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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
Leptospirosis is one of the most important neglected tropical bacterial diseases in Latin America and the Caribbean . However , very little is known about the circulating etiological agents of leptospirosis in this region . In this study , we describe the serological and molecular features of leptospires isolated from ...	Leptospirosis is an emerging zoonotic disease caused by infection with pathogenic strains of Leptospira . Isolation of Leptospira strains is rare , making it difficult to assess their distribution worldwide . In this study , we characterized cultures of Leptospira obtained from more than one hundred leptospirosis patie...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases", "leptospirosis" ]	2013	Serovar Diversity of Pathogenic Leptospira Circulating in the French West Indies
The vertebrate neural plate contains distinct domains of gene expression , prefiguring the future brain areas . In this study , we draw an extended expression map of the rostral neural plate that reveals discrete domains inside the presumptive posterior forebrain . We show , by fate mapping , that these well-defined ce...	During the earliest stages of development , the brain is first formed as a simple sheet of cells called the neural plate . Although the plate looks homogenous , it contains distinct domains that can be identified by differential gene expression . These domains correspond to distinct future brain areas . In this study ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "danio", "(zebrafish)", "eukaryotes", "vertebrates", "teleost", "fishes", "neuroscience", "animals" ]	2007	The Prethalamus Is Established during Gastrulation and Influences Diencephalic Regionalization
Ghana is affected by regular cholera epidemics and an annual average of 3 , 066 cases since 2000 . In 2014 , Ghana experienced one of its largest cholera outbreaks within a decade with more than 20 , 000 notified infections . In order to attribute this rise in cases to a newly emerging strain or to multiple simultaneou...	The bacterium Vibrio cholerae is mainly transmitted faecal-orally via human-to-human contact or via environmental water sources in which V . cholerae is able to persist . West Africa , including Ghana , is regularly affected by Cholera epidemics , in particular during rainy seasons . In 2014 , Ghana experienced an exce...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "pathogens", "vibrio", "drugs", "tropical", "diseases", "microbiology", "geographical", "locations", "toxicology", "toxic", "agents", "bacterial", "diseases"...	2016	Molecular Epidemiology and Antibiotic Susceptibility of Vibrio cholerae Associated with a Large Cholera Outbreak in Ghana in 2014
As genetic information is transmitted through successive generations , it passes between pluripotent cells in the early embryo and germ cells in the developing foetus and adult animal . Tex19 . 1 encodes a protein of unknown function , whose expression is restricted to germ cells and pluripotent cells . During male spe...	The germ cells—eggs in females and sperm in males—are responsible for passing genetic information from one generation to the next . As any genetic changes that arise in the germ cells can be transmitted to the next generation , germ cells are a prime target for the activity of mobile genetic elements . Mobile genetic e...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "developmental", "biology/cell", "differentiation", "developmental", "biology/germ", "cells", "genetics", "and", "genomics/gene", "function", "developmental", "biology/stem", "cells" ]	2008	Deletion of the Pluripotency-Associated Tex19.1 Gene Causes Activation of Endogenous Retroviruses and Defective Spermatogenesis in Mice
Gene duplication is an important evolutionary mechanism that can result in functional divergence in paralogs due to neo-functionalization or sub-functionalization . Consistent with functional divergence after gene duplication , recent studies have shown accelerated evolution in retained paralogs . However , little is k...	How a protein is controlled is intimately linked to its function . Therefore , evolution can drive the functional divergence of proteins by tweaking their regulation , even if enzymatic capacities are preserved . Changes in posttranslational regulation ( protein phosphorylation , degradation , subcellular localization ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phylogenetic", "analysis", "evolutionary", "modeling", "biology", "and", "life", "sciences", "comparative", "genomics", "molecular", "evolution", "computational", "biology", "evolutionary", "biology", "gene", "duplication", "molecular", "biology", "techniques", "molecular"...	2014	Detecting Functional Divergence after Gene Duplication through Evolutionary Changes in Posttranslational Regulatory Sequences
The London Declaration ( 2012 ) was formulated to support and focus the control and elimination of ten neglected tropical diseases ( NTDs ) , with targets for 2020 as formulated by the WHO Roadmap . Five NTDs ( lymphatic filariasis , onchocerciasis , schistosomiasis , soil-transmitted helminths and trachoma ) are to be...	Neglected tropical diseases ( NTDs ) are a group of infectious diseases that occur mostly in poor , warm countries . NTDs are caused by various bacteria and parasites , such as worms . They can either be cured or prevented through drugs and other interventions , such as control of insects that spread the infection . Th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "disabilities", "demography", "tropical", "diseases", "parasitic", "diseases", "bacterial", "diseases", "global", "health", "neglected", "tropical", "diseases", "population", "biology", "infectious", "disease", ...	2016	Concerted Efforts to Control or Eliminate Neglected Tropical Diseases: How Much Health Will Be Gained?
We determine knotting probabilities and typical sizes of knots in double-stranded DNA for chains of up to half a million base pairs with computer simulations of a coarse-grained bead-stick model: Single trefoil knots and composite knots which include at least one trefoil as a prime factor are shown to be common in DNA ...	We develop a coarse-grained model of double-stranded DNA which is solely based on experimentally determined knotting probabilities of short DNA strands . Our analysis is motivated by the emergence of DNA nanopore sequencing technology . The main advantage of nanopore sequencing in comparison to next-generation devices ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "engineering", "and", "technology", "dna", "electrophoresis", "mathematical", "models", "materials", "science", "nanotechnology", "molecular", "biology", "techniques", "dna", "macromolecules", "materials", "by", "structure", "research", "and", ...	2016	A Monte Carlo Study of Knots in Long Double-Stranded DNA Chains
Whole genome duplication has shaped eukaryotic evolutionary history and has been associated with drastic environmental change and species radiation . While the most common fate of WGD duplicates is a return to single copy , retained duplicates have been found enriched for highly interacting genes . This pattern has bee...	The evolution of eukaryotes is characterized by drastic changes in their genome content . Genome expansions have often occurred by duplication of the entire genome . It is generally not know whether organisms gain any adaptive advantage from these mutations . However , they appear to become fixed in response to environ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "evolution", "evolutionary", "modeling", "biology", "and", "life", "sciences", "computational", "biology", "evolutionary", "biology" ]	2014	A Synergism between Adaptive Effects and Evolvability Drives Whole Genome Duplication to Fixation
It is estimated that India has more deaths from rabies than any other country . However , existing estimates are indirect and rely on non-representative studies . We examined rabies deaths in the ongoing Million Death Study ( MDS ) , a representative survey of over 122 , 000 deaths in India that uses enhanced types of ...	Rabies , a disease of antiquity , has been partially controlled in many countries and eliminated in a few . However , according to the World Health Organization , rabies continues to kill thousands of people in India each year , more than in any other country . We used an enhanced type of verbal autopsy ( a structured ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "social", "and", "behavioral", "sciences", "science", "policy", "biology", "veterinary", "science" ]	2012	Deaths from Symptomatically Identifiable Furious Rabies in India: A Nationally Representative Mortality Survey
The factors contributing to chronic Chagas' heart disease remain unknown . High nitric oxide ( NO ) levels have been shown to be associated with cardiomyopathy severity in patients . Further , NO produced via inducible nitric oxide synthase ( iNOS/NOS2 ) is proposed to play a role in Trypanosoma cruzi control . However...	Chagas disease , a neglected tropical disease caused by the protozoan Trypanosoma cruzi , afflicts from 8 to 15 million people in the Latin America . Chronic chagasic cardiomyopathy ( CCC ) is the most frequent manifestation of Chagas disease . Currently , patient management only mitigates CCC symptoms . The pathogenic...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunopathology", "immunology", "biology" ]	2012	Inducible Nitric Oxide Synthase in Heart Tissue and Nitric Oxide in Serum of Trypanosoma cruzi-Infected Rhesus Monkeys: Association with Heart Injury
To escape CD8+ T-cell immunity , human cytomegalovirus ( HCMV ) US11 redirects MHC-I for rapid ER-associated proteolytic degradation ( ERAD ) . In humans , classical MHC-I molecules are encoded by the highly polymorphic HLA-A , -B and -C gene loci . While HLA-C resists US11 degradation , the specificity for HLA-A and H...	The human immune system can cover the presentation of a wide array of pathogen derived antigens owing to the three extraordinary polymorphic MHC class I ( MHC-I ) gene loci , called HLA-A , -B and -C in humans . Studying the HLA peptide ligands of human cytomegalovirus ( HCMV ) infected cells , we realized that the HCM...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "hela", "cells", "gene", "regulation", "pathogens", "biological", "cultures", "immunology", "microbiology", "fibroblasts", ...	2019	HLA-B locus products resist degradation by the human cytomegalovirus immunoevasin US11
Courtship is pivotal for successful mating . However , courtship is challenging for the Cryptococcus neoformans species complex , comprised of opportunistic fungal pathogens , as the majority of isolates are α mating type . In the absence of mating partners of the opposite mating type , C . deneoformans can undergo uni...	Sexual reproduction plays a pivotal role in shaping fungal population structure and diversity in nature . The global human fungal pathogen Cryptococcus neoformans species complex evolved distinct sexual cycles: bisexual reproduction between mating partners of the opposite mating types , and unisexual reproduction with ...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Conclusion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "social", "sciences", "fungi", "model", "organisms", "animal", "behavior", "experimental...	2019	Unisexual reproduction promotes competition for mating partners in the global human fungal pathogen Cryptococcus deneoformans
