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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
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Developing physiologically-based pharmacokinetic ( PBPK ) models for chemicals can be resource-intensive , as neither chemical-specific parameters nor in vivo pharmacokinetic data are easily available for model construction . Previously developed , well-parameterized , and thoroughly-vetted models can be a great resour... | Physiologically-based pharmacokinetic ( PBPK ) models are complex kinetic models describing the absorption , distribution , metabolism and excretion of chemicals in humans or animals in vivo . They can be utilized in many applications , such as dosimetry testing , toxicological investigations , and chemical risk assess... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"body",
"fluids",
"chemical",
"compounds",
"organic",
"compounds",
"toluene",
"physiological",
"parameters",
"aromatic",
"hydrocarbons",
"pharmacology",
"drug",
"metabolism",
"hydrocarbons",
"chemistry",
"iodides",
"hematology",
"x... | 2016 | Developing a Physiologically-Based Pharmacokinetic Model Knowledgebase in Support of Provisional Model Construction |
We present a theory of decision-making in the presence of multiple choices that departs from traditional approaches by explicitly incorporating entropic barriers in a stochastic search process . We analyze response time data from an on-line repository of 15 million blitz chess games , and show that our model fits not j... | Decision-making has been studied in great detail relying on binary choices , modeled as the noisy accumulation of a decision variable to a threshold . We show that it breaks down when used to describe real-life human decision involving multiple options . We show instead that including obstacles in the diffusion model (... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"recreation",
"decision",
"theory",
"decision",
"making",
"engineering",
"and",
"technology",
"applied",
"mathematics",
"social",
"sciences",
"mathematical",
"models",
"neuroscience",
"problem",
"solving",
"decision",
"analysis",
"cognitive",
"psychology",
"mathematics",
... | 2018 | An entropic barriers diffusion theory of decision-making in multiple alternative tasks |
Kinetic models provide the means to understand and predict the dynamic behaviour of enzymes upon different perturbations . Despite their obvious advantages , classical parameterizations require large amounts of data to fit their parameters . Particularly , enzymes displaying complex reaction and regulatory ( allosteric... | Kinetic models enable understanding and prediction of the dynamic behaviour of enzymatic reactions . Different frameworks have been proposed to parameterize enzymatic reactions using approximate expressions while maintaining thermodynamic consistency . Approximate expressions have been particularly sought and used , as... | [
"Abstract",
"Introduction",
"Models",
"Results",
"Discussion"
] | [] | 2015 | A General Framework for Thermodynamically Consistent Parameterization and Efficient Sampling of Enzymatic Reactions |
Adeno-associated viruses ( AAV ) are Dependoparvoviruses that have shown promise as recombinant vectors for gene therapy . While infectious pathways of AAV are well studied , gaps remain in our understanding of host factors affecting vector genome expression . Here , we map the role of ring finger protein 121 ( RNF121 ... | Recombinant AAV vectors are at the forefront of clinical gene therapy . There is a need to better understand the mechanisms dictating AAV transduction in the host . Here , we identify a network of host proteins involving RNF121 , p97 and the DNA damage machinery as potent factors regulating AAV genome transcription . O... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"transfection",
"luciferase",
"enzymes",
"messenger",
"rna",
"microbiology",
"enzymology",
"dna",
"damage",
"immunoprecipitation",
"dna",
"molecular",
"biology",
"techniques",
"research",
"and",
"analysis",
"methods",
"genome",
"complexity",
"genomics",
"proteins",
"oxido... | 2019 | Ring finger protein 121 is a potent regulator of adeno-associated viral genome transcription |
Little is known of the direct microbicidal activity of T cells in leprosy , so a lipopeptide consisting of the N-terminal 13 amino acids lipopeptide ( LipoK ) of a 33-kD lipoprotein of Mycobacterium leprae , was synthesized . LipoK activated M . leprae infected human dendritic cells ( DCs ) to induce the production of ... | We observed that LipoK ( Mycobacterium leprae lipopeptide with 13 amino acids ) is capable of inducing a good immune response in M . leprae infected human dendritic cells ( DCs ) . These activated DCs had up-regulated expression of costimulatory molecule CD86 as well as CD83 ( well known maturation marker ) on their su... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"immunology",
"biology",
"immune",
"response"
] | 2011 | A Lipopeptide Facilitate Induction of Mycobacterium leprae Killing in Host Cells |
The translocation of single-stranded DNA ( ssDNA ) across membranes of two cells is a fundamental biological process occurring in both bacterial conjugation and Agrobacterium pathogenesis . Whereas bacterial conjugation spreads antibiotic resistance , Agrobacterium facilitates efficient interkingdom transfer of ssDNA f... | The importation of genetic material into cells is a common and fundamental mechanism occurring in bacterial conjugation , DNA uptake , and Agrobacterium plant infection and is , for instance , responsible for antibiotic resistance spread . Previous studies suggested that this process relied only on the activity of comp... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"microbiology",
"biophysics"
] | 2008 | VirE2: A Unique ssDNA-Compacting Molecular Machine |
Recognition of intracellular pathogenic bacteria by members of the nucleotide-binding domain and leucine-rich repeat containing ( NLR ) family triggers immune responses against bacterial infection . A major response induced by several Gram-negative bacteria is the activation of caspase-1 via the Nlrc4 inflammasome . Up... | Shigella are bacterial pathogens that are the cause of bacillary dysentery . An important feature of Shigella is their ability to invade the cytoplasm of host epithelial cells and macrophages . A major component of host recognition of Shigella invasion is the activation of the inflammasome , a molecular platform that d... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"bacterial",
"diseases",
"infectious",
"diseases",
"immunity",
"innate",
"immunity",
"immunology",
"biology"
] | 2014 | Shigella Type III Secretion Protein MxiI Is Recognized by Naip2 to Induce Nlrc4 Inflammasome Activation Independently of Pkcδ |
Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies . Here , we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454... | The ability of HIV-1 and other highly variable pathogens to rapidly mutate to escape vaccine-induced immune responses represents a major hurdle to the development of effective vaccines to these highly persistent pathogens . Application of next-generation or deep sequencing technologies to the study of host pathogens co... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"immune",
"cells",
"clinical",
"immunology",
"immunity",
"hiv",
"immunology",
"biology",
"viral",
"diseases"
] | 2012 | Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection |
While an increasing number of conserved small regulatory RNAs ( sRNAs ) are known to function in general bacterial physiology , the roles and modes of action of sRNAs from horizontally acquired genomic regions remain little understood . The IsrK sRNA of Gifsy-1 prophage of Salmonella belongs to the latter class . This ... | As the function of conserved core-genome-encoded small RNAs ( sRNA ) reflects the basic lifestyle of bacteria , the function of non-conserved island-encoded sRNAs remains enigmatic . The island-encoded sRNA IsrK belongs to Gifsy-1 prophage of Salmonella . Here , we report a complex mechanism in which the IsrK RNA funct... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"nucleic",
"acid",
"synthesis",
"pathology",
"and",
"laboratory",
"medicine",
"bacteriophages",
"pathogens",
"messenger",
"rna",
"microbiology",
"dna",
"transcription",
"viruses",
"bacterial",
"diseases",
"enterobacteriaceae",
"mol... | 2016 | Gifsy-1 Prophage IsrK with Dual Function as Small and Messenger RNA Modulates Vital Bacterial Machineries |
The spirochete Borrelia recurrentis is the causal agent of louse-borne relapsing fever and is transmitted to humans by the infected body louse Pediculus humanus . We have recently demonstrated that the B . recurrentis surface receptor , HcpA , specifically binds factor H , the regulator of the alternative pathway of co... | Borrelia recurrentis , the causal agent of louse-borne relapsing fever is transmitted to humans via infected body lice . Infection with B . recurrentis has been achieved only in humans and is accompanied by a systemic inflammatory disease , multiple relapses of fever and massive spirochetemia . A key virulence factor o... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases/bacterial",
"infections",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"immunology/immunity",
"to",
"infections",
"immunology/innate",
"immunity"
] | 2010 | Human Complement Regulators C4b-Binding Protein and C1 Esterase Inhibitor Interact with a Novel Outer Surface Protein of Borrelia recurrentis |
For making decisions in everyday life we often have first to infer the set of environmental features that are relevant for the current task . Here we investigated the computational mechanisms underlying the evolution of beliefs about the relevance of environmental features in a dynamical and noisy environment . For thi... | When making decisions in our everyday life ( e . g . where to eat ) we first have to identify a set of environmental features that are relevant for the decision ( e . g . the distance to the place , current time or the price ) . Although we are able to make such inferences almost effortlessly , this type of problems is... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Modeling the Evolution of Beliefs Using an Attentional Focus Mechanism |
NF-κB pathways are key signaling cascades of the Drosophila innate immune response . One of them , the Immune Deficiency ( IMD ) pathway , is under a very tight negative control . Although molecular brakes exist at each step of this signaling module from ligand availability to transcriptional regulation , it remains un... | In multicellular organism such as mammals or insects , activation of innate immune responses occurs following detection of microbes by dedicated receptors called pattern recognition receptors . Such immune activation is taking place in immune competent tissue such as the skin , the digestive and respiratory epithelia a... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"skin",
