Dynamics Using Pairwise RNA FISH Data
The ongoing global spread of Tomato yellow leaf curl virus ( TYLCV; Genus Begomovirus , Family Geminiviridae ) represents a serious looming threat to tomato production in all temperate parts of the world . Whereas determining where and when TYLCV movements have occurred could help curtail its spread and prevent future ...	Tomato yellow leaf curl virus ( TYLCV ) poses a serious threat to tomato production throughout the temperate regions of the world . Our analysis , using a suite of bioinformatic tools applied to all publically available TYLCV genome sequences , suggests that the virus probably arose somewhere in the Middle East between...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "computational", "biology/evolutionary", "modeling", "molecular", "biology/molecular", "evolution", "virology/emerging", "viral", "diseases", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2010	The Spread of Tomato Yellow Leaf Curl Virus from the Middle East to the World
As part of a broader collaborative network of exome sequencing studies , we developed a jointly called data set of 5 , 685 Ashkenazi Jewish exomes . We make publicly available a resource of site and allele frequencies , which should serve as a reference for medical genetics in the Ashkenazim ( hosted in part at https:/...	The Ashkenazim are a people with ancestry in northern-European Jewish groups . A founder effect caused a bottleneck in this population approximately one thousand years ago , resulting in a group of enriched alleles in their genetic makeup . A higher documented prevalence of Crohn’s Disease in the Ashkenazim indicates t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "crohn's", "disease", "population", "genetics", "immunology", "variant", "genotypes", "alleles", "genetic", "mapping", "clinical", "medicine", "genetic", "predisposition", "gastroenterology", ...	2018	Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population
Tick feeding causes extreme morbidity and mortality to humans through transmission of pathogens and causes severe economic losses to the agricultural industry by reducing livestock yield . Salivary gland secretions are essential for tick feeding and thus , reducing or preventing saliva secretions into the vertebrate ho...	Tick feeding results in negative health and economic consequences worldwide and there has been continued interest in the development of products with novel mechanisms of action for control of tick populations . Kir channels have been shown to be a significant ion conductance pathway in arthropods and are critical for p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "neurochemistry", "body", "fluids", "ixodes", "chemical", "compounds", "saliva", "animals", "organic", "compounds", "neuroscience", "hormones", "physiological", "processes", "salivation", "amines", "neurotransmitters...	2019	Inward rectifier potassium (Kir) channels mediate salivary gland function and blood feeding in the lone star tick, Amblyomma americanum
Both endocrine and exocrine pancreatic cells arise from pancreatic-duodenal homeobox 1 ( pdx1 ) -positive progenitors . The molecular mechanisms controlling cell fate determination and subsequent proliferation , however , are poorly understood . Unlike endocrine cells , less is known about exocrine cell specification ....	The pancreas is a vital organ comprising endocrine and exocrine components . Both endocrine and exocrine cells derive from a common pool of progenitors present in the gut endoderm during embryogenesis . The molecular mechanisms regulating cell fate decisions and lineage-specific proliferation are not fully understood ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology" ]	2008	Exdpf Is a Key Regulator of Exocrine Pancreas Development Controlled by Retinoic Acid and ptf1a in Zebrafish
Oscillatory activity robustly correlates with task demands during many cognitive tasks . However , not only are the network mechanisms underlying the generation of these rhythms poorly understood , but it is also still unknown to what extent they may play a functional role , as opposed to being a mere epiphenomenon . H...	Oscillations are ubiquitous in the brain and often correlate with distinct cognitive tasks . Nonetheless their role in shaping network dynamics , and hence in driving behavior during such tasks is poorly understood . Here we provide a comprehensive study of the effect of periodic drive on neuronal networks exhibiting m...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "resonance", "frequency", "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "membrane", "potential", "electrophysiology", "neuroscience", "learning", "and", "memory", "cognitive", "neuroscience", "cognition", "memory", "computer", "and...	2018	Network mechanisms underlying the role of oscillations in cognitive tasks
Schistosomiasis is a helminthic disease that affects more than 200 million people . An effective vaccine would be a major step towards eliminating the disease . Studies suggest that T follicular helper ( Tfh ) cells provide help to B cells to generate the long-term humoral immunity , which would be a crucial component ...	Schistosomiasis affects more than 200 million people worldwide and causes more than 280 , 000 deaths per year . Current control strategies are based on chemotherapy , but recurrent reinfection of people living in endemic areas makes researchers search for an effective vaccine to provide long-term protection against sch...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Distribution of Peripheral Memory T Follicular Helper Cells in Patients with Schistosomiasis Japonica
Permethrin is the active component of topical creams widely used to treat human scabies . Recent evidence has demonstrated that scabies mites are becoming increasingly tolerant to topical permethrin and oral ivermectin . An effective approach to manage pesticide resistance is the addition of synergists to counteract me...	Synergists are commonly used in combination with pesticides to suppress metabolism-based resistance and increase the efficacy of the agents . They are also useful as tools for laboratory investigation of specific resistance mechanisms based on their ability to inhibit specific metabolic pathways . To determine the role...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "chemistry/biochemistry", "dermatology/skin", "infections" ]	2009	The Effect of Insecticide Synergists on the Response of Scabies Mites to Pyrethroid Acaricides