The chemotactic response of cells to graded fields of chemical cues is a complex process that requires the coordination of several intracellular activities . Fundamental steps to obtain a front vs . back differentiation in the cell are the localized distribution of internal molecules and the amplification of the extern...	The ability of cells to respond to chemical signals present in the environment is of upmost importance for life . In the developing embryo , cells crawl along graded fields of chemical cues to aggregate into organized patterns . This process is an example of chemotaxis . It is a complex phenomenon , where external sign...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "science/applications", "cell", "biology/cell", "signaling", "mathematics", "neuroscience/neurodevelopment", "computational", "biology", "chemical", "biology/chemical", "biology", "of", "the", "cell" ]	2009	Autocatalytic Loop, Amplification and Diffusion: A Mathematical and Computational Model of Cell Polarization in Neural Chemotaxis
Salivary hyaluronidases have been described in a few bloodsucking arthropods . However , very little is known about the presence of this enzyme in various bloodsucking insects and no data are available on its effect on transmitted microorganisms . Here , we studied hyaluronidase activity in thirteen bloodsucking insect...	Hyaluronidases are enzymes degrading the extracellular matrix of vertebrates . Bloodsucking insects use them to cleave the skin of the host , enlarge the feeding lesion and acquire the blood meal . In addition , resulting fragments of extracellular matrix modulate local immune response of the host , which may positivel...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/skin", "infections" ]	2008	Hyaluronidase of Bloodsucking Insects and Its Enhancing Effect on Leishmania Infection in Mice
The liver is the central organ for detoxification of xenobiotics in the body . In pharmacokinetic modeling , hepatic metabolization capacity is typically quantified as hepatic clearance computed as degradation in well-stirred compartments . This is an accurate mechanistic description once a quasi-equilibrium between bl...	The liver continuously removes xenobiotic compounds from the blood in the mammalian body . Most computational models represent the liver as composed of few well-stirred subcompartments so that a spatially resolved simulation of hepatic perfusion and compound distribution right after drug administration is currently not...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "computer", "science", "mathematical", "computing", "liver", "diseases", "mathematics", "materials", "science", "gastroenterology", "and", "hepatology", "drugs", "and", "devices", "drug", "distribution", "porous", "materials", "computerized", "simulations", "d...	2014	Spatio-Temporal Simulation of First Pass Drug Perfusion in the Liver
Worldwide more than 2 billion people are infected with helminths , predominantly in developing countries . Co-infections with viruses such as human immunodeficiency virus ( HIV ) are common due to the geographical overlap of these pathogens . Helminth and viral infections induce antagonistic cytokine responses in their...	The coincidental infection of a host with two different pathogens is widespread in low-income countries . Regions where helminth infections are endemic strongly overlap with areas where the incidence of viral infections such as HIV is high . HIV is a major public health issue causing more than 1 million deaths per year...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "viral", "transmission", "and", "infection", "spleen", "immunology", "microbiology", "parasitic", "diseases", "nematode", "...	2016	Filariae-Retrovirus Co-infection in Mice is Associated with Suppressed Virus-Specific IgG Immune Response and Higher Viral Loads
Human immunodeficiency virus type 1 ( HIV-1 ) invades the central nervous system ( CNS ) shortly after systemic infection and can result in the subsequent development of HIV-1–associated dementia ( HAD ) in a subset of infected individuals . Genetically compartmentalized virus in the CNS is associated with HAD , sugges...	Infection of the central nervous system ( CNS ) with human immunodeficiency virus type 1 ( HIV-1 ) can lead to the development of HIV-1–associated dementia , a severe neurological disease that results in cognitive and motor impairment . Individuals that are chronically infected with HIV-1 sometimes display unique viral...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/infectious", "diseases", "of", "the", "nervous", "system", "virology/immunodeficiency", "viruses" ]	2009	Compartmentalized Human Immunodeficiency Virus Type 1 Originates from Long-Lived Cells in Some Subjects with HIV-1–Associated Dementia
The reported incidence of dengue fever increased dramatically in recent years in China . This study aimed to investigate and to assess the effectiveness of intervention implemented in a dengue outbreak in Ningbo City , Zhejiang Province , China . Data of a dengue outbreak were collected in Ningbo City in China by a fie...	Dengue has led to heavy disease burden in China . The reported incidence of the disease increased dramatically in recent years and cases have expanded from southern to central and northern part of China . In this study , the findings include that DENV-1 can transmit rapidly with a short period of time and leads to high...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "animals", "simulation", "and", "modeling", "viruses", "developmental", "biology", "rna", "viruses", "molecular", "bio...	2019	Incidence dynamics and investigation of key interventions in a dengue outbreak in Ningbo City, China
The identification of protein binding sites in promoter sequences is a key problem to understand and control regulation in biochemistry and biotechnological processes . We use a computational method to analyze promoters from a given genome . Our approach is based on a physical model at the mesoscopic level of protein-D...	Binding of specific proteins to particular sites in the DNA sequence is a fundamental issue for gene regulation in molecular biology and genetic engineering . A deep understanding of cell physiology requires the analysis of a plethora of genes involving characterization of their promoter architectures that determine th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "statistical", "mechanics", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters
In adults , motion perception is mediated by an extensive network of occipital , parietal , temporal , and insular cortical areas . Little is known about the neural substrate of visual motion in infants , although behavioural studies suggest that motion perception is rudimentary at birth and matures steadily over the f...	While it is known that the visual brain is immature at birth , there is little firm information about the developmental timeline of the visual system in humans . Despite this , it is commonly assumed that the cortex matures slowly , with primary visual areas developing first , followed by higher associative regions . H...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	BOLD Response Selective to Flow-Motion in Very Young Infants
Inflammasomes are cytosolic multi-protein complexes that detect infection or cellular damage and activate the Caspase-1 ( CASP1 ) protease . The NAIP5/NLRC4 inflammasome detects bacterial flagellin and is essential for resistance to the flagellated intracellular bacterium Legionella pneumophila . The effectors required...	Inflammasomes are multi-protein complexes that detect infection and other stimuli and activate the Caspase-1 ( CASP1 ) protease . The effectors required downstream of NAIP5/NLRC4 to restrict bacterial replication remain unclear . Active CASP1 cleaves and activates the pore-forming protein gasdermin D ( GSDMD ) to induc...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "bacteriology", "cell", "death", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathogens", "immunology", "cell", "processes", "microbiology", "electromagnetic", ...	2019	Gasdermin-D and Caspase-7 are the key Caspase-1/8 substrates downstream of the NAIP5/NLRC4 inflammasome required for restriction of Legionella pneumophila
Epidemiological studies have shown that one of the strongest risk factors for prostate cancer is a family history of the disease , suggesting that inherited factors play a major role in prostate cancer susceptibility . Germline mutations in BRCA2 predispose to breast and ovarian cancer with its predominant tumour suppr...	In Western countries , prostate cancer is the most common male cancer and the second biggest cause of cancer-related deaths in men . Men with a familial history of either breast or ovarian cancer have an elevated predisposition to prostate cancer , suggesting there is a genetic element to this disease . Indeed , the in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology/prostate", "cancer", "genetics", "and", "genomics/cancer", "genetics" ]	2010	Brca2 and Trp53 Deficiency Cooperate in the Progression of Mouse Prostate Tumourigenesis
Toll-like receptor 3 ( TLR3 ) senses dsRNA intermediates produced during RNA virus replication to activate innate immune signaling pathways through adaptor protein TRIF . Many viruses have evolved strategies to block TLR3-mediated interferon signaling via targeting TRIF . Here we studied how hepatitis C virus ( HCV ) a...	We previously reported that hepatitis C virus ( HCV ) NS4B inhibits the RIG-I–like receptors ( RLR ) -mediated interferon signaling . Here we studied whether NS4B antagonizes the TLR3-mediated interferon signaling in the HCV infection . We found that NS4B protein inhibited TLR3-mediated interferon signaling by down-reg...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "metabolic", "processes", "immunology", "microbiology", "immune", "receptor", "signaling", "viruses", "signal", "inhibition", "rna", "viruses", "membrane", ...	2018	Hepatitis C virus NS4B induces the degradation of TRIF to inhibit TLR3-mediated interferon signaling pathway
Trypanosoma cruzi calreticulin ( TcCRT ) is a virulence factor that binds complement C1 , thus inhibiting the activation of the classical complement pathway and generating pro-phagocytic signals that increase parasite infectivity . In a previous work , we characterized a clonal cell line lacking one TcCRT allele ( TcCR...	Trypanosoma cruzi is a protozoan parasite which infects 9 million people in Latin America . Currently there is no vaccine to prevent this disease . Therefore , different approaches or alternatives are urgently needed to identify new protective immunogens . Live vaccines are likely to be most effective in inducing prote...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "gene", "regulation", "genetics", "molecular", "genetics", "protozoology", "biology", "microbiology" ]	2014	A Monoallelic Deletion of the TcCRT Gene Increases the Attenuation of a Cultured Trypanosoma cruzi Strain, Protecting against an In Vivo Virulent Challenge
Gastrointestinal ( GI ) mucosal dysfunction predicts and likely contributes to non-infectious comorbidities and mortality in HIV infection and persists despite antiretroviral therapy . However , the mechanisms underlying this dysfunction remain incompletely understood . Neutrophils are important for containment of path...	HIV infection results in chronic immune activation that leads to increased risk of other diseases and premature death , and this has been linked to gastrointestinal tract ( GI ) damage in infected individuals . In this study , we investigated neutrophils , a cell involved in the immune response to pathogens , in colore...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "urology", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "gut", "bacteria", "pathology", "and", "laboratory", "medicine", "biopsy", "microbiome", "pathogens", "immunology", "microbiology", "surgical", "and", "invasi...	2019	Increased mucosal neutrophil survival is associated with altered microbiota in HIV infection