"cell",
"death",
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"integumentary",
"system",
"cell",
"processes",
"developmental",
"biology",
"respiratory",
"system",
"pupae",
"epidermis",
"trachea",
"lipids",
"fats",
"gene",
"expression",
"l... | 2017 | Inhibition of a NF-κB/Diap1 Pathway by PGRP-LF Is Required for Proper Apoptosis during Drosophila Development |
A vaccine against schistosomiasis would have a great impact in disease elimination . Sm29 and Sm22 . 6 are two parasite tegument proteins which represent promising antigens to compose a vaccine . These antigens have been associated with resistance to infection and reinfection in individuals living in endemic area for t... | The development of a vaccine against schistosomiasis together with chemotherapy would have a great impact in the disease control and elimination . Sm29 and Sm22 . 6 are two promising antigens that have been associated with resistance to infection/reinfection in humans and also successfully induce protection in trials u... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Sm29, but Not Sm22.6 Retains its Ability to Induce a Protective Immune Response in Mice Previously Exposed to a Schistosoma mansoni Infection |
While it is widely held that an organism's genomic information should remain constant , several protein families are known to modify it . Members of the AID/APOBEC protein family can deaminate DNA . Similarly , members of the ADAR family can deaminate RNA . Characterizing the scope of these events is challenging . Here... | Most biomedical , genomic research begins with the painstaking assembly of a “reference genome” for the organism of interest . Implicit in this process is an assumption that genomic information is constant throughout an organism . There are enzymes , however , that can change , or “edit , ” genomic information so that ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/genome",
"projects",
"computational",
"biology/genomics",
"computer",
"science/information",
"technology",
"genetics",
"and",
"genomics/bioinformatics"
] | 2010 | A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing, and DNA Editing |
Rift Valley fever ( RVF ) is a viral zoonosis that primarily affects animals resulting in considerable economic losses due to death and abortions among infected livestock . RVF also affects humans with clinical symptoms ranging from an influenza-like illness to a hemorrhagic fever . Over the past years , RVF virus ( RV... | Rift Valley fever ( RVF ) is a zoonotic viral disease posing an increasing threat to animals and humans worldwide . Recent severe outbreaks of the disease in animal and human populations in endemic regions and outside the disease's traditional geographic boundaries necessitate the need for evaluating the diagnostic per... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"applied",
"microbiology",
"emerging",
"infectious",
"diseases",
"virology",
"biology",
"microbiology",
"viral",
"disease",
"diagnosis"
] | 2013 | International External Quality Assessment of Molecular Detection of Rift Valley Fever Virus |
Despite free of charge biomedical treatment , the cost burden of Buruli ulcer disease ( Bu ) hospitalisation in Central Cameroon accounts for 25% of households' yearly earnings , surpassing the threshold of 10% , which is generally considered catastrophic for the household economy , and calling into question the sustai... | The cost burden of free of charge Buruli ulcer disease ( Bu ) hospital treatment is not sustainable for a majority of patients and their families in Central Cameroon . The long term nature of Bu taxes the patients' and their families' resources often to a breaking point , consequently often leading to the abandonment o... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/social",
"and",
"behavioral",
"determinants",
"of",
"health",
"public",
"health",
"and",
"epidemiology/infectious",
"diseases",
"public",
"health",
"and",
"epidemiology/health",
"services",
"research",
"and",
"economics",
"public",... | 2008 | “It Is Me Who Endures but My Family That Suffers”: Social Isolation as a Consequence of the Household Cost Burden of Buruli Ulcer Free of Charge Hospital Treatment |
Endometriosis is a gynecological disease defined by the extrauterine growth of endometrial-like cells that cause chronic pain and infertility . The disease is limited to primates that exhibit spontaneous decidualization , and diseased cells are characterized by significant defects in the steroid-dependent genetic pathw... | Women develop endometriosis when endometrial tissue with altered sensitivity to ovarian hormones grows outside the uterus . The persistent survival of these cells results in chronic pelvic pain and infertility . Although the origin of the disease remains a mystery , it only occurs in women and menstruating primates , s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"developmental",
"biology",
"menstrual",
"abnormalities",
"reproductive",
"system",
"obstetrics",
"and",
"gynecology",
"genetics",
"epigenetics",
"biology",
"dna",
"modification",
"anatomy",
"and",
"physiology",
"sexual",
"reproduction",
"cell",
"differentiation... | 2014 | Genome-Wide DNA Methylation Analysis Predicts an Epigenetic Switch for GATA Factor Expression in Endometriosis |
The high environmental adaptability of bacteria is contingent upon their ability to sense changes in their surroundings . Bacterial pathogen entry into host poses an abrupt and dramatic environmental change , during which successful pathogens gauge multiple parameters that signal host localization . The facultative hum... | To thrive in the human body and cause disease , bacterial pathogens rely on the expression of a battery of genes , termed virulence genes . However , to activate these genes , the bacterium must “know” that it is no longer free-roaming , and has invaded a host . Like all life forms , bacterial pathogens must acquire th... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"pathology",
"and",
"laboratory",
"medicine",
"chemical",
"compounds",
"pathogens",
"immunology",
"microbiology",
"organic",
"compounds",
"electromagnetic",
"radiation",
"dna",
"transcription",
... | 2017 | L-glutamine Induces Expression of Listeria monocytogenes Virulence Genes |
LJ001 is a lipophilic thiazolidine derivative that inhibits the entry of numerous enveloped viruses at non-cytotoxic concentrations ( IC50≤0 . 5 µM ) , and was posited to exploit the physiological difference between static viral membranes and biogenic cellular membranes . We now report on the molecular mechanism that r... | The threat of emerging and re-emerging viruses underscores the need to develop broad-spectrum antivirals . LJ001 is a non-cytotoxic , membrane-targeted , broad-spectrum antiviral previously reported to inhibit the entry of many lipid-enveloped viruses . Here , we delineate the molecular mechanism that underlies LJ001's... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicinal",
"chemistry",
"virology",
"chemistry",
"chemical",
"reactions",
"biology",
"antivirals",
"microbiology",
"photochemical",
"reactions"
] | 2013 | A Mechanistic Paradigm for Broad-Spectrum Antivirals that Target Virus-Cell Fusion |
Leishmania uses the amino acid L-arginine as a substrate for arginase , enzyme that produces urea and ornithine , last precursor of polyamine pathway . This pathway is used by the parasite to replicate and it is essential to establish the infection in the mammalian host . L-arginine is not synthesized by the parasite ,... | Leishmania alternates its life cycle between the invertebrate host , in which the promastigote forms reside at pH 7 . 0 and approximately 25°C; and the mammalian host , in which the amastigote forms reside at pH 5 . 0 and approximately 37°C . These environmental changes submit the parasite to dynamic undergo modificati... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"blood",
"cells",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"microbiology",
"parasitic",
"diseases",
"protozoan",
"life",
"cycles",
"parasitic",
"protozoans",
"membrane",
"proteins",
"developmental",
"biology",
"protozoans",
"leishmania",
... | 2017 | L-arginine availability and arginase activity: Characterization of amino acid permease 3 in Leishmania amazonensis |
Many genes involved in the immune response of Anopheles gambiae , the main malaria vector in Africa , have been identified , but whether naturally occurring polymorphisms in these genes underlie variation in resistance to the human malaria parasite , Plasmodium falciparum , is currently unknown . Here we carried out a ... | Anopheles gambiae is the main malaria vector in Africa , transmitting the parasite when it blood feeds on human hosts . The parasite undergoes several developmental stages in the mosquito to complete its life cycle , during which time it is confronted by the mosquito's immune system . The resistance of mosquitoes to ma... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genetics",
"and",
"genomics/microbial",
"evolution",
"and",
"genomics",
"genetics",
"and",
"genomics/functional",
"genomics",
"genetics",
"and",
"genomics/genetics",
"of",
"the",
"immune",
"system",
"genetics",
"and",
"genomics/complex",
"traits",
"immunology/immune",
"r... | 2010 | Polymorphisms in Anopheles gambiae Immune Genes Associated with Natural Resistance to Plasmodium falciparum |
Quorum sensing ( QS ) is a bacterial cell-cell communication process that relies on the production and detection of extracellular signal molecules called autoinducers . QS allows bacteria to perform collective activities . Vibrio cholerae , a pathogen that causes an acute disease , uses QS to repress virulence factor p... | The disease cholera , caused by the pathogenic bacterium Vibrio cholerae , is a major health concern in developing regions . In order to be virulent , V . cholerae must precisely control the timing of production of virulence factors . To do this , V . cholerae uses a cell-cell communication process called quorum sensin... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"medicinal",
"chemistry",
"chemistry",
"biology",
"microbiology"
] | 2012 | Broad Spectrum Pro-Quorum-Sensing Molecules as Inhibitors of Virulence in Vibrios |
Caulobacter crescentus undergoes an asymmetric cell division controlled by a genetic circuit that cycles in space and time . We provide a universal strategy for defining the coding potential of bacterial genomes by applying ribosome profiling , RNA-seq , global 5′-RACE , and liquid chromatography coupled with tandem ma... | Caulobacter crescentus is a model system for studying asymmetric cell division , a fundamental process that , through differential gene expression in the two daughter cells , enables the generation of cells with different fates . To explore how the genome directs and maintains asymmetry upon cell division , we performe... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genome",
"expression",
"analysis",