Inferring the combinatorial regulatory code of transcription factors ( TFs ) from genome-wide TF binding profiles is challenging . A major reason is that TF binding profiles significantly overlap and are therefore highly correlated . Clustered occurrence of multiple TFs at genomic sites may arise from chromatin accessi...	Transcription factors ( TFs ) are proteins that bind to DNA and regulate gene expression . Recent technological advances make it possible to map TF binding patterns across the whole genome . Multiple single-gene studies showed that combinatorial binding of multiple transcription factors determines the gene transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "algorithms", "genome", "analysis", "tools", "computer", "science", "genomics", "genetic", "networks", "functional", "genomics", "regulatory", "networks", "biology", "computational", "biology", "computing", "methods", "computer", "inferencing", "genetics", "and", "genomic...	2012	A Graphical Modelling Approach to the Dissection of Highly Correlated Transcription Factor Binding Site Profiles
Human cytomegalovirus ( HCMV ) is an important , ubiquitous pathogen that causes severe clinical disease in immunocompromised individuals , such as organ transplant recipients and infants infected in utero . Antiviral chemotherapy remains problematic due to toxicity of the available compounds and the emergence of virus...	Human cytomegalovirus ( HCMV ) is a major global health concern and a vaccine to prevent HCMV disease is a widely recognized medical need . However , no vaccine has been licensed to date . A major obstacle for the development of a vaccine is a lack of knowledge of the nature and specificities of protective responses th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "serum", "medicine", "and", "health", "sciences", "immune", "physiology", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "cytomegalovirus", "infection", "vi...	2017	Protective capacity of neutralizing and non-neutralizing antibodies against glycoprotein B of cytomegalovirus
Accurate timing of action potentials is required for neurons in auditory brainstem nuclei to encode the frequency and phase of incoming sound stimuli . Many such neurons express “high threshold” Kv3-family channels that are required for firing at high rates ( >∼200 Hz ) . Kv3 channels are expressed in gradients along t...	In order to detect the nature and location of a sound stimulus , neurons in the central auditory system have to fire at very high rates with extreme temporal precision . Specifically , they have to be able to follow changes in an auditory stimulus at rates of up to 2000 Hz or more and to lock their action potentials to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	2012	Gradients and Modulation of K+ Channels Optimize Temporal Accuracy in Networks of Auditory Neurons
Ammonia is a major signal that regulates nitrogen fixation in most diazotrophs . Regulation of nitrogen fixation by ammonia in the Gram-negative diazotrophs is well-characterized . In these bacteria , this regulation occurs mainly at the level of nif ( nitrogen fixation ) gene transcription , which requires a nif-speci...	GlnR is a global transcription regulator of nitrogen metabolism in Bacillus and other Gram-positive bacteria . GlnR generally functions as repressor and inhibits gene transcription under excess nitrogen . Our study for the first time reveals that GlnR simultaneously acted as an activator and a repressor for nitrogen fi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "bacillus", "microbiology", "dna-binding", "proteins", "plant", "physiology", "organic", "compounds", "dna", "transcription",...	2018	Positive and negative regulation of transferred nif genes mediated by indigenous GlnR in Gram-positive Paenibacillus polymyxa
Diseases caused by Aedes-borne viruses , such as dengue , Zika , chikungunya , and yellow fever , are emerging and reemerging globally . The causes are multifactorial and include global trade , international travel , urbanisation , water storage practices , lack of resources for intervention , and an inadequate evidenc...	Aedes aegypti and A . albopictus are mosquito species that thrive in towns and cities and can transmit viruses to humans that cause diseases , such as dengue , Zika , chikungunya , and yellow fever . The geographic range of human infection with these viruses is rapidly expanding globally . Even when preventative or the...	[ "Abstract", "Introduction", "Conclusion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "animals", "review", "infectious", "disease", "control", "insect", "vectors", "zoology", "public", "and", "occupational", "health", "infectious", "diseases", "agrochemicals", "epidemiology", "disease", "vectors", ...	2018	Integrated Aedes management for the control of Aedes-borne diseases
RNA secondary structure plays a central role in the replication and metabolism of all RNA viruses , including retroviruses like HIV-1 . However , structures with known function represent only a fraction of the secondary structure reported for HIV-1NL4-3 . One tool to assess the importance of RNA structures is to examin...	We have taken advantage of the rapid evolution of primate lentiviruses to assess the conservation of secondary structure in the viral RNA genome . We determined the structure of the SIVmac239 RNA genome to allow a detailed comparison with the previously determined structure of the HIV-1NL4-3 genome . In comparing the t...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "rna", "viral", "evolution", "rna", "structure", "infectious", "diseases", "nucleic", "acids", "virology", "hiv", "biology", "microbiology", "viral", "diseases" ]	2013	Comparison of SIV and HIV-1 Genomic RNA Structures Reveals Impact of Sequence Evolution on Conserved and Non-Conserved Structural Motifs
Empirical evidence suggests the incentive value of an option is affected by other options available during choice and by options presented in the past . These contextual effects are hard to reconcile with classical theories and have inspired accounts where contextual influences play a crucial role . However , each acco...	Research has shown that decision-making is dramatically influenced by context . Two types of influence have been identified , one dependent on options presented in the past ( between-choice effects ) and the other dependent on options currently available ( within-choice effects ) . Whether these two types of effects ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "decision", "theory", "medicine", "and", "health", "sciences", "decision", "making", "applied", "mathematics", "social", "sciences", "neuroscience", "learning", "and", "memory", "cognitive", "psychology", "mathematics", "statistics", "(mathematics)", "cognition", "memory"...	2017	A unifying Bayesian account of contextual effects in value-based choice

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