Terminating protein translation accurately and efficiently is critical for both protein fidelity and ribosome recycling for continued translation . The three bacterial release factors ( RFs ) play key roles: RF1 and 2 recognize stop codons and terminate translation; and RF3 promotes disassociation of bound release fact...	Proteins are the cellular workhorses , performing essentially all of the functions required for cell and organismal survival . But , it takes a great deal of energy to make proteins , making it critical that proteins are made accurately and in the proper time frame . After a ribosome synthesizes a protein , release fac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "operons", "carbohydrates", "organic", "compounds", "glucose", "genome", "analysis", "translation", "termination", "molecular", "biology", "techniques", "dna", "cellular", "structures", "and", "organelles", "genetic", "footprinting", "research", "...	2017	Global analysis of translation termination in E. coli
Post-exposure prophylaxis ( PEP ) against rabies infection consists of a combination of passive immunisation with plasma-derived human or equine immune globulins and active immunisation with vaccine delivered shortly after exposure . Since anti-rabies immune globulins are expensive and scarce , there is a need for chea...	Rabies is an infectious disease causing 59 , 000 deaths and millions are exposed each year worldwide . Post-exposure prophylaxis ( PEP ) against rabies consists of a combination of passive ( immune globulins ) and active immunisation ( vaccine ) directly after viral exposure . Currently used plasma-derived anti-rabies ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "viral", "vaccines", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vaccines", "preventive", "medicine", "animal", "models", "viruses", "r...	2016	Post-exposure Treatment with Anti-rabies VHH and Vaccine Significantly Improves Protection of Mice from Lethal Rabies Infection
Viruses are masters of evolution due to high frequency mutations and genetic recombination . In spite of the significance of viral RNA recombination that promotes the emergence of drug-resistant virus strains , the role of host and environmental factors in RNA recombination is poorly understood . Here we report that th...	Viral RNA recombination plays a major role in virus evolution . Yet , we know little about the roles of host and environmental factors in viral RNA recombination . In this work , using TBSV and yeast as a model host , we show that MET22 nucleotidase suppresses viral RNA recombination . In vitro experiments with a cell-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology/virus", "evolution", "and", "symbiosis", "virology" ]	2010	The Combined Effect of Environmental and Host Factors on the Emergence of Viral RNA Recombinants
Body size in Drosophila larvae , like in other animals , is controlled by nutrition . Nutrient restriction leads to catabolic responses in the majority of tissues , but the Drosophila mitotic imaginal discs continue growing . The nature of these differential control mechanisms that spare distinct tissues from starvatio...	Growth of organs , or anabolism , is tightly controlled by nutritional and hormonal cues such as insulin-like peptides that also suppress autophagy through their receptors and downstream growth pathway . Starvation conditions induce growth arrest and catabolism ( involving autophagy ) in some tissues while sparing the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Experimental", "Procedures" ]	[ "animal", "models", "developmental", "biology", "signal", "transduction", "drosophila", "melanogaster", "animal", "genetics", "model", "organisms", "organism", "development", "cell", "division", "cell", "growth", "molecular", "development", "genetics", "biology", "molecul...	2013	Two-Tiered Control of Epithelial Growth and Autophagy by the Insulin Receptor and the Ret-Like Receptor, Stitcher
Based on spatiotemporal clustering of human dengue virus ( DENV ) infections , transmission is thought to occur at fine spatiotemporal scales by horizontal transfer of virus between humans and mosquito vectors . To define the dimensions of local transmission and quantify the factors that support it , we examined relati...	Dengue is the leading cause of mosquito-borne viral infections globally . An improved understanding of the spatial and temporal distribution of dengue virus ( DENV ) transmission between humans and the principal vector , Aedes aegypti , can enhance prevention programs . Human DENV infection is known to occur at very fi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "viral", "transmission", "and", "infection", "dengue", "microbiology", "viral", "vectors", "neglected", "tropical", "diseases", "infectious", "diseases", "dengue", "fever", "biology", "vectors", "and", "hosts", "p...	2012	Fine Scale Spatiotemporal Clustering of Dengue Virus Transmission in Children and Aedes aegypti in Rural Thai Villages
Asymmetric strand segregation has been proposed as a mechanism to minimize effective mutation rates in epithelial tissues . Under asymmetric strand segregation , the double-stranded molecule that contains the oldest DNA strand is preferentially targeted to the somatic stem cell after each round of DNA replication . Thi...	Through my investigations of the fidelity of epigenetic inheritance , I became intrigued by the interplay of genetic and epigenetic fidelities . Cairns proposed in 1975 that the lifetime risk of epithelial cancers would be reduced if chromosomes containing the oldest DNA strands were selectively segregated to somatic s...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "developmental", "biology/aging", "cell", "biology/developmental", "molecular", "mechanisms", "evolutionary", "biology", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/cancer", "genetics" ]	2009	Asymmetric Strand Segregation: Epigenetic Costs of Genetic Fidelity?
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress transposable elements . It was previously thought that mammals possess four DNA methyltransferase paralogs—Dnmt1 , Dnmt3a , Dnmt3b and Dnmt3l—that establish and maintain cytosine-5 methylation . Here we identify a fifth para...	Half of human genomes are made up of transposons , which are mobile genetic elements that pose a constant threat to genome stability . As a defense strategy , transposons are methylated to prevent their expression and restrain their mobility . We have generated a mutant mouse , called ‘rahu’ , that fails to methylate t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "spermatocytes", "retrotransposons", "germ", "cells", "genetic", "elements", "sequence", "motif", "analysis", "epigenetics", "dna", "mammalian", "genomics", "dna", "methylation", "chromatin", "sperm", "research", "and", "analysis", "methods", "sequence", "analysis", "ch...	2017	rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline
Ankyrin repeat proteins are elastic materials that unfold and refold sequentially , repeat by repeat , under force . Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C . We show that the b...	Here we use molecular dynamics simulation to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with binding partner S6-C . Tandem repeat proteins like Gankyrin comprise tandem arrays of small structural motifs that pack linearly to produce elongated architectures...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "computational", "biology", "biophysics" ]	2013	Effects of Ligand Binding on the Mechanical Properties of Ankyrin Repeat Protein Gankyrin
The chromosomal program of meiotic prophase , comprising events such as laying down of meiotic cohesins , synapsis between homologs , and homologous recombination , must be preceded and enabled by the regulated induction of meiotic prophase genes . This gene regulatory program is poorly understood , particularly in org...	The formation of haploid gametes from diploid germ cells requires a specialized reductive cell division known as meiosis . This reductive division is enabled by chromosomal events that occur during meiotic prophase , including synapsis and crossing-over of homologous chromosomes . These chromosomal events involve meios...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Gene Regulatory Program for Meiotic Prophase in the Fetal Ovary
The rK39 recombinant protein is derived from a specific antigen produced by the Leishmania donovani complex , and has been used in the last two decades for the serodiagnosis of visceral leishmaniasis . We present here a systematic review and meta-analysis of studies evaluating serologic assays to diagnose visceral leis...	Visceral Leishmaniasis ( VL ) is a neglected tropical disease for which serodiagnostic tests are available , but not yet widely implemented in rural areas . The rK39 recombinant protein is derived from a kinesin-like protein of parasites belonging to the Leishmania donovani complex , and has been used in the last two d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "laboratory", "sciences", "diagnostic", "medicine", "parasitic", "diseases" ]	2012	Comparative Study of rK39 Leishmania Antigen for Serodiagnosis of Visceral Leishmaniasis: Systematic Review with Meta-Analysis
In 2014 , the United States experienced an epidemic of acute flaccid myelitis ( AFM ) cases in children coincident with a nationwide outbreak of enterovirus D68 ( EV-D68 ) respiratory disease . Up to half of the 2014 AFM patients had EV-D68 RNA detected by RT-PCR in their respiratory secretions , although EV-D68 was on...	Reports of polio-like paralysis , referred to as acute flaccid myelitis ( AFM ) , have recently emerged in association with infections caused by enterovirus D68 ( EV-D68 ) . In the second half of 2014 , 120 cases of AFM , mostly in young children , were reported during a nationwide outbreak of EV-D68 respiratory diseas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "respiratory", "infections", "nervous", "system", "neuroscience", "pulmonology", "motor", "neurons", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "mammalian", "genomics", "research", "and", "an...	2017	A mouse model of paralytic myelitis caused by enterovirus D68
FtsZ , the primary protein of the bacterial Z ring guiding cell division , has been recently shown to engage in intriguing treadmilling dynamics along the circumference of the division plane . When coreconstituted in vitro with FtsA , one of its natural membrane anchors , on flat supported membranes , these proteins as...	FtsZ is a tubulin homologue and the primary protein of the bacterial Z ring that guides cell division . In vivo , but also in reconstituted systems , FtsZ shows an intriguing treadmilling dynamic along circular tracks of approximately 1 micrometer in diameter . In cells , this treadmilling along the circumference of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "glycosylamines", "classical", "mechanics", "enzymes", "condensed", "matter", "physics", "enzymology", "guanosine", "geometry", "luminescent", "proteins", "mathematics", "yellow", "fluorescent", "protein", "materials", "science", "damage", "mechan...	2018	Treadmilling analysis reveals new insights into dynamic FtsZ ring architecture
The reovirus fusion-associated small transmembrane ( FAST ) proteins function as virus-encoded cellular fusogens , mediating efficient cell–cell rather than virus–cell membrane fusion . With ectodomains of only ∼20–40 residues , it is unclear how such diminutive viral fusion proteins mediate the initial stages ( i . e ...	Much of our current understanding of how proteins mediate membrane fusion derives from the study of enveloped virus fusion proteins . These fusion protein complexes function autonomously to co-ordinately regulate virus–cell attachment and subsequent membrane merger . In contrast , the reovirus Fusion-Associated Small T...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/viral", "infections", "biochemistry/macromolecular", "assemblies", "and", "machines", "virology/host", "invasion", "and", "cell", "entry", "cell", "biology/cell", "adhesion", "cell", "biology...	2008	A Virus-Encoded Cell–Cell Fusion Machine Dependent on Surrogate Adhesins