"caulobacter",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"microbiology",
"genomic",
"databases",
"prokaryotic",
"models",
"model",
"organisms",
"genome",
"analysis",
"bacteria",
"research",
"and",
"analysis",
... | 2014 | The Coding and Noncoding Architecture of the Caulobacter crescentus Genome |
Critical transitions are sudden , often irreversible , changes that can occur in a large variety of complex systems; signals that warn of critical transitions are therefore highly desirable . We propose a new method for early warning signals that integrates multiple sources of information and data about the system thro... | Fisheries , coral reefs , productive farmland , planetary climate , neural activity in the brain , and financial markets are all complex systems that can be susceptible to sudden changes leading to drastic re-organization or collapse . A variety of signals based on analysis of time-series data have been proposed that w... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"mathematics",
"ecology",
"biology",
"nonlinear",
"dynamics"
] | 2012 | Early Warning Signals for Critical Transitions: A Generalized Modeling Approach |
Bdelloid rotifers are microinvertebrates with unique characteristics: they have survived tens of millions of years without sexual reproduction; they withstand extreme desiccation by undergoing anhydrobiosis; and they tolerate very high levels of ionizing radiation . Recent evidence suggests that subtelomeric regions of... | Bdelloid rotifers are tiny invertebrates with unusual characteristics: they withstand stresses , such as desiccation and high levels of ionising radiation , that kill other animals , and they have survived over millions of years without sexual reproduction , which contradicts theories on the evolutionary advantages of ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genomics",
"functional",
"genomics",
"genetics",
"biology",
"evolutionary",
"biology",
"evolutionary",
"genetics",
"genetics",
"and",
"genomics"
] | 2012 | Biochemical Diversification through Foreign Gene Expression in Bdelloid Rotifers |
Syphilis is a chronic disease caused by the bacterium Treponema pallidum subsp . pallidum . Treponema pallidum disseminates widely throughout the host and extravasates from the vasculature , a process that is at least partially dependent upon the ability of T . pallidum to interact with host extracellular matrix ( ECM ... | The Treponema pallidum protein , Tp0751 , possesses adhesive properties and has been previously reported to mediate attachment to the host extracellular matrix components laminin , fibronectin , and fibrinogen . Herein we demonstrate that Tp0751 adopts an eight-stranded beta barrel-containing lipocalin structure , and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biotechnology",
"synthetic",
"biotechnology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"fibrinogen",
"engineering",
"and",
"technology",
"pathogens",
"synthetic",
"biology",
"microbiology",
"peptide",
"libraries",
"molecular",
... | 2016 | The Structure of Treponema pallidum Tp0751 (Pallilysin) Reveals a Non-canonical Lipocalin Fold That Mediates Adhesion to Extracellular Matrix Components and Interactions with Host Cells |
Spike timing dependent plasticity ( STDP ) has been observed experimentally in vitro and is a widely studied neural algorithm for synaptic modification . While the functional role of STDP has been investigated extensively , the effect of rhythms on the precise timing of STDP has not been characterized as well . We use ... | Rhythms are well studied phenomena in many animal species . Brain rhythms in the gamma frequency range ( 30–90 Hz ) are thought to play a role in attention and memory . In this paper , we are interested in how cortical gamma rhythms interact with information specific inputs that also have a significant gamma frequency ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"neuroscience",
"neuroscience/theoretical",
"neuroscience",
"neuroscience/sensory",
"systems"
] | 2009 | Cortical Gamma Rhythms Modulate NMDAR-Mediated Spike Timing Dependent Plasticity in a Biophysical Model |
EHBP-1 ( Ehbp1 ) is a conserved regulator of endocytic recycling , acting as an effector of small GTPases including RAB-10 ( Rab10 ) . Here we present evidence that EHBP-1 associates with tubular endosomal phosphatidylinositol-4 , 5-bisphosphate [PI ( 4 , 5 ) P2] enriched membranes through an N-terminal C2-like ( NT-C2... | Endosomes are intracellular organelles that sort protein and lipid components integral to the membrane , as well as more loosely associated lumenal content , for delivery to distinct intracellular destinations . Endosomes associated with recycling cargo back to the plasma membrane are often tubular in morphology , and ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"motility",
"medicine",
"and",
"health",
"sciences",
"vesicles",
"actin",
"filaments",
"vacuoles",
"microtubules",
"cellular",
"structures",
"and",
"organelles",
"cytoskeleton",
"digestive",
"system",
"endosomes",
"contractile",
"proteins",
"actins",
"proteins",
... | 2016 | RAB-10 Promotes EHBP-1 Bridging of Filamentous Actin and Tubular Recycling Endosomes |
Echinococcus multilocularis is the source of alveolar echinococcosis , a potentially fatal zoonotic disease . This investigation assessed the presence of E . multilocularis infection in definitive hosts in the Chenaran region of Razavi Khorasan Province , northeastern Iran . Fecal samples from 77 domestic and stray dog... | Echinococcus multilocularis causes alveolar echinococcosis , a serious zoonotic disease present in many areas of the world . The parasite is maintained in nature through a life cycle in which adult worms in the intestine of carnivores transmit infection to small mammals , predominantly rodents , via eggs in the feces .... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"biology",
"microbiology",
"zoology",
"parasitology",
"helminthology"
] | 2011 | Detection of Echinococcus multilocularis in Carnivores in Razavi Khorasan Province, Iran Using Mitochondrial DNA |
There is a strong need for computational frameworks that integrate different biological processes and data-types to unravel cellular regulation . Current efforts to reconstruct transcriptional regulatory networks ( TRNs ) focus primarily on proximal data such as gene co-expression and transcription factor ( TF ) bindin... | Cellular networks , such as metabolic and transcriptional regulatory networks ( TRNs ) , do not operate independently but work together in unison to determine cellular phenotypes . Further , the phenotype and architecture of one network constrains the topology of other networks . Hence , it is critical to study network... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2013 | Metabolic Constraint-Based Refinement of Transcriptional Regulatory Networks |
Syphilis , a sexually transmitted disease caused by spirochetal bacterium Treponema pallidum , can progress to affect the central nervous system , causing neurosyphilis . Accumulating evidence suggest that regulatory T cells ( Tregs ) may play an important role in the pathogenesis of syphilis . However , little is know... | Syphilis , caused by the bacterium Treponema pallidum , can progress to affect the central nervous system ( CNS ) and cause damage in the brain and spinal cord , which is called neurosyphilis . While many affected neurosyphilis patients may not have any symptoms , some of the patients will develop severe symptoms that ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2013 | Regulatory T Cells in Peripheral Blood and Cerebrospinal Fluid of Syphilis Patients with and without Neurological Involvement |
Many genes are recruited to the nuclear periphery upon transcriptional activation . The mechanism and functional significance of this recruitment is unclear . We find that recruitment of the yeast INO1 and GAL1 genes to the nuclear periphery is rapid and independent of transcription . Surprisingly , these genes remain ... | Eukaryotic cells control the spatial arrangement of chromosomes; the localization of genes can both reflect and contribute to their transcriptional state . A number of genes in the simple eukaryote brewer's yeast are “recruited” to the nuclear periphery through interactions with the nuclear pore complex when they are e... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"yeast",
"and",
"fungi",
"eukaryotes",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2007 | H2A.Z-Mediated Localization of Genes at the Nuclear Periphery Confers Epigenetic Memory of Previous Transcriptional State |
The abrupt origin and rapid diversification of the flowering plants during the Cretaceous has long been considered an “abominable mystery . ” While the cause of their high diversity has been attributed largely to coevolution with pollinators and herbivores , their ability to outcompete the previously dominant ferns and... | The angiosperms , commonly referred to as the flowering plants , are the dominant plants in most terrestrial ecosystems , but how they came to be so successful is considered one of the most profound mysteries in evolutionary biology . Prevailing hypotheses have suggested that the angiosperms rose to dominance through a... | [
"Abstract",
"Introduction",
"Results",
"and",
"discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"taxonomy",
"plant",
"anatomy",
"stem",
"anatomy",
"ferns",
"stomata",
"phylogenetics",
"plant",
"science",
"data",
"management",
"plant",
"genomics",
"plants",
"flowering",
"plants",
"leaf",
"veins",
"computer",
"and",
"information",
"sciences",
"pla... | 2018 | Genome downsizing, physiological novelty, and the global dominance of flowering plants |
Exposure to Plasmodium falciparum is associated with circulating “atypical” memory B cells ( atMBCs ) , which appear similar to dysfunctional B cells found in HIV-infected individuals . Functional analysis of atMBCs has been limited , with one report suggesting these cells are not dysfunctional but produce protective a... | A subset of “atypical” memory B cells found in individuals with high exposure to P . falciparum has been hypothesized to be dysfunctional , based on phenotypic similarities to analogous cells found in HIV-infected individuals . However , the functional capabilities of these cells have been poorly characterized in the s... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | FCRL5 Delineates Functionally Impaired Memory B Cells Associated with Plasmodium falciparum Exposure |
Immunological memory is a hallmark of B and T lymphocytes that have undergone a previous encounter with a given antigen . It is assumed that memory cells mediate better protection of the host upon re-infection because of improved effector functions such as antibody production , cytotoxic activity and cytokine secretion... | The immune system comprises white blood cells that belong to the innate or the adaptive immune arms . Adaptive immune cells such as T and B lymphocytes can give rise to memory cells which mediate long-lived immunity against pathogens . During a recall infection , innate immune phagocytic cells such as monocytes and neu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"immune",
"cells",
"cytokines",
"immune",
"activation",
"immunity",
"to",
"infections",
"immunology",
"microbiology",
"lymphoid",
"organs",
"host-pathogen",
"interaction",
"animal",
"models",
"adaptive",
"immunity",
"mechanisms",
"of",
"resistance",
"and",
"susceptibility... | 2011 | Inflammatory Monocytes and Neutrophils Are Licensed to Kill during Memory Responses In Vivo |
The fragile X-related disorders result from expansion of a CGG/CCG microsatellite in the 5’ UTR of the FMR1 gene . We have previously demonstrated that the MSH2/MSH3 complex , MutSβ , that is important for mismatch repair , is essential for almost all expansions in a mouse model of these disorders . Here we show that t... | The repeat expansion diseases are a group of human genetic disorders that are caused by expansion of a specific microsatellite in a single affected gene . How this expansion occurs is unknown , but previous work in various models for different diseases in the group , including the fragile X-related disorders ( FXDs ) ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"reproductive",
"system",
"dna-binding",
"proteins",
"nucleotides",
"animal",
"models",
"germ",
"cells",
"model",
"organisms",
"molecular",
"biology",
"techniques",
"genotyping",
"extraction",
"techniques",
"sperm",
"research",
"... | 2016 | A MutSβ-Dependent Contribution of MutSα to Repeat Expansions in Fragile X Premutation Mice? |
The study of dynamic functions of large-scale biological networks has intensified in recent years . A critical component in developing an understanding of such dynamics involves the study of their hierarchical organization . We investigate the temporal hierarchy in biochemical reaction networks focusing on: ( 1 ) the e... | Cellular metabolism describes the complex web of biochemical transformations that are necessary to build the structural components , to convert nutrients into “usable energy” by the cell , and to degrade or excrete the by-products . A critical aspect toward understanding metabolism is the set of dynamic interactions be... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"and",
"Methods"
] | [
"mathematics",
"biochemistry/chemical",
"biology",
"of",
"the",
"cell",
"biochemistry/bioinformatics",
"computational",
"biology/metabolic",
"networks",
"biotechnology/bioengineering",
"biochemistry/theory",
"and",
"simulation"
] | 2008 | Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks |
Endogenous small interfering RNAs ( siRNAs ) are a class of naturally occuring regulatory RNAs found in fungi , plants , and animals . Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however , the specific roles of most endogenous siRNAs are unclear . The helicase gene ... | Endogenous small interfering RNAs ( siRNAs ) are a class of small RNAs present in fungi , plants , and animals . Small RNAs , including microRNAs , are known to regulate the expression levels of genes , silence invading elements such as transposons , and act in cell division . However , the function of many endogenous ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"rna",
"interference",
"animal",
"models",
"caenorhabditis",
"elegans",
"model",
"organisms",
"epigenetics",
"gene",
"expression",
"biology",
"molecular",
"biology",
"systems",
"biology",
"rna",
"rna",
"processing",
"nucleic",
"acids",
"genetics",
"molecular",
"cell",
... | 2011 | The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications |
NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding . By sliding nucleosomes , NURF is able to alter chromatin dynamics to control transcription and genome organization . Previous biochemical and genetic analysis of the specificity-subunit o... | In eukaryotes DNA is folded and compacted into manageable units by wrapping around a protein spool of histone proteins to form nucleosomes . By varying the position and dynamics of nucleosomes using energy-dependent chromatin remodeling enzymes , genes can be selectively turned off or on in cells , controlling developm... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immunology",
"invertebrate",
"genomics",
"animals",
"animal",
"models",
"nucleosome",
"mapping",
"insulators",
"drosophila",
"melanogaster",
"model",
"organisms",
"materials",
... | 2016 | Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators |
Somatostatin-expressing , low threshold-spiking ( LTS ) cells and fast-spiking ( FS ) cells are two common subtypes of inhibitory neocortical interneuron . Excitatory synapses from regular-spiking ( RS ) pyramidal neurons to LTS cells strongly facilitate when activated repetitively , whereas RS-to-FS synapses depress .... | The brain consists of circuits of neurons that signal to one another via synapses . There are two classes of neurons: excitatory cells , which cause other neurons to become more active , and inhibitory neurons , which cause other neurons to become less active . It is thought that the activity of excitatory neurons is k... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"circuit",
"models",
"computational",
"neuroscience",
"biology",
"neuroscience"
] | 2011 | LTS and FS Inhibitory Interneurons, Short-Term Synaptic Plasticity, and Cortical Circuit Dynamics |
Rabies , a fatal but preventable zoonosis , is a major public health problem in developing countries . In Cambodia the disease burden is largely underestimated because patients with encephalitis following dog bites are rarely hospitalized and die at home . Since 1998 Institut Pasteur in Cambodia ( IPC ) , Phnom Penh ha... | In Cambodia , rabies still elicits fear in the communities . Since 1998 the Institut Pasteur in Cambodia ( IPC ) , Phnom Penh has been the only source of free post-exposure prophylaxis ( PEP ) and post mortem diagnosis . During 1998–2007 , on average ∼12 , 400 patients received PEP annually at IPC ( range 8 , 907–14 , ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"public",
"health",
"and",
"epidemiology/infectious",
"diseases"
] | 2009 | Rabies Situation in Cambodia |
Chikungunya virus ( CHIKV ) is a mosquito-transmitted alphavirus that causes high fever , rash , and recurrent arthritis in humans . It has efficiently adapted to Aedes albopictus , which also inhabits temperate regions , including Europe and the United States of America . In the past , CHIKV has mainly affected develo... | The chikungunya virus ( CHIKV ) glycoprotein E2 mediates cell attachment and consists of three domains A , B and C . Since the cell entry process of CHIKV is not understood in detail , we analyzed the binding properties of the three E2 domains with proteins expressed in E . coli or as Fc-fusion proteins and the role of... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"cell",
"binding",
"flow",
"cytometry",
"cell",
"physiology",
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"togaviruses",
"chikungunya",
"infection",
"viral",
"transmission",
"and",
"infection",
"293t",
"cells",
"pathogens",
"... | 2017 | Identification of Functional Determinants in the Chikungunya Virus E2 Protein |
Neurocysticercosis ( NCC ) , a helminth infection of the brain , is a major cause of seizures . The mediators responsible for seizures in NCC are unknown , and their management remains controversial . Substance P ( SP ) is a neuropeptide produced by neurons , endothelial cells and immunocytes . The current studies exam... | Neurocysticercosis ( NCC ) , is a helminth infection of the brain that is caused by Taenia solium . NCC is the major cause of acquired seizures worldwide . Live Taenia solium parasites in the brain of NCC patients are surrounded by little or no inflammation . Seizures are thought to result not from parasitic infection ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"infectious",
"diseases",
"global",
"health",
"parasitic",
"diseases"
] | 2012 | Substance P Causes Seizures in Neurocysticercosis |
Plasmodium vivax and Hepatitis B virus ( HBV ) are globally outspread in similar geographic regions . The concurrence of both infections and its association with some degree of protection against symptomatic and/or severe vivax malaria has been already described . Nevertheless , data on how host response to both pathog... | The determinants of the diverse clinical presentations of Plasmodium vivax malaria are not completely understood . Previous studies have reported that P . vivax-HBV coinfection is associated with increased odds of presenting with asymptomatic malaria , but little is known about the immune mechanisms driving such associ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"parasite",
"groups",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"plasmodium",
"pathogens",
"immunology",
"tropical",
"diseases",
"microbiology",
"biomarkers",
... | 2019 | Chronic hepatitis B virus infection drives changes in systemic immune activation profile in patients coinfected with Plasmodium vivax malaria |
Envenoming induced by Bothrops snakebites is characterized by drastic local tissue damage that involves an intense inflammatory reaction and local hyperalgesia which are not neutralized by conventional antivenom treatment . Herein , the effectiveness of photobiomodulation to reduce inflammatory hyperalgesia induced by ... | Envenoming caused by Bothrops snakes is characterized by drastic local tissue damage involving hemorrhage , blistering , myonecrosis , prominent inflammatory response and intense pain . The most effective treatment for Bothrops snakebites is antivenom therapy , which is very efficient in reversing systemic effects of e... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"toxins",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"cytokines",
"engineering",
"and",
"technology",
"nervous",
"system",
"lasers",
"immunology",
"tropical",
"diseases",
... | 2016 | Analgesic Effect of Photobiomodulation on Bothrops Moojeni Venom-Induced Hyperalgesia: A Mechanism Dependent on Neuronal Inhibition, Cytokines and Kinin Receptors Modulation |
Champagne coat color in horses is controlled by a single , autosomal-dominant gene ( CH ) . The phenotype produced by this gene is valued by many horse breeders , but can be difficult to distinguish from the effect produced by the Cream coat color dilution gene ( CR ) . Three sires and their families segregating for CH... | The purpose of this study was to uncover the molecular basis for the champagne hair color dilution phenotype in horses . Here , we report a DNA base substitution in the second exon of the horse gene SLC36A1 that changes an amino acid in the transmembrane domain of the protein from threonine to arginine . The phenotypic... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"genetics",
"and",
"genomics/gene",
"discovery",
"genetics",
"and",
"genomics/comparative",