Chemicals that are highly prevalent in our environment , such as phthalates and pesticides , have been linked to problems associated with reproductive health . However , rapid assessment of their impact on reproductive health and understanding how they cause such deleterious effects , remain challenging due to their fa...	The ever-increasing number of new chemicals introduced into our environment poses a significant problem for risk assessment . In addition , assessing the direct impact of toxicants on human meiosis remains challenging . We successfully utilized a high-throughput platform in the nematode C . elegans , a genetically trac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "caenorhabditis", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "germ", "cells", "animal", "models", "dna", "damag...	2019	Assessing effects of germline exposure to environmental toxicants by high-throughput screening in C. elegans
According to the ‘ceRNA hypothesis’ , microRNAs ( miRNAs ) may act as mediators of an effective positive interaction between long coding or non-coding RNA molecules , carrying significant potential implications for a variety of biological processes . Here , inspired by recent work providing a quantitative description o...	The discovery of RNA interference has revolutionized the decades’ old view of RNAs as mere intermediaries between DNA and proteins in the gene expression workflow . MicroRNAs ( or miRNAs ) , in particular , have been shown to be able to both stabilize the protein output by buffering transcriptional noise and to create ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "channel", "capacity", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "dna", "transcription", "micrornas", "post-transcriptional", "gene", "regulation", "transcription", "factors", "computer", "and", "information", "sciences", "transcriptional", ...	2016	Probing the Limits to MicroRNA-Mediated Control of Gene Expression
In Enterococcus faecalis , sex pheromone-mediated transfer of antibiotic resistance plasmids can occur under unfavorable conditions , for example , when inducing pheromone concentrations are low and inhibiting pheromone concentrations are high . To better understand this paradox , we adapted fluorescence in situ hybrid...	Within a given niche , expression levels of individual cells ( and resulting functional behaviors ) may differ substantially from the mean of the population due to stochasticity or microenvironment heterogeneity . Quantification of bacterial gene expression at the single cell level provides a more informative picture o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "plasmids", "microbiology", "antibiotic", "resistance", "genetic", "elements", "enterococcus", "forms", "of", "dna", "dna", "pharmacology", "ba...	2017	Stochasticity in the enterococcal sex pheromone response revealed by quantitative analysis of transcription in single cells
Recent insights suggest that non-specific and/or promiscuous enzymes are common and active across life . Understanding the role of such enzymes is an important open question in biology . Here we develop a genome-wide method , PROPER , that uses a permissive PSI-BLAST approach to predict promiscuous activities of metabo...	Many enzymes can perform secondary functions at low affinities or rates , but such ‘promiscuous’ functions have never been predicted on a genome-wide scale . Here , we present the first genome-wide method to predict promiscuous functions of metabolic genes , which we apply to E . coli . Notably , we predict and validat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "computational", "biology", "enzymology", "database", "searching", "bacillus", "microbiology", "gene", "function", "prokaryotic", "models", "mod...	2016	Systems-Wide Prediction of Enzyme Promiscuity Reveals a New Underground Alternative Route for Pyridoxal 5’-Phosphate Production in E. coli
Activation of pattern recognition receptors and proper regulation of downstream signaling are crucial for host innate immune response . Upon infection , the NF-κB and interferon regulatory factors ( IRF ) are often simultaneously activated to defeat invading pathogens . Mechanisms concerning differential activation of ...	Host innate immune signaling plays critical roles in defeating pathogen infection . In response to viral infection , cellular signaling events cumulate in the activation of NF-κB and interferon regulatory factors . How these two signaling ramifications are differentially regulated remains an open question . Here we rep...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An Internally Translated MAVS Variant Exposes Its Amino-terminal TRAF-Binding Motifs to Deregulate Interferon Induction
Gene expression is controlled by the combinatorial effects of regulatory factors from different biological subsystems such as general transcription factors ( TFs ) , cellular growth factors and microRNAs . A subsystem’s gene expression may be controlled by its internal regulatory factors , exclusively , or by external ...	The dynamics of a biological system can be controlled by its own internal mechanisms and external perturbations . To gain intuition on this , we may draw a comparison with a mass hanging from a spring . The mass will move naturally by itself but its dynamics is also affected by one’s pulling it . That is , the dynamics...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetic", "oscillators", "developmental", "biology", "mathematics", "linear", "algebra", "algebra", "gene", "regulatory", "networks", "embryogenesis", "gene", "expression", "genetics", "gene", "regulation", "biology", "and", "life", "sciences", "physical", "sciences", ...	2016	DREISS: Using State-Space Models to Infer the Dynamics of Gene Expression Driven by External and Internal Regulatory Networks
A recent study reported neutralizing antibodies to West Nile virus ( WNV ) in horses from four ranches of southern Pantanal . To extend that study , a serosurvey for WNV and 11 Brazilian flaviviruses was conducted with 760 equines , 238 sheep and 61 caimans from 17 local cattle ranches . Among the tested equines , 32 w...	West Nile virus is maintained in cycles between birds and mosquitoes and recently reemerged as a worldwide major public health and veterinarian concern as the cause of human and equine encephalitis outbreaks . Recent studies have reported serological evidence of West Nile virus circulation in Pantanal , west-central re...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "emerging", "viral", "diseases", "virology", "biology", "microbiology" ]	2014	Serological Evidence of Widespread Circulation of West Nile Virus and Other Flaviviruses in Equines of the Pantanal, Brazil
Cells respond to their environment by modulating protein levels through mRNA transcription and post-transcriptional control . Modest observed correlations between global steady-state mRNA and protein measurements have been interpreted as evidence that mRNA levels determine roughly 40% of the variation in protein levels...	Cells respond to their environment by making proteins using transcription and translation of mRNA . Modest observed correlations between global steady-state mRNA and protein measurements have been interpreted as evidence that mRNA levels determine roughly 40% of the variation in protein levels , indicating dominant pos...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast
Intrinsic antiviral resistance represents the first line of intracellular defence against virus infection . During herpes simplex virus type-1 ( HSV-1 ) infection this response can lead to the repression of viral gene expression but is counteracted by the viral ubiquitin ligase ICP0 . Here we address the mechanisms by ...	Viruses must evade several antiviral defences in order to establish a productive infection . These include antibody- and cell-mediated acquired immunity and interferon-regulated innate immunity . Recently , a third arm of antiviral defence has been discovered , so called intrinsic immunity . This aspect of antiviral re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2011	A Viral Ubiquitin Ligase Has Substrate Preferential SUMO Targeted Ubiquitin Ligase Activity that Counteracts Intrinsic Antiviral Defence
The frequent dispensability of duplicated genes in budding yeast is heralded as a hallmark of genetic robustness contributed by genetic redundancy . However , theoretical predictions suggest such backup by redundancy is evolutionarily unstable , and the extent of genetic robustness contributed from redundancy remains c...	Eukaryotic cells show remarkable robustness against external perturbations , which has been thought to be attributed , at least in part , to the extensive gene duplication events in eukaryotic genomes . By duplication , genes are likely to gain redundant copies for backup purposes , however , this notion contradicts th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/molecular", "genetics", "computational", "biology/systems", "biology", "evolutionary", "biology/bioinformatics", "evolutionary", "biology/genomics" ]	2010	The Cellular Robustness by Genetic Redundancy in Budding Yeast
Neuroimaging has identified many correlates of emotion but has not yet yielded brain representations predictive of the intensity of emotional experiences in individuals . We used machine learning to identify a sensitive and specific signature of emotional responses to aversive images . This signature predicted the inte...	Emotions are an important aspect of human experience and behavior; yet , we do not have a clear understanding of how they are processed in the brain . We have identified a neural signature of negative emotion—a neural activation pattern distributed across the brain that accurately predicts how negative a person will fe...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2015	A Sensitive and Specific Neural Signature for Picture-Induced Negative Affect
Animal-vegetal ( AV ) polarity of most vertebrate eggs is established during early oogenesis through the formation and disassembly of the Balbiani Body ( Bb ) . The Bb is a structure conserved from insects to humans that appears as a large granule , similar to a mRNP granule composed of mRNA and proteins , that in addi...	The totipotent egg of most vertebrates is polarized in a so called animal-vegetal axis that is essential to early embryonic development . The animal-vegetal axis is established in the early oocyte by the dissociation of the Balbiani Body ( Bb ) . The Bb is a large RNA-protein granule , conserved from insects to mammals...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "reproductive", "system", "vertebrates", "animals", "xenopus", "germ", "cells", "animal", "models", "oocytes", "model", "organisms", "amphibians", "experimental", "organism", "systems", "forms", "of", "dna", "dna", "cellular", ...	2017	Microtubule-actin crosslinking factor 1 (Macf1) domain function in Balbiani body dissociation and nuclear positioning
Despite its role in homogenizing populations , hybridization has also been proposed as a means to generate new species . The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes , allowing a hybrid population to occupy ecological niches u...	Understanding the origin of species is one of the central challenges in evolutionary biology . It has been suggested that hybridization could generate new species because hybrids can display novel combinations of traits that induce reproductive isolation from their parental species ( called “hybrid speciation” ) . Exis...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities
In all eukaryotes , histone variants are incorporated into a subset of nucleosomes to create functionally specialized regions of chromatin . One such variant , H2A . Z , replaces histone H2A and is required for development and viability in all animals tested to date . However , the function of H2A . Z in development re...	To fit within a cell's nucleus , DNA is wrapped around protein spools composed of the histones H3 , H4 , H2A , and H2B . One spool and the DNA wrapped around it are called a nucleosome , and all of the packaged DNA in a cell's nucleus is collectively called “chromatin . ” Chromatin is important because it modulates acc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "molecular", "biology/histone", "modification", "developmental", "biology", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/epigenetic...	2008	The Genomic Distribution and Function of Histone Variant HTZ-1 during C. elegans Embryogenesis
Proper functioning of working memory involves the expression of stimulus-selective persistent activity in pyramidal neurons of the prefrontal cortex ( PFC ) , which refers to neural activity that persists for seconds beyond the end of the stimulus . The mechanisms which PFC pyramidal neurons use to discriminate between...	Memory , referred to as the ability to retain , store and recall information , represents one of the most fundamental cognitive functions in daily life . A significant feature of memory processes is selectivity to particular events or items that are important to our survival and relevant to specific situations . For lo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "working", "memory", "cognitive", "neuroscience", "computational", "neuroscience", "single", "neuron", "function", "biology", "neuroscience", "coding", "mechanisms" ]	2012	Predictive Features of Persistent Activity Emergence in Regular Spiking and Intrinsic Bursting Model Neurons
The point of attachment of spindle microtubules to metaphase chromosomes is known as the centromere . Plant and animal centromeres are epigenetically specified by a centromere-specific variant of Histone H3 , CENH3 ( a . k . a . CENP-A ) . Unlike canonical histones that are invariant , CENH3 proteins are accumulating s...	As populations evolve into new species they acquire mutations that are compatible with their own genetic background , but often lead to defects when crossed to others . Here , we show that naturally evolved differences in the centromere-specific histone H3 ( CENH3 ) can contribute to this process . Unlike canonical his...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Naturally Occurring Differences in CENH3 Affect Chromosome Segregation in Zygotic Mitosis of Hybrids
The omnipresence of allosteric regulation together with the fundamental role of structural dynamics in this phenomenon have initiated a great interest to the detection of regulatory exosites and design of corresponding effectors . However , despite a general consensus on the key role of dynamics most of the earlier eff...	Recent advances in the development of allosteric drugs allow one to fully appreciate the sheer power of allosteric effectors in the avoiding toxicity , receptor desensitization and modulatory rather than on/off mode of action , compared to the traditional orthosteric compounds . The detection of allosteric sites is one...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "allosteric", "regulation", "cell", "physiology", "medicine", "and", "health", "sciences", "crystal", "structure", "engineering", "and", "technology", "condensed", "matter", "physics", "enzymology", "protein", "structure", "pharmacology", "crystallography", "thermodynamics"...	2018	Reversing allosteric communication: From detecting allosteric sites to inducing and tuning targeted allosteric response
During plant-pathogen interactions , the plant may mount several types of defense responses to either block the pathogen completely or ameliorate the amount of disease . Such responses include release of reactive oxygen species ( ROS ) to attack the pathogen , as well as formation of cell wall appositions ( CWAs ) to p...	Reactive oxygen species ( ROS ) are antimicrobial compounds and also serve as stimulators and products of plant defense reactions . ROS appear to be active in the critical zone where pathogens and plants come in contact . Therefore , understanding the source , the role , and the destination of ROS in each interacting p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/plant-biotic", "interactions", "plant", "biology/plant-biotic", "interactions", "cell", "biology/cellular", "death", "and", "stress", "responses", "cell", "biology/microbial", "growth", "and", "development", "pathology/molecular", "pathology", "cell", "biology/pla...	2011	HYR1-Mediated Detoxification of Reactive Oxygen Species Is Required for Full Virulence in the Rice Blast Fungus
Calcium ( Ca ) sparks are elementary events of biological Ca signaling . A normal Ca spark has a brief duration in the range of 10 to 100 ms , but long-lasting sparks with durations of several hundred milliseconds to seconds are also widely observed . Experiments have shown that the transition from normal to long-lasti...	Calcium ( Ca ) sparks , resulting from Ca-induced Ca release , are elementary events of biological Ca signaling . Sparks are normally brief , but long-lasting sparks have been widely observed experimentally under various conditions . The underlying mechanisms of spark duration or termination and the corresponding deter...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Long-Lasting Sparks: Multi-Metastability and Release Competition in the Calcium Release Unit Network
This work examines the computational architecture used by the brain during the analysis of the spectral envelope of sounds , an important acoustic feature for defining auditory objects . Dynamic causal modelling and Bayesian model selection were used to evaluate a family of 16 network models explaining functional magne...	The past decade has seen a phenomenal rise in applications of functional magnetic resonance imaging for both research and clinical applications . Most of the applications , however , concentrate on finding the regions of the brain that mediate the processing of a cognitive/motor task without determining the interaction...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience", "homo", "(human)" ]	2007	Hierarchical Processing of Auditory Objects in Humans
Human immunodeficiency virus ( HIV ) persistence in latently infected resting memory CD4+ T-cells is the major barrier to HIV cure . Cellular histone deacetylases ( HDACs ) are important in maintaining HIV latency and histone deacetylase inhibitors ( HDACi ) may reverse latency by activating HIV transcription from late...	The major barrier to curing HIV is the long term persistence of latently infected resting memory T-cells in HIV-infected patients on antiretroviral therapy ( ART ) . One strategy being pursued to eliminate latently infected cells is to activate HIV production from latently infected cells with the aim of killing latentl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "immunodeficiency", "viruses", "infectious", "diseases", "hiv", "infections", "medicine", "and", "health", "sciences", "medical", "microbiology", "hiv", "viral", "pathogens", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "vir...	2014	Activation of HIV Transcription with Short-Course Vorinostat in HIV-Infected Patients on Suppressive Antiretroviral Therapy
Recognizing that certain biological functions can be associated with specific DNA sequences has led various fields of biology to adopt the notion of the genetic part . This concept provides a finer level of granularity than the traditional notion of the gene . However , a method of formally relating how a set of parts ...	Deciphering the genetic code has been one of the major milestones in our understanding of how genetic information is stored in DNA sequences . However , only part of the genetic information is captured by the simple rules describing the correspondence between gene and proteins . The molecular mechanisms of gene express...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "computational", "biology/synthetic", "biology", "genetics", "and", "genomics/complex", "traits", "computer", "science/numerical", "analysis", "and", "theoretical", "computing", "genetics", "and", "genomics/gene", "function", "computational", "biology/systems", "biology" ]	2009	Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars
RNA-protein binding is critical to gene regulation , controlling fundamental processes including splicing , translation , localization and stability , and aberrant RNA-protein interactions are known to play a role in a wide variety of diseases . However , molecular understanding of RNA-protein interactions remains limi...	RNA-protein binding is critical to gene regulation , and aberrant RNA-protein interactions play a role in a wide variety of diseases . However , molecular understanding of these interactions remains limited because of the difficulty of ascertaining the motifs that bind each protein . To address this challenge , we have...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "rna-binding", "proteins", "applied", "mathematics", "simulation", "and", "modeling", "algorithms", "mathematics", "clustering", "algorithms", "immunoprecipitation", "sequence", "motif", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "rna", ...	2018	SARNAclust: Semi-automatic detection of RNA protein binding motifs from immunoprecipitation data
Fatty acid ( FA ) binding proteins ( FABPs ) of helminths are implicated in acquisition and utilization of host-derived hydrophobic substances , as well as in signaling and cellular interactions . We previously demonstrated that secretory hydrophobic ligand binding proteins ( HLBPs ) of Taenia solium metacestode ( TsM ...	Neurocysticercosis ( NC ) , an infection of the central nervous system with Taenia solium metacestode ( TsM ) , constitutes a leading cause of adult-onset seizures in endemic areas . Like other helminths , TsM is incapable of synthesizing lipid molecules . It should be equipped with a specialized system for lipid trans...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2012	Structural and Binding Properties of Two Paralogous Fatty Acid Binding Proteins of Taenia solium Metacestode
In 2010 , WHO recommended the use of new short-course treatment regimens in kala-azar elimination efforts for the Indian subcontinent . Although phase 3 studies have shown excellent results , there remains a lack of evidence on a wider treatment population and the safety and effectiveness of these regimens under field ...	Treatment is one of key strategies for visceral leishmaniasis control and elimination . Historically a number of monotherapy drugs for VL treatment were used in India including pentavalent antimonials , amphotericin B deoxycholate ( AmB ) , and miltefosine ( MF ) . With the limited number of drugs available there was a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "kala-azar", "medicine", "and", "health", "sciences", "clinical", "research", "design", "drugs", "geographical", "locations", "microbiology", "india", "tropical", "diseases", "antifungals", "parasitic", "diseases", "anemia", "research", "design", "pharma...	2018	Field safety and effectiveness of new visceral leishmaniasis treatment regimens within public health facilities in Bihar, India
The majority of recently emerging infectious diseases in humans is due to cross-species pathogen transmissions from animals . To establish a productive infection in new host species , viruses must overcome barriers to replication mediated by diverse and rapidly evolving host restriction factors such as protein kinase R...	The spread of microbes from animals to humans has been responsible for most recently emerging human infectious diseases , including AIDS , bird flu , and SARS . Therefore , understanding the evolutionary and molecular mechanisms underlying cross-species transmission is of critical importance for public health . After e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "mechanisms", "of", "resistance", "and", "susceptibility", "viral", "immune", "evasion", "virology", "microbial", "evolution", "host-pathogen", "interaction", "biology", "microbiology", "evolutionary", "biology", "viral", "diseases", ...	2014	Adaptive Gene Amplification As an Intermediate Step in the Expansion of Virus Host Range
Genetic diversity is maintained by continuing generation and removal of variants . While examining over 800 , 000 DNA variants in wild isolates of Caenorhabditis elegans , we made a discovery that the proportions of variant types are not constant across the C . elegans genome . The variant proportion is defined as the ...	DNA variants in the world population of a species reflect the genetic diversity of the species . While examining variants in whole-genome sequenced wild isolates of the nematode worm Caenorhabditis elegans , we discovered apparent correlations between the recombination rate and the proportion of many variant types . To...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "invertebrates", "caenorhabditis", "invertebrate", "genomics", "animals", "animal", "models", "regression", "analysis", "mutation", "caenorhabditis", "elegans", "model", "organisms", "mathematics", "statistics", "(mathematics)", "experimental", "organism", "systems", "dna", ...	2017	Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans
Nitric oxide ( NO ) regulates neuronal function and thus is critical for tuning neuronal communication . Mechanisms by which NO modulates protein function and interaction include posttranslational modifications ( PTMs ) such as S-nitrosylation . Importantly , cross signaling between S-nitrosylation and prenylation can ...	One way neurons communicate with each other and with other tissues , such as muscle , is by releasing chemical compounds known as neurotransmitters at sites of interaction known as synapses . This synaptic transmission can be finely regulated by both the releasing neuron and the receiving neuron or muscle cell . Many s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "neurochemistry", "neuromuscular", "junctions", "vesicles", "nervous", "system", "green", "fluorescent", "protein", "electrophysiology", "neuroscience", "prenylation", "animals", "animal", "models", "farnesylation", ...	2018	Nitric oxide-mediated posttranslational modifications control neurotransmitter release by modulating complexin farnesylation and enhancing its clamping ability
Most identified Drosophila appendage-patterning genes encode DNA-binding proteins , whose cross-regulatory interactions remain to be better characterized at the molecular level , notably by studying their direct binding to tissue-specific transcriptional enhancers . A fine-tuned spatio-temporal expression of bric-a-bra...	In insects , leg and antenna are homologous limbs , though derive from a single ancestral appendage . In Drosophila , leg and antennal development along the proximo-distal ( P-D ) axis relies on relatively-well known genetic cascades , in which most appendage-patterning genes encode transcription factors ( TF ) . Howev...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "molecular", "cell", "biology", "genetics", "biology", "genomics", "evolutionary", "biology" ]	2013	Drosophila Distal-less and Rotund Bind a Single Enhancer Ensuring Reliable and Robust bric-a-brac2 Expression in Distinct Limb Morphogenetic Fields
Toxoplasma gondii has evolved a number of strategies to evade immune responses in its many hosts . Previous genetic mapping of crosses between clonal type 1 , 2 , and 3 strains of T . gondii , which are prevalent in Europe and North America , identified two rhoptry proteins , ROP5 and ROP18 , that function together to ...	Parasites and the hosts they infect are in constant struggle with each other for survival . On the one hand , the host needs to control parasite growth , while the parasite needs to evade the host response long enough to allow for efficient transmission . The parasite Toxoplasma gondii has evolved virulence factors ROP...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Rhoptry Proteins ROP5 and ROP18 Are Major Murine Virulence Factors in Genetically Divergent South American Strains of Toxoplasma gondii
The widespread use of antibiotics is selecting for a variety of resistance mechanisms that seriously challenge our ability to treat bacterial infections . Resistant bacteria can be selected at the high concentrations of antibiotics used therapeutically , but what role the much lower antibiotic concentrations present in...	Antibiotic resistance has emerged as a very significant health care problem due to the extensive use and misuse of antibiotics in human and veterinary medicine and in agriculture . It remains unclear where most of the resistant bacteria have been selected , and in particular if the low antibiotic concentrations that ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "microbiology", "evolutionary", "biology", "population", "biology" ]	2011	Selection of Resistant Bacteria at Very Low Antibiotic Concentrations
The steroid hormone ecdysone coordinates insect growth and development , directing the major postembryonic transition of forms , metamorphosis . The steroid-deficient ecdysoneless1 ( ecd1 ) strain of Drosophila melanogaster has long served to assess the impact of ecdysone on gene regulation , morphogenesis , or reprodu...	Steroid hormones perform pivotal roles in animal development , sexual maturation , reproduction , and physiology . Also insects possess a hormonal steroid , commonly known as ecdysone , that was originally found to promote ecdyses in growing larvae and their metamorphosis to adults . Since the discovery of ecdysone-ind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "endocrine", "signaling", "animal", "genetics", "gene", "function", "genetics", "of", "disease", "developmental", "biology", "organism", "development", "molecular", "development", "genetic", "engineering", "gene", "expression", "nuclear", "receptor", "sig...	2014	Unexpected Role of the Steroid-Deficiency Protein Ecdysoneless in Pre-mRNA Splicing
Behaving in the real world requires flexibly combining and maintaining information about both continuous and discrete variables . In the visual domain , several lines of evidence show that neurons in some cortical networks can simultaneously represent information about the position and identity of objects , and maintai...	Forming a coherent picture of our surrounding environment requires combining visual information about the position of objects ( where information ) with information about their identity ( what information ) . It also requires the ability to maintain this combined information for short periods of time after the stimulus...	[ "Abstract", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/cognitive", "neuroscience", "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2008	Representing Where along with What Information in a Model of a Cortical Patch
Clathrin and the multi-subunit adaptor protein complex AP2 are central players in clathrin-mediated endocytosis by which the cell selectively internalizes surface materials . Here , we report the essential role of clathrin and AP2 in phagocytosis of apoptotic cells . In Caenorhabditis elegans , depletion of the clathri...	Phagocytosis of apoptotic cells is an indispensable part of the cell death program . During phagocytosis , the evolutionarily conserved CED-1 family phagocytic receptors recognize cell corpses and transduce engulfment signals to induce the formation and maturation of phagosomes . However , it remains largely unknown ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetics", "biology", "model", "organisms" ]	2013	Clathrin and AP2 Are Required for Phagocytic Receptor-Mediated Apoptotic Cell Clearance in Caenorhabditis elegans
The Americas have suffered a dramatic epidemic of Zika since May in 2015 , when Zika virus ( ZIKV ) was first detected in Brazil . Mosquitoes belonging to subgenus Stegomyia of Aedes , particularly Aedes aegypti , are considered the primary vectors of ZIKV . However , the rapid spread of the virus across the continent ...	The pandemic Zika epidemic has affected nearly all American countries . The etiological agent is a mosquito-borne-virus originated from Africa that spread to Asia and more recently , to the Pacific region and the Americas . We experimentally demonstrated that the common house nightly biting mosquito Culex quinquefascia...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "geographical", "locations", "microbiology", "saliva", "animals", "viral", "vectors", "vir...	2016	Culex quinquefasciatus from Rio de Janeiro Is Not Competent to Transmit the Local Zika Virus
Paracoccidioidomycosis ( PCM ) is the most prevalent deep mycosis in Latin America and is caused by fungi from the Paracoccidioides genus . Virulence factors are important fungal characteristics that support the development of disease . Aspartyl proteases ( Saps ) are virulence factors in many human fungal pathogens th...	Paracoccidioidomycosis is a systemic fungal disease occurring in Latin America and more prevalent in South America . The disease is caused by the dimorphic fungus Paracoccidioides spp . , its pathogenesis is multifactorial and few virulence factors have been recognized in this fungus . Some virulence factors , like the...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "yeast", "infections", "immune", "cells", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "fungi", "experimental", "organism", "systems", "paraco...	2018	Secreted aspartyl proteinase (PbSap) contributes to the virulence of Paracoccidioides brasiliensis infection
The risk of severe adverse events following treatment of onchocerciasis with ivermectin in areas co-endemic with loiasis currently compromises the development of control programmes and the treatment of co-infected individuals . We therefore assessed whether doxycycline treatment could be used without subsequent ivermec...	The control of onchocerciasis in Africa relies on the sustained delivery of ivermectin . In certain areas , annual treatments delivered with high population coverage for at least 15–17 years can break transmission . In other endemic settings this strategy alone is thought to be insufficient to eradicate the disease . O...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "microbiology/parasitology", "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Macrofilaricidal Activity after Doxycycline Only Treatment of Onchocerca volvulus in an Area of Loa loa Co-Endemicity: A Randomized Controlled Trial
The transition from mitotic to meiotic cell cycles is essential for haploid gamete formation and fertility . Stimulated by retinoic acid gene 8 ( Stra8 ) is an essential gatekeeper of meiotic initiation in vertebrates; yet , the molecular role of STRA8 remains principally unknown . Here we demonstrate that STRA8 functi...	Meiotic initiation is a key feature of sexual reproduction that launches an intricate chromosomal program involving DNA double strand breaks ( DSBs ) , homolog pairing , cohesion , synapsis , and recombination . Vertebrate gene Stra8 is an essential gatekeeper of meiotic initiation . However , the molecular role of STR...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "meiosis", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "reproductive", "system", "spermatocytes", "vesicles", "cell", "cycle", "and", "cell", "division", "drugs", "cell", "processes", "antimalarials", "germ", "cells", "ph...	2019	Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice
Meiotic crossovers ( COs ) shape genetic diversity by mixing homologous chromosomes at each generation . CO distribution is a highly regulated process . CO assurance forces the occurrence of at least one obligatory CO per chromosome pair , CO homeostasis smoothes out the number of COs when faced with variation in precu...	In species that reproduce sexually , diploid individuals have two copies of each chromosome , inherited from their father and mother . During a special cell division called meiosis , these two sets of chromosomes are mixed by homologous recombination to give genetically unique chromosomes that will be transmitted to th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "cytoskeletal", "proteins", "meiosis", "molecular", "motors", "kinesins", "cell", "biology", "synapsis", "proteins", "microtubule", "motors", "cell", "cycle", "and", "cell", "division", "genetics", "biology", "and", "life", "sciences", "dna", "cell", ...	2014	The Kinesin AtPSS1 Promotes Synapsis and is Required for Proper Crossover Distribution in Meiosis
Microbial translocation ( MT ) is the process by which microbes or microbial products translocate from the intestine to the systemic circulation . MT is a common cause of systemic immune activation in HIV infection and is associated with reduced frequencies of CD4+ T cells; no data exist , however , on the role of MT i...	Hookworm infections affect more than half a billion people worldwide and cause morbidity in the form of intestinal injury and blood loss . Host immunologic factors that influence the pathogenesis of disease in these individuals are not completely understood . Circulating microbial products such as LPS and markers assoc...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "gastroenterology", "and", "hepatology", "immunology", "biology" ]	2012	Evidence of Microbial Translocation Associated with Perturbations in T Cell and Antigen-Presenting Cell Homeostasis in Hookworm Infections
Conformational changes in allosteric regulation can to a large extent be described as motion along one or a few coherent degrees of freedom . The states involved are inherent to the protein , in the sense that they are visited by the protein also in the absence of effector ligands . Previously , we developed the measur...	What are the molecular mechanisms of allosteric communication in proteins ? We base our analysis on the hypothesis that a folded protein has a number of conformational degrees of freedom , which describe fluctuations around the native conformation and switching from/to functional states . Transitions between the protei...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "protein", "chemistry", "theoretical", "biology", "biological", "data", "management", "biophysic", "al", "simulations", "biology", "computational", "biology", "biophysics" ]	2011	Coherent Conformational Degrees of Freedom as a Structural Basis for Allosteric Communication
In many species , oocyte meiosis is carried out in the absence of centrioles . As a result , microtubule organization , spindle assembly , and chromosome segregation proceed by unique mechanisms . Here , we report insights into the principles underlying this specialized form of cell division , through studies of C . el...	When cells divide , they must assemble a microtubule-based structure called a spindle on which the chromosomes are segregated . While in most cell types the microtubules that comprise the spindle are nucleated and organized by centriole-containing centrosomes , female reproductive cells ( oocytes ) of many species lack...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "rna", "interference", "microtubules", "anaphase", "chromosome", "structure", "and", "function", "caenorhabditis", "metaphase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "germ", "cells", "animal", "models", "development...	2017	Interplay between microtubule bundling and sorting factors ensures acentriolar spindle stability during C. elegans oocyte meiosis
How nonenveloped viruses such as simian virus 40 ( SV40 ) trigger the lytic release of their progeny is poorly understood . Here , we demonstrate that SV40 expresses a novel later protein termed VP4 that triggers the timely lytic release of its progeny . Like VP3 , VP4 synthesis initiates from a downstream AUG start co...	The release of viral particles from an infected host cell is essential for a virus to spread within the host organism . Cytolytic viruses such as the common cold , poliovirus , and simian virus 40 ( SV40 ) release their progeny by inducing lysis or death of the host cell . For efficient viral spreading , it is critical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "nonenveloped", "viral", "release", "viroporin", "cell", "biology", "simian", "virus", "40", "virology", "membrane", "lysis", "cell", "lysis" ]	2007	A Very Late Viral Protein Triggers the Lytic Release of SV40
Experiments with drug-induced epilepsy in rat brains and epileptic human brain region reveal that focal cooling can suppress epileptic discharges without affecting the brain’s normal neurological function . Findings suggest a viable treatment for intractable epilepsy cases via an implantable cooling device . However , ...	Focal cooling of the epileptic brain region has been shown to consistently suppress epileptic activity and it is hoped that this treatment can be developed in the future into an implantable cooling device . However , it is still not clearly understood how cooling suppresses epileptic activity . This study uses a comput...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "action", "potentials", "membrane", "potential", "brain", "electrophysiology", "electrophysiology", "neuroscience", "clinical", "medicine", "ganglion", "cells", "brain", "mapping", "in...	2017	Differential temperature sensitivity of synaptic and firing processes in a neural mass model of epileptic discharges explains heterogeneous response of experimental epilepsy to focal brain cooling
Chlamydia trachomatis is an important human pathogen that replicates inside the infected host cell in a unique vacuole , the inclusion . The formation of this intracellular bacterial niche is essential for productive Chlamydia infections . Despite its importance for Chlamydia biology , a holistic view on the protein co...	The important human pathogen Chlamydia trachomatis causes 100 million new infections each year world-wide . It replicates inside the infected host cell in a unique vacuole , the inclusion . Currently , the nature , and specifically the protein composition of the inclusion , is poorly defined . Here , we described the h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Proteome of the Isolated Chlamydia trachomatis Containing Vacuole Reveals a Complex Trafficking Platform Enriched for Retromer Components
The epileptic network is characterized by pathologic , seizure-generating ‘foci’ embedded in a web of structural and functional connections . Clinically , seizure foci are considered optimal targets for surgery . However , poor surgical outcome suggests a complex relationship between foci and the surrounding network th...	Localization-related epilepsy is a debilitating condition where seizures begin in dysfunctional brain regions , and is often resistant to medication . The challenge for treating patients is mapping connections between cortical structures that vary with time and drive seizure dynamics . While it is well known that whole...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Dynamic Network Drivers of Seizure Generation, Propagation and Termination in Human Neocortical Epilepsy
The GI tract is preferentially targeted during acute/early HIV-1 infection . Consequent damage to the gut plays a central role in HIV pathogenesis . The basis for preferential targeting of gut tissues is not well defined . Recombinant proteins and synthetic peptides derived from HIV and SIV gp120 bind directly to integ...	HIV is gut-tropic . Disruption of GALT plays an important role in HIV -mediated immune dysfunction . α4β7 is a receptor that facilitates homing of lymphocytes to GALT . α4β7high CD4+ T cells are early targets of HIV infection . The HIV envelope protein gp120 binds to α4β7; however , a link between this interaction and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "ions", "microbiology", "vertebrates", "viral", "structure", "a...	2018	Select gp120 V2 domain specific antibodies derived from HIV and SIV infection and vaccination inhibit gp120 binding to α4β7
Prediction of antibiotic resistance phenotypes from whole genome sequencing data by machine learning methods has been proposed as a promising platform for the development of sequence-based diagnostics . However , there has been no systematic evaluation of factors that may influence performance of such models , how they...	Machine learning-based prediction of antibiotic resistance from bacterial genome sequences represents a promising tool to rapidly determine the antibiotic susceptibility profile of clinical isolates and reduce the morbidity and mortality resulting from inappropriate and ineffective treatment . However , while there has...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "united", "states", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "drugs", "geographical", "locations", "microbiology", "neisseria", "gonorrhoeae", "organisms", "north", "america", "anti...	2019	Evaluation of parameters affecting performance and reliability of machine learning-based antibiotic susceptibility testing from whole genome sequencing data
Chikungunya virus is a vector-borne alphavirus transmitted by the bites of infected female Ae . aegypti and Ae . albopictus . In Brazil between 2014 and 2016 almost 320 thousand autochthonous human cases were reported and in Florida numerous imported CHIKV viremic cases ( > 3 , 800 ) demonstrate the potential high risk...	Chikungunya is considered a serious mosquito-borne disease in many tropical and subtropical countries throughout the world . It is already an epidemic disease in Brazil and poses as a potential risk in Florida . It is mainly transmitted by mosquitoes Aedes aegypti and Aedes albopictus . These mosquito species are commo...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "united", "states", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "sali...	2018	Chikungunya virus vector competency of Brazilian and Florida mosquito vectors
A pandemic-capable influenza virus requires a hemagglutinin ( HA ) surface glycoprotein that is immunologically unseen by most people and is capable of supporting replication and transmission in humans . HA stabilization has been linked to 2009 pH1N1 pandemic potential in humans and H5N1 airborne transmissibility in th...	Many genetically diverse influenza viruses circulate among wild aquatic birds . Occasionally , one causes an outbreak in domestic poultry , swine , other animals , or humans . Zoonotic influenza viruses rarely cause a human pandemic . The hemagglutinin ( HA ) surface glycoprotein is the major surface antigen . A pandem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "vertebrates", "orthomyxoviruses", "animals", "mammals", "viruses", "rna", "viruses", ...	2017	H1N1 influenza viruses varying widely in hemagglutinin stability transmit efficiently from swine to swine and to ferrets