"genomics",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/gene",
"function",
"genetics",
"and",
"genomics"
] | 2008 | Missense Mutation in Exon 2 of SLC36A1 Responsible for Champagne Dilution in Horses |
H1 linker histones facilitate higher-order chromatin folding and are essential for mammalian development . To achieve high-resolution mapping of H1 variants H1d and H1c in embryonic stem cells ( ESCs ) , we have established a knock-in system and shown that the N-terminally tagged H1 proteins are functionally interchang... | Embryonic stem cells ( ESCs ) possess unique chromatin and epigenetic signatures , which are important in defining the identity and genome plasticity of pluripotent stem cells . Although ESC epigenomes have been extensively characterized , the genome localization of histone H1 variants , the chromatin structural protei... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"chromosome",
"structure",
"and",
"function",
"gene",
"regulation",
"dna",
"transcription",
"gene",
"function",
"histone",
"modification",
"genome",
"sequencing",
"developmental",
"biology",
"stem",
"cells",
"epigenetics",
"molecular",
"genetics",
"chromatin",
"chromosome... | 2013 | High-Resolution Mapping of H1 Linker Histone Variants in Embryonic Stem Cells |
Human movement is a key behavioral factor in many vector-borne disease systems because it influences exposure to vectors and thus the transmission of pathogens . Human movement transcends spatial and temporal scales with different influences on disease dynamics . Here we develop a conceptual model to evaluate the impor... | Vector-borne diseases constitute a largely neglected and enormous burden on public health in many resource-challenged environments , demanding efficient control strategies that could be developed through improved understanding of pathogen transmission . Human movement—which determines exposure to vectors—is a key behav... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"ecology/behavioral",
"ecology",
"infectious",
"diseases/neglected",
"tropical",
"diseases",
"infectious",
"diseases/viral",
"infections",
"public",
"health",
"and",
"epidemiology/social",
"and",
"behavioral",
"determinants",
"of",
"health",
"ecology... | 2009 | The Role of Human Movement in the Transmission of Vector-Borne Pathogens |
Genetic variants underlying complex traits , including disease susceptibility , are enriched within the transcriptional regulatory elements , promoters and enhancers . There is emerging evidence that regulatory elements associated with particular traits or diseases share similar patterns of transcriptional activity . A... | We discover that genetic variants associated with specific diseases have more in common with each other than we have previously seen . Specifically , variants associated with the same disease tend to be in parts of the genome that are turned on or off in similar complex patterns across many different cell types . We di... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"and",
"health",
"sciences",
"crohn's",
"disease",
"gene",
"regulation",
"immunology",
"ulcerative",
"colitis",
"colitis",
"cell",
"signaling",
"clinical",
"medicine",
"mathematics",
"gastroenterology",
"and",
"hepatolo... | 2018 | Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease |
Functional genomics screens using multi-parametric assays are powerful approaches for identifying genes involved in particular cellular processes . However , they suffer from problems like noise , and often provide little insight into molecular mechanisms . A bottleneck for addressing these issues is the lack of comput... | Genome-scale functional genomics screens are important tools for investigating the function of genes . Technological progress allows for the simultaneous measurement of multiple parameters quantifying the response of cells to gene perturbations such as RNA interference . Such multi-dimensional screens provide rich data... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"signal",
"transduction",
"functional",
"genomics",
"cell",
"biology",
"genetics",
"biology",
"and",
"life",
"sciences",
"genomics",
"molecular",
"cell",
"biology",
"computational",
"biology"
] | 2014 | Revealing Molecular Mechanisms by Integrating High-Dimensional Functional Screens with Protein Interaction Data |
Due to the risk of severe vaccine-associated adverse events , yellow fever vaccination in Brazil is only recommended in areas considered at risk for disease . From September 2008 through June 2009 , two outbreaks of yellow fever in previously unvaccinated populations resulted in 21 confirmed cases with 9 deaths ( case-... | Yellow fever is a viral hemorrhagic disease transmitted by mosquitos , endemic in tropical regions of Africa and South America . Large urban outbreaks of yellow fever have been eliminated in the Americas , where most yellow fever cases result from human exposure to jungle or forested environments . Vaccination is effec... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"yellow",
"fever",
"immunizations",
"medicine",
"infectious",
"diseases",
"veterinary",
"diseases",
"veterinary",
"virology",
"zoonotic",
"diseases",
"viral",
"diseases",
"public",
"health",
"veterinary",
"science"
] | 2014 | Yellow Fever Outbreaks in Unvaccinated Populations, Brazil, 2008–2009 |
Nucleos ( t ) ide analog therapy blocks DNA synthesis by the hepatitis B virus ( HBV ) reverse transcriptase and can control the infection , but treatment is life-long and has high costs and unpredictable long-term side effects . The profound suppression of HBV by the nucleos ( t ) ide analogs and their ability to cure... | Current therapy for HBV blocks DNA synthesis by the viral reverse transcriptase and can control the infection indefinitely , but treatment rarely cures patients . More patients could be cured by suppressing HBV replication further using a new drug in combination with the existing ones . The HBV RNAseH is a logical drug... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"drugs",
"and",
"devices",
"viral",
"enzymes",
"microbiology",
"hepatitis",
"pharmacology",
"infectious",
"diseases",
"proteins",
"hiv",
"biology",
"recombinant",
"proteins",
"viral",
"replication",
"drug",
"discovery",
"biochemistry",
"hiv",
"diagnosis",
"a... | 2013 | The Hepatitis B Virus Ribonuclease H Is Sensitive to Inhibitors of the Human Immunodeficiency Virus Ribonuclease H and Integrase Enzymes |
Diseases of protein folding arise because of the inability of an altered peptide sequence to properly engage protein homeostasis components that direct protein folding and function . To identify global principles of misfolding disease pathology we examined the impact of the local folding environment in alpha-1-antitryp... | The function of all proteins is dependent on achieving the correct folded state , a process referred to as protein homeostasis or proteostasis . Cellular proteostasis is maintained by diverse signaling pathways , including the heat shock response ( HSR ) , which protects proteins in the face of acute stress . However ,... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"heat",
"shock",
"response",
"cellular",
"stress",
"responses",
"medicine",
"and",
"health",
"sciences",
"cell",
"biology",
"proteins",
"protein",
"structure",
"biology",
"and",
"life",
"sciences",
"cell",
"processes",
"cystic",
"fibrosis",
"transmembr... | 2014 | Modulation of the Maladaptive Stress Response to Manage Diseases of Protein Folding |
The development of a functional nervous system requires tight control of neurite growth and guidance by extracellular chemical cues . Neurite growth is astonishingly sensitive to shallow concentration gradients , but a widely observed feature of both growth and guidance regulation , with important consequences for deve... | For the brain to become wired up during development , growing nerve fibres use molecular guidance factors to navigate over long distances and find their appropriate targets . However , the ability of nerve fibres to do this is severely limited by the loss of both growth and guidance as the concentration of guidance fac... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"physiology",
"cytokines",
"pathology",
"and",
"laboratory",
"medicine",
"immunology",
"signaling",
"networks",
"neurites",
"neuroscience",
"collagens",
"developmental",
"biology",
"signal",
... | 2018 | Control of neurite growth and guidance by an inhibitory cell-body signal |
Salmonella Typhimurium ( S . Tm ) is a common cause of self-limiting diarrhea . The mucosal inflammation is thought to arise from a standoff between the pathogen's virulence factors and the host's mucosal innate immune defenses , particularly the mucosal NAIP/NLRC4 inflammasome . However , it had remained unclear how t... | Salmonella Typhimurium is a common cause of foodborne diarrhea . The disease symptoms arise already a few hours after infection . However , it had remained unclear how the immune system can mount the responses eliciting the disease symptoms so quickly . Earlier work in a mouse model had shown that the gut epithelium ex... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"blood",
"cells",
"flow",
"cytometry",
"anatomical",
"pathology",
"innate",
"immune",
"system",
"medicine",
"and",
"health",
"sciences",
"immune",
"cells",
"immune",
"physiology",
"pathology",
"and",
"laboratory",
"medicine",
"cytokines",
"immunology",
"cytopathology",
... | 2016 | An NK Cell Perforin Response Elicited via IL-18 Controls Mucosal Inflammation Kinetics during Salmonella Gut Infection |
Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species . Populations of leatherback turtles ( Dermochelys coriacea ) in the eastern Pacific have declined by >90% during the past two ... | Highly migratory marine animals routinely cross international borders during extensive migrations over thousands of kilometers , thus requiring conservation strategies with information about habitat use and movement patterns . Critically endangered leatherback turtles ( Dermochelys coriacea ) in the eastern Pacific hav... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology",
"science",
"policy",
"evolutionary",
"biology"
] | 2008 | Persistent Leatherback Turtle Migrations Present Opportunities for Conservation |
Viral RNA-host protein interactions are critical for replication of flaviviruses , a genus of positive-strand RNA viruses comprising major vector-borne human pathogens including dengue viruses ( DENV ) . We examined three conserved host RNA-binding proteins ( RBPs ) G3BP1 , G3BP2 and CAPRIN1 in dengue virus ( DENV-2 ) ... | Dengue virus is the most prevalent arbovirus in the world and an increasingly significant public health problem . Development of vaccines and therapeutics has been slowed by poor understanding of viral pathogenesis . Especially , how the virus subverts the host interferon response , a powerful branch of the innate immu... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"biology",
"and",
"life",
"sciences",