The surface proteins of human influenza A viruses experience positive selection to escape both human immunity and , more recently , antiviral drug treatments . In bacteria and viruses , immune-escape and drug-resistant phenotypes often appear through a combination of several mutations that have epistatic effects on pat...	Epistasis describes non-additive interactions among genetic sites: the consequence of a mutation at one site may depend on the status of the genome at other sites . In an extreme case , a mutation may have no effect if it arises on one genetic background , but a strong effect on another background . Epistatic mutations...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "public", "health", "and", "epidemiology/infectious", "diseases", "evolutionary", "biology", "public", "health", "and", "epidemiology...	2011	Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins
The AID / APOBEC genes are a family of cytidine deaminases that have evolved in vertebrates , and particularly mammals , to mutate RNA and DNA at distinct preferred nucleotide contexts ( or “hotspots” ) on foreign genomes such as viruses and retrotransposons . These enzymes play a pivotal role in intrinsic immunity def...	The APOBEC family of cytidine deaminases are important enzymes in most vertebrates . The ancestral member of this gene family is activation induced deaminase ( AID ) , which mutates the Immunoglobulin loci in B Cells during antibody affinity maturation in jawed vertebrates . The APOBEC family has expanded particularly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "microbial", "mutation", "medicine", "and", "health", "sciences", "retrotransposons", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "mutation", "rna", "viruses", "dna", "viruses", "gene...	2017	The preferred nucleotide contexts of the AID/APOBEC cytidine deaminases have differential effects when mutating retrotransposon and virus sequences compared to host genes
New therapeutics are needed for neglected tropical diseases including Human African trypanosomiasis ( HAT ) , a progressive and fatal disease caused by the protozoan parasites Trypanosoma brucei gambiense and T . b . rhodesiense . There is a need for simple , efficient , cost effective methods to identify new molecules...	Drug discovery for neglected tropical diseases must use efficient methods due to limited resources . One preferred drug discovery strategy is target-based drug discovery . In this strategy it is assumed that drug action begins with binding of a drug to its target . However , while binding is required , it is not suffic...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzymology", "parasitic", "protozoans", "protozoans", "pharmaceutics", "pharmacology", "enzyme", "inhibitors", "chemical", "dissociation", "competitive", "inhibitors", "behavior", "chemistry", "drug", "therapy", "drug", "discovery",...	2016	A Four-Point Screening Method for Assessing Molecular Mechanism of Action (MMOA) Identifies Tideglusib as a Time-Dependent Inhibitor of Trypanosoma brucei GSK3β
The oscillating concentration of intracellular calcium is one of the most important examples for collective dynamics in cell biology . Localized releases of calcium through clusters of inositol 1 , 4 , 5-trisphosphate receptor channels constitute elementary signals called calcium puffs . Coupling by diffusing calcium l...	Intracellular calcium oscillations and waves are paramount cellular signals . The frequency of global release events regulates , for example , expression of genes . Knowledge about the mechanism of oscillations and the factors that determine their frequency is crucial when aiming at the control of downstream processes ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "ion", "channel", "gating", "ion", "channels", "systems", "science", "mathematics", "stochastic", "processes", "calcium", "signaling", "computer", "and", "information", "sciences", "proteins", "calcium", "channels", "nonlinear", "dynamics", "biophysics", "probability", ...	2015	Modulation of Elementary Calcium Release Mediates a Transition from Puffs to Waves in an IP3R Cluster Model
Genome-scale datasets have been used extensively in model organisms to screen for specific candidates or to predict functions for uncharacterized genes . However , despite the availability of extensive knowledge in model organisms , the planning of genome-scale experiments in poorly studied species is still based on th...	Microarray expression experiments allow fast functional profiling of an organism's entire genome and significant efforts are devoted to analyzing the resulting data . Available genome sequences are also increasing quickly . However , it is unexplored how to use available functional genomics data to direct large-scale e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics" ]	2010	Systematic Planning of Genome-Scale Experiments in Poorly Studied Species
Retroviruses are not expected to encode miRNAs because of the potential problem of self-cleavage of their genomic RNAs . This assumption has recently been challenged by experiments showing that bovine leukemia virus ( BLV ) encodes miRNAs from intragenomic Pol III promoters . The BLV miRNAs are abundantly expressed in ...	The recent discovery of miRNA expression by retroviruses is a matter of active debate and some controversy . Several retroviruses including human immunodeficiency virus ( HIV ) potentially encode functional small non-coding RNAs that are nevertheless undetectable in vivo . While these miRNAs regulate multiple host and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "livestock", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "ruminants", "gene", "regulation", "enzymes", "immunology", "rna", "extraction", "enzymology", "vertebrates", "microbiology", "animals", "mammals", "organisms", "mic...	2016	Bovine Leukemia Virus Small Noncoding RNAs Are Functional Elements That Regulate Replication and Contribute to Oncogenesis In Vivo
Correct developmental timing is essential for plant fitness and reproductive success . Two important transitions in shoot development—the juvenile-to-adult vegetative transition and the vegetative-to-reproductive transition—are mediated by a group of genes targeted by miR156 , SQUAMOSA PROMOTER BINDING PROTEIN ( SBP ) ...	In Arabidopsis , miR156 acts by repressing the expression of 10 SQUAMOSA PROMOTOR BINDING PROTEIN-LIKE ( SPL ) genes . The phenotype of plants over-expressing miR156 demonstrates that these genes control many aspects of plant development and physiology , but the functions of individual miR156-regulated SPL genes , and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "floral", "meristem", "gene", "regulation", "brassica", "plant", "physiology", "mutation", "plant", "science", "model", "organisms", "plants", "flowering", "plants", "research", "and", "analysis", "methods", "arabidopsis", "thaliana", "gene", "expr...	2016	Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana
Scabies is an infectious skin disease caused by the mite Sarcoptes scabiei and has been classified as one of the six most prevalent epidermal parasitic skin diseases infecting populations living in poverty by the World Health Organisation . The role of the complement system , a pivotal component of human innate immunit...	Scabies is a skin infection caused by parasitic scabies mites . There are an estimated 300 million cases globally , with the majority of infections occurring in the world's poorest communities . In Australia , scabies is common in remote Indigenous communities where the infection rate is 16 times higher than the non-In...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dermatology", "infectious", "diseases", "innate", "immune", "system", "medicine", "and", "health", "sciences", "skin", "infections", "clinical", "immunology", "immunity", "sexually", "transmitted", "diseases", "scabies", "neglected", "tropical", "diseases", "biology", ...	2014	Scabies Mite Inactive Serine Proteases Are Potent Inhibitors of the Human Complement Lectin Pathway
Admixture—the mixing of genomes from divergent populations—is increasingly appreciated as a central process in evolution . To characterize and quantify patterns of admixture across the genome , a number of methods have been developed for local ancestry inference . However , existing approaches have a number of shortcom...	When divergent populations hybridize , their offspring obtain portions of their genomes from each parent population . Although the average ancestry proportion in each descendant is equal to the proportion of ancestors from each of the ancestral populations , the contribution of each ancestry type is variable across the...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "invertebrates", "markov", "models", "population", "genetics", "ploidy", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "mathematics", "inversions", "experimental", "organism", "systems", "population", "biology...	2017	A Hidden Markov Model Approach for Simultaneously Estimating Local Ancestry and Admixture Time Using Next Generation Sequence Data in Samples of Arbitrary Ploidy
Differentiation of extracellular Leishmania promastigotes within their sand fly vector , termed metacyclogenesis , is considered to be essential for parasites to regain mammalian host infectivity . Metacyclogenesis is accompanied by changes in the local parasite environment , including secretion of complex glycoconjuga...	Millions of people around the world are at risk of infection with single-celled Leishmania parasites that cause a wide range of infectious diseases of the immune system , the leishmaniases . There is no effective vaccine for these infections while available drugs have toxic side-effects and resistance is an increasing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "microbiology", "sand", "flies", "cloning", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "developmental", "biology", "protozoans", "leishmania", "molecular", "biology", "techniques", "insect", ...	2017	Leishmania HASP and SHERP Genes Are Required for In Vivo Differentiation, Parasite Transmission and Virulence Attenuation in the Host
Antimonials are still being used for visceral leishmaniasis ( VL ) treatment among HIV co-infected patients in East-Africa due to the shortage of alternative safer drugs like liposomal amphotericin B . Besides tolerability , emergence of resistance to antimonials is a major concern . This study was aimed at assessing t...	The co-infection of VL and HIV is a very challenging clinical problem especially in the East-Africa region . Though liposomal amphotericin B is the recommended treatment option for VL-HIV co-infection , it is often not available in practice in Ethiopia . Thus several patients are still being treated with antimonials th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "leishmaniasis", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "veterinary", "science" ]	2014	High Parasitological Failure Rate of Visceral Leishmaniasis to Sodium Stibogluconate among HIV Co-infected Adults in Ethiopia
Gliotoxin , and other related molecules , are encoded by multi-gene clusters and biosynthesized by fungi using non-ribosomal biosynthetic mechanisms . Almost universally described in terms of its toxicity towards mammalian cells , gliotoxin has come to be considered as a component of the virulence arsenal of Aspergillu...	The pathogenic fungus Aspergillus fumigatus causes disease in immunocompromised individuals such as cancer patients . The fungus makes a small molecule called gliotoxin which helps A . fumigatus bypass the immune system in ill people , and cause disease . Although a small molecule , gliotoxin biosynthesis is enabled by...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology/biocatalysis", "infectious", "diseases/respiratory", "infections", "microbiology/immunity", "to", "infections", "chemical", "biology/biocatalysis", "biotechnology/applied", "microbiology", "biotechnology/chemical", "biology", "of", "the", "cell", "infectious", "disea...	2010	Self-Protection against Gliotoxin—A Component of the Gliotoxin Biosynthetic Cluster, GliT, Completely Protects Aspergillus fumigatus Against Exogenous Gliotoxin

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