"immunology",
"microbiology",
"medicine",
"and",
"health",
"sciences"
] | 2014 | G3BP1, G3BP2 and CAPRIN1 Are Required for Translation of Interferon Stimulated mRNAs and Are Targeted by a Dengue Virus Non-coding RNA |
As scientific advances in perturbing biological systems and technological advances in data acquisition allow the large-scale quantitative analysis of biological function , the robustness of organisms to both transient environmental stresses and inter-generational genetic changes is a fundamental impediment to the ident... | Advances in the ways that living systems can be perturbed in order to study how they function and sharp reductions in the cost of computer resources have allowed the collection of large amounts of data . The aim of biological system modeling is to analyze this data in order to pin down the precise interactions of molec... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"systems",
"biology",
"biology",
"computational",
"biology"
] | 2014 | A Network Characteristic That Correlates Environmental and Genetic Robustness |
Pheromones are used for conspecific communication by many animals . In Drosophila , the volatile male-specific pheromone 11-cis vaccenyl acetate ( cVA ) supplies an important signal for gender recognition . Sensing of cVA by the olfactory system depends on multiple components , including an olfactory receptor ( OR67d )... | Pheromones are chemicals produced and released by animals for social communication with other members of their species . For example , male fruit flies produce a volatile pheromone that is sensed by both males and females , and which functions in gender recognition . This volatile male pheromone , called 11-cis vacceny... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"and",
"life",
"sciences"
] | 2014 | Requirement for Drosophila SNMP1 for Rapid Activation and Termination of Pheromone-Induced Activity |
Chronic kidney disease ( CKD ) is an increasing global public health concern , particularly among populations of African ancestry . We performed an interrogation of known renal loci , genome-wide association ( GWA ) , and IBC candidate-gene SNP association analyses in African Americans from the CARe Renal Consortium . ... | Chronic kidney disease ( CKD ) is an increasing global public health problem and disproportionately affects populations of African ancestry . Many studies have shown that genetic variants are associated with the development of CKD; however , similar studies are lacking in African ancestry populations . The CARe consort... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"genome-wide",
"association",
"studies",
"medicine",
"chronic",
"kidney",
"disease",
"quantitative",
"traits",
"tubulointerstitial",
"disease",
"biology",
"heredity",
"genetic",
"association",
"studies",
"genetics",
"human",
"genetics",
"genetics",
"of",
"disease",
"nephr... | 2011 | Genetic Association for Renal Traits among Participants of African Ancestry Reveals New Loci for Renal Function |
Non-autonomous cell-death is a cardinal feature of the disintegration of neural networks in neurodegenerative diseases , but the molecular bases of this process are poorly understood . The neural retina comprises a mosaic of rod and cone photoreceptors . Cone and rod photoreceptors degenerate upon rod-specific expressi... | The secondary demise of healthy neurons upon the degeneration of neurons harboring primary genetic defect ( s ) is hallmark to neurodegenerative diseases . However , the factors and mechanisms driving these cell-death processes are not understood , a severe limitation which has hampered the therapeutic development of n... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"death",
"molecular",
"neuroscience",
"neurobiology",
"of",
"disease",
"and",
"regeneration",
"gene",
"regulation",
"neuroscience",
"animal",
"models",
"model",
"organisms",
"molecular",
"genetics",
"biology",
"mouse",
"visual",
"system",
"cellular",
"neuroscien... | 2013 | Distinct and Atypical Intrinsic and Extrinsic Cell Death Pathways between Photoreceptor Cell Types upon Specific Ablation of Ranbp2 in Cone Photoreceptors |
Lymphatic filariasis can be associated with development of serious pathology in the form of lymphedema , hydrocele , and elephantiasis in a subset of infected patients . Dysregulated host inflammatory responses leading to systemic immune activation are thought to play a central role in filarial disease pathogenesis . W... | Lymphatic filariasis afflicts over 120 million people worldwide . While the infection is mostly clinically asymptomatic , approximately 40 million people suffer from overt , morbid clinical pathology , characterized by swelling of the scrotal area and lower limbs ( hydrocele and lymphedema ) . Host immunologic factors ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"clinical",
"immunology",
"immunology"
] | 2012 | Circulating Microbial Products and Acute Phase Proteins as Markers of Pathogenesis in Lymphatic Filarial Disease |
We have developed a manufacturing strategy that can improve the safety and genetic stability of recombinant live-attenuated chimeric dengue vaccine ( DENVax ) viruses . These viruses , containing the pre-membrane ( prM ) and envelope ( E ) genes of dengue serotypes 1–4 in the replicative background of the attenuated de... | Transmitted by Aedes spp . mosquitoes found worldwide , dengue is the most important mosquito-borne viral disease in the world . The incidence of dengue has increased 30-fold over the past 50 years , and is now endemic in over 100 countries . Vaccination is believed to be one of the most effective strategies in dengue ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"virology",
"viral",
"vaccines",
"biology",
"microbiology"
] | 2013 | Genetic and Phenotypic Characterization of Manufacturing Seeds for a Tetravalent Dengue Vaccine (DENVax) |
Iron is essential for a wide range of cellular processes . Here we show that the bZIP-type regulator HapX is indispensable for the transcriptional remodeling required for adaption to iron starvation in the opportunistic fungal pathogen Aspergillus fumigatus . HapX represses iron-dependent and mitochondrial-localized ac... | Due to its requirement for a wide range of cellular processes , iron is an essential nutrient for virtually every organism . The mammalian immune system utilizes iron-withholding mechanisms to deny access to free iron . Therefore , pathogens must overcome extreme iron limitation . Patients with suppressed immune system... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Methods"
] | [
"biochemistry",
"genetics",
"and",
"genomics/gene",
"expression",
"genetics",
"and",
"genomics/functional",
"genomics",
"infectious",
"diseases/fungal",
"infections",
"microbiology/microbial",
"physiology",
"and",
"metabolism",
"microbiology/microbial",
"growth",
"and",
"develo... | 2010 | HapX-Mediated Adaption to Iron Starvation Is Crucial for Virulence of Aspergillus fumigatus |
The fusion of two distinct prominences into one continuous structure is common during development and typically requires integration of two epithelia and subsequent removal of that intervening epithelium . Using confocal live imaging , we directly observed the cellular processes underlying tissue fusion , using the sec... | Tissue fusion , the process by which two independent prominences become united to form one continuous structure , is common during development , and its failure leads to multiple structural birth defects . In this study , we directly examine the cellular and molecular mechanisms by which tissue fusion occurs using the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Convergence and Extrusion Are Required for Normal Fusion of the Mammalian Secondary Palate |
Venezuelan equine encephalitis ( VEE ) is a re-emerging , mosquito-borne viral disease with the potential to cause fatal encephalitis in both humans and equids . Recently , detection of endemic VEE caused by enzootic strains has escalated in Mexico , Peru , Bolivia , Colombia and Ecuador , emphasizing the importance of... | Venezuelan equine encephalitis virus ( VEEV ) is transmitted to humans and horses by mosquitoes in Mexico , Central and South America . These infections can lead to fatal encephalitis in humans as well as horses , donkeys and mules , and there are no licensed vaccines or treatments available for humans . VEEV circulate... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"ecology",
"viral",
"transmission",
"and",
"infection",
"vector",
"biology",
"virology",
"biology",
"microbiology"
] | 2012 | Genetic and Anatomic Determinants of Enzootic Venezuelan Equine Encephalitis Virus Infection of Culex (Melanoconion) taeniopus |
How the molecular mechanisms of stress response are integrated at the cellular level remains obscure . Here we show that the cellular polarity machinery in the fission yeast Schizosaccharomyces pombe undergoes dynamic adaptation to thermal stress resulting in a period of decreased Cdc42 activity and altered , monopolar... | Heat stress , caused by fluctuations in ambient temperature , occurs frequently in nature . How organisms adapt and maintain regular patterns of growth over a range of environmental conditions remain poorly understood . Our work in the simple unicellular yeast Schizosaccharomyces pombe suggests that the heat stress-ass... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2013 | Hsp70-Hsp40 Chaperone Complex Functions in Controlling Polarized Growth by Repressing Hsf1-Driven Heat Stress-Associated Transcription |
Neurotrophic interactions occur in Drosophila , but to date , no neurotrophic factor had been found . Neurotrophins are the main vertebrate secreted signalling molecules that link nervous system structure and function: they regulate neuronal survival , targeting , synaptic plasticity , memory and cognition . We have id... | Neurotrophins are secreted proteins that link nervous system structure and function in vertebrates . They regulate neuronal survival , thus adjusting cell populations , and connectivity , enabling the formation of neuronal circuits . They also regulate patterns of dendrites and axons , synaptic function , memory , lear... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"developmental",
"biology",
"evolutionary",
"biology",
"neuroscience",
"molecular",
"biology",
"genetics",
"and",
"genomics"
] | 2008 | Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation |
Hepadnavirus at very low doses establishes in woodchucks asymptomatic , serologically undetectable but molecularly evident persistent infection . This primary occult infection ( POI ) preferentially engages the immune system and initiates virus-specific T cell response in the absence of antiviral antibody induction . T... | Introduction of highly sensitive molecular assays for detection of hepatitis B virus ( HBV ) identified the existence of persistent occult HBV infection years after recovery from an episode of hepatitis B and in individuals exposed to HBV but without symptoms and classical markers of infection . Because HBV integrates ... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"infectious",
"diseases",
"infectious",
"disease",
"immunology",
"medicine",
"and",
"health",
"sciences",
"infectious",
"hepatitis",
"hepatitis",
"b",
"hepatitis",
"clinical",
"immunology",
"gastroenterology",
"and",
"hepatology",
"biology",
"and",
"life",
"sciences",
"... | 2014 | Primary Seronegative but Molecularly Evident Hepadnaviral Infection Engages Liver and Induces Hepatocarcinoma in the Woodchuck Model of Hepatitis B |
PARN is one of several deadenylase enzymes present in mammalian cells , and as such the contribution it makes to the regulation of gene expression is unclear . To address this , we performed global mRNA expression and half-life analysis on mouse myoblasts depleted of PARN . PARN knockdown resulted in the stabilization ... | Almost all cellular mRNAs terminate in a 3′ poly ( A ) tail , the removal of which can induce both translational silencing and mRNA decay . Mammalian cells encode many poly ( A ) -specific exoribonucleases , but their individual roles are poorly understood . Here , we undertook an analysis of the role of PARN deadenyla... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"medicine",
"genome",
"expression",
"analysis",
"functional",
"genomics",
"gene",
"regulation",
"anatomy",
"and",
"physiology",
"rna",
"stability",
"muscle",
"molecular",
"genetics",
"musculoskeletal",
"system",
"cell",
"adhesion",
"extracellular",
"matrix",
"gene",
"ex... | 2012 | The PARN Deadenylase Targets a Discrete Set of mRNAs for Decay and Regulates Cell Motility in Mouse Myoblasts |
There is limited information on antivenom pharmacokinetics . This study aimed to investigate the pharmacokinetics of an Indian snake antivenom in humans with Russell’s viper bites . Patient data and serial blood samples were collected from patients with Russell’s viper ( Daboia russelii ) envenoming in Sri Lanka . All ... | Snake envenoming is a neglected tropical disease that affects hundreds of thousands of people in the rural tropics . Antivenom is the main treatment for snake bites but there is limited information on the pharmacokinetics and appropriate dosing regimen . Most studies have been done in animals and dosing guidelines are ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Population Pharmacokinetics of an Indian F(ab')2 Snake Antivenom in Patients with Russell's Viper (Daboia russelii) Bites |
Human movement is likely an important risk factor for environmentally-transmitted pathogens . While epidemiologic studies have traditionally focused on household risk factors , individual movement data could provide critical additional information about risk of exposure to such pathogens . We conducted global positioni... | Environmental features of urban slums including inadequate sanitation , substandard housing , and population crowding predispose residents to numerous infections . Despite this shared environment , not all slum residents , even within households , have equal risk of infection with specific pathogens and we do not know ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"ecology",
"and",
"environmental",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"global",
"positioning",
"system",
"engineering",
"and",
"technology",
"pathogens",
"tropical",
"diseases",
"geographical",
"locations",
... | 2018 | Fine-scale GPS tracking to quantify human movement patterns and exposure to leptospires in the urban slum environment |
Environmentally mediated infectious disease transmission models provide a mechanistic approach to examining environmental interventions for outbreaks , such as water treatment or surface decontamination . The shift from the classical SIR framework to one incorporating the environment requires codifying the relationship... | Many infectious disease interventions , including water treatment , hand hygiene , and surface decontamination , target pathogens in the environment . Explicitly modeling the concentration of pathogens in the environment within transmission models can be a useful way to consider not only the impact of such mitigation e... | [
"Abstract",
"Introduction",
"Models",
"and",
"methods",
"Results",
"and",
"discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"vibrio",
"microbiology",
"cryptosporidium",
"parasitic",
"protozoans",
"physiological",
"processes",
"statistical",
"data",
"vibrio",
"cholerae",
"protozoans",
"mathematics"... | 2017 | Dose-response relationships for environmentally mediated infectious disease transmission models |
Rabbit Hemorrhagic disease virus ( RHDV ) , a calicivirus of the Lagovirus genus , and responsible for rabbit hemorrhagic disease ( RHD ) , kills rabbits between 48 to 72 hours post infection with mortality rates as high as 50–90% . Caliciviruses , including noroviruses and RHDV , have been shown to bind histo-blood gr... | Rabbit hemorrhagic disease virus ( RHDV ) , detected as late as 1984 , has spread to large parts of the world , threatening rabbit populations and other species dependent on rabbits in many European countries . Mortality has been shown to be as high as 90% and rabbits are killed 48 to 72 hours after infection . Related... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Material",
"and",
"Methods"
] | [
"veterinary",
"diseases",
"emerging",
"infectious",
"diseases",
"veterinary",
"microbiology",
"virology",
"microbial",
"pathogens",
"biology",
"evolutionary",
"biology",
"microbiology",
"host-pathogen",
"interaction",
"evolutionary",
"genetics",
"animal",
"management",
"veter... | 2011 | Histo-Blood Group Antigens Act as Attachment Factors of Rabbit Hemorrhagic Disease Virus Infection in a Virus Strain-Dependent Manner |
The sole report of annual leptospirosis incidence in continental Africa of 75–102 cases per 100 , 000 population is from a study performed in August 2007 through September 2008 in the Kilimanjaro Region of Tanzania . To evaluate the stability of this estimate over time , we estimated the incidence of acute leptospirosi... | Leptospirosis is an infectious disease that causes a fever . It can be severe or fatal . Understanding how many people get leptospirosis helps to determine priorities in allocating resources for disease diagnosis , treatment , and prevention . There are few data about leptospirosis incidence in sub-Saharan African coun... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"leptospira",
"pathology",
"and",
"laboratory",
"medicine",
"infectious",
"disease",
"epidemiology",
"pathogens",
"tropical",
"diseases",
"geographical",
"locations",
"microbiology",
"census",
"bacterial",
"diseases",
"research",
"... | 2016 | Comparison of the Estimated Incidence of Acute Leptospirosis in the Kilimanjaro Region of Tanzania between 2007–08 and 2012–14 |
Woolly mammoths inhabited Eurasia and North America from late Middle Pleistocene ( 300 ky BP [300 , 000 years before present] ) , surviving through different climatic cycles until they vanished in the Holocene ( 3 . 6 ky BP ) . The debate about why the Late Quaternary extinctions occurred has centred upon environmental... | What caused the woolly mammoth's extinction ? Climate warming in the Holocene might have driven the extinction of this cold-adapted species , yet the species had survived previous warming periods , suggesting that the more-plausible cause was human expansion . Testing these competing hypotheses has been hampered by the... | [
"Abstract",
"Introduction",
"Results",
"and",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"ecology"
] | 2008 | Climate Change, Humans, and the Extinction of the Woolly Mammoth |
The formation of virus movement protein ( MP ) -containing punctate structures on the cortical endoplasmic reticulum is required for efficient intercellular movement of Red clover necrotic mosaic virus ( RCNMV ) , a bipartite positive-strand RNA plant virus . We found that these cortical punctate structures constitute ... | Intercellular movement of plant viruses is the crucial step during systemic viral infections . Red clover necrotic mosaic virus ( RCNMV ) , a bipartite positive-strand RNA plant virus , forms movement protein ( MP ) -containing punctate structures on the cortical endoplasmic reticulum in infected cells , which are requ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology",
"virology",
"biology",
"and",
"life",
"sciences",
"microbiology",
"molecular",
"cell",
"biology",
"cellular",
"structures",
"and",
"organelles"
] | 2014 | GAPDH-A Recruits a Plant Virus Movement Protein to Cortical Virus Replication Complexes to Facilitate Viral Cell-to-Cell Movement |
DNA–protein interactions are involved in many essential biological activities . Because there is no simple mapping code between DNA base pairs and protein amino acids , the prediction of DNA–protein interactions is a challenging problem . Here , we present a novel computational approach for predicting DNA-binding prote... | Many essential biological activities require interactions between DNA and proteins . These proteins usually use certain amino acids , called DNA-binding sites , to recognize their specific DNA targets . To facilitate the search of its specific DNA targets , a DNA-binding protein often associates with nonspecific DNA an... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"computational",
"biology/macromolecular",
"structure",
"analysis",
"biophysics/macromolecular",
"assemblies",
"and",
"machines",
"biophysics/structural",
"genomics",
"computational",
"biology/protein",
"structure",
"prediction"
] | 2009 | From Nonspecific DNA–Protein Encounter Complexes to the
Prediction of DNA–Protein Interactions |
Recent years have seen a rapid increase in the number of rabies cases in China and an expansion in the geographic distribution of the virus . In spite of the seriousness of the outbreak and increasing number of fatalities , little is known about the phylogeography of the disease in China . In this study , we report an ... | Rabies is a major problem in developing countries and responsible for more than 55 , 000 deaths annually . More than half of the cases occur in Asia and China has the second highest incidence of rabies after India . Human rabies cases in China decreased during the early 1990s but the virus began to re-emerge in the lat... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"public",
"health",
"and",
"epidemiology",
"spatial",
"epidemiology",
"phylogenetics",
"rabies",
"neglected",
"tropical",
"diseases",
"population",
"biology",
"veterinary",
"science",
"infectious",
"diseases",
"veterinary",
"diseases",
"zoonotic",
"diseases",
... | 2012 | The Spatial and Temporal Dynamics of Rabies in China |
The emerging arthritogenic , mosquito-borne chikungunya virus ( CHIKV ) causes severe disease in humans and represents a serious public health threat in countries where Aedes spp mosquitoes are present . This study describes for the first time the successful production of CHIKV virus-like particles ( VLPs ) in insect c... | Viruses that are transmitted by mosquitoes represent major threats for human health all over the world . One of these viruses is the Chikungunya virus ( CHIKV ) . CHIKV is transmitted by the Asian Tiger mosquito , which is making ground to more temperate regions such as Europe , and thereby increasing the risk of CHIKV... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"infectious",
"diseases",
"viral",
"vaccines",
"adaptive",
"immunity",
"viruslike",
"particles",
"emerging",
"infectious",
"diseases",
"immunity",
"virology",
"neglected",
"tropical",
"diseases",
"biology",
"microbiology",
"arboviral",
"infections",
"infectious"... | 2013 | Effective Chikungunya Virus-like Particle Vaccine Produced in Insect Cells |
In female mammals , activation of Xist ( X-inactive specific transcript ) is essential for establishment of X chromosome inactivation . During early embryonic development in mice , paternal Xist is preferentially expressed whereas maternal Xist ( Xm-Xist ) is silenced . Unlike autosomal imprinted genes , Xist imprintin... | X-inactive specific transcript ( Xist ) is essential a large non-coding RNA for establishment of X chromosome inactivation in female mammals . The aberrant X chromosome inactivation critically affects cellular viability . Therefore , spatiotemporal regulation of Xist expression is required for proper development . In m... | [
"Abstract",
"Introduction",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"condensation",
"gene",
"regulation",
"rna",
"analysis",
"condensed",
"matter",
"physics",
"germ",
"cells",
"developmental",
"biology",
"oocytes",
"epigenetics",
"molecular",
"biology",
"techniques",
"embryos",
"mammalian",
"genomics",
"chromatin",
"research",
"and",
"a... | 2016 | Maintenance of Xist Imprinting Depends on Chromatin Condensation State and Rnf12 Dosage in Mice |
Human African Trypanosomiasis ( HAT ) , a disease caused by protozoan parasites transmitted by tsetse flies , is an important neglected tropical disease endemic in remote regions of sub-Saharan Africa . Although the determination of the burden of HAT has been based on incidence , mortality and morbidity rates , the tru... | Sleeping sickness affects people often living in remote rural areas and those who mainly depend on subsistence agriculture . We carried out a study among former sleeping sickness patients in Kenya to find out the socio-economic challenges they faced in seeking treatment and the coping strategies they used to deal with ... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"children",
"medicine",
"and",
"health",
"sciences",
"education",
"african",
"trypanosomiasis",
"sociology",
"tropical",
"diseases",
"geographical",
"locations",
"social",
"sciences",
"parasitic",
"diseases",
"health",
"care",
"age",
"groups",
"human",
"families",
"negl... | 2017 | The socio-economic burden of human African trypanosomiasis and the coping strategies of households in the South Western Kenya foci |
Malaria drug resistance contributes to up to a million annual deaths . Judicious deployment of new antimalarials and vaccines could benefit from an understanding of early molecular events that promote the evolution of parasites . Continuous in vitro challenge of Plasmodium falciparum parasites with a novel dihydroorota... | Malaria parasites kill up to a million people around the world every year . Emergence of resistance to drugs remains a key obstacle against elimination of malaria . In the laboratory , parasites can efficiently acquire resistance to experimental antimalarials by changing DNA at the target locus . This happens efficient... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biochemistry",
"genome",
"evolution",
"parasite",
"evolution",
"parasitology",
"biology",
"genomics",
"microbiology",
"drug",
"discovery"
] | 2013 | Asexual Populations of the Human Malaria Parasite, Plasmodium falciparum, Use a Two-Step Genomic Strategy to Acquire Accurate, Beneficial DNA Amplifications |
The speed of stem cell differentiation has to be properly coupled with self-renewal , both under basal conditions for tissue maintenance and during regeneration for tissue repair . Using the Drosophila midgut model , we analyze at the cellular and molecular levels the differentiation program required for robust regener... | Adult tissue/organ function is maintained by stem cells . Key question in stem cell biology is how the pool of stem cells can be robustly expanded yet timely contracted through differentiation according to the need of a tissue . Over the last years , the mechanisms underlying stem cell activation have been extensively ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"cancers",
"and",
"neoplasms",
"cloning",
"animals",
"notch",
"signaling",
"cell",
"differentiation",
"oncology",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
... | 2017 | A genetic framework controlling the differentiation of intestinal stem cells during regeneration in Drosophila |
The retinoblastoma tumor suppressor ( Rb ) is a potent and ubiquitously expressed cell cycle regulator , but patients with a germline Rb mutation develop a very specific tumor spectrum . This surprising observation raises the possibility that mechanisms that compensate for loss of Rb function are present or activated i... | The retinoblastoma tumor suppressor Rb belongs to a family of cell cycle inhibitors along with the related proteins p107 and p130 . Strong evidence indicates that the three family members have both specific and overlapping functions and expression patterns in mammalian cells , including in cancer cells . However , the ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"cell",
"biology/gene",
"expression"
] | 2010 | Tandem E2F Binding Sites in the Promoter of the p107 Cell Cycle Regulator Control p107 Expression and Its Cellular Functions |
The incidence of human brucellosis in Kyrgyzstan has been increasing in the last years and was identified as a priority disease needing most urgent control measures in the livestock population . The latest species identification of Brucella isolates in Kyrgyzstan was carried out in the 1960s and investigated the circul... | Brucellosis is a bacterial disease causing abortion in cattle , sheep , and goats . It is transmissible to humans by direct transmission and the consumption of untreated milk . Brucellosis has become more and more frequent in Kyrgyzstan in the last decades , and its control has been made a priority . Knowing the bacter... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion",
"Conclusion"
] | [
"medicine",
"infectious",
"diseases",
"public",
"health",
"and",
"epidemiology",
"veterinary",
"epidemiology",
"veterinary",
"microbiology",
"medical",
"microbiology",
"epidemiology",
"biology",
"microbiology",
"public",
"health",
"veterinary",
"science"
] | 2013 | Molecular Epidemiology and Antibiotic Susceptibility of Livestock Brucella melitensis Isolates from Naryn Oblast, Kyrgyzstan |
Many emerging infections are RNA virus spillovers from animal reservoirs . Reservoir identification is necessary for predicting the geographic extent of infection risk , but rarely are taxonomic levels below the animal species considered as reservoir , and only key circumstances in nature and methodology allow intrinsi... | Reservoirs of zoonotic viruses are usually equated with a particular wildlife species . It is rarely assessed whether genetic groups below the species level may instead represent the actual reservoir , though this would have major implications on estimations of the zoonosis’ spatial distribution . Here we investigate w... | [
"Abstract",
"Introduction",
"Methods",
"Data",
"Archiving",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"pathology",
"and",
"laboratory",
"medicine",
"pathogens",
"rna",
"extraction",
"microbiology",
"vertebrates",
"geographical",
"locations",
"animals",
"mammals",
"viruses",
"rna",
"viruses",
"phylogenetic",
"analysis",
"mitochondri... | 2017 | When Viruses Don’t Go Viral: The Importance of Host Phylogeographic Structure in the Spatial Spread of Arenaviruses |
Resistance emergence against antileishmanial drugs , particularly Sodium Antimony Gluconate ( SAG ) has severely hampered the therapeutic strategy against visceral leishmaniasis , the mechanism of resistance being indistinguishable . Cysteine leucine rich protein ( CLrP ) , was recognized as one of the overexpressed pr... | Leishmania causes complex of pathologies called Leishmaniasis and among the several forms visceral leishmaniasis is the precarious one as being fatal , if left untreated . Emergence of resistance against several antileishmanials particularly Sodium Antimony Gluconate ( SAG ) has severely battered the therapeutic strate... | [
"Abstract",
"Introduction",
"Materials",
"and",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | Over-Expression of Cysteine Leucine Rich Protein Is Related to SAG Resistance in Clinical Isolates of Leishmania donovani |
Brain-wide interactions generating complex neural dynamics are considered crucial for emergent cognitive functions . However , the irreducible nature of nonlinear and high-dimensional dynamical interactions challenges conventional reductionist approaches . We introduce a model-free method , based on embedding theorems ... | Advances in recording technologies have enabled the acquisition of neuronal dynamics data at unprecedented scale and resolution , but the increase in data complexity challenges reductionist model-based approaches . Motivated by generic theorems of dynamical systems , we characterize model-free , nonlinear embedding rel... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [] | 2015 | Untangling Brain-Wide Dynamics in Consciousness by Cross-Embedding |
Dogs , with their breed-determined limited genetic background , are great models of human disease including cancer . Canine B-cell lymphoma and hemangiosarcoma are both malignancies of the hematologic system that are clinically and histologically similar to human B-cell non-Hodgkin lymphoma and angiosarcoma , respectiv... | To shed light on the genetic predisposition to cancers of the hematologic system , we performed genome-wide association analysis of affected and non-affected pet dogs . Dogs naturally develop the same diseases as humans , including cancer , and the relatively limited genetic diversity within different breeds makes gene... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [] | 2015 | Genome-wide Association Study Identifies Shared Risk Loci Common to Two Malignancies in Golden Retrievers |
Mutation is fundamental to evolution , because it generates the genetic variation on which selection can act . In nature , genetic changes often increase the mutation rate in systems that range from viruses and bacteria to human tumors . Such an increase promotes the accumulation of frequent deleterious or neutral alle... | Mutation is of central importance in biology . It creates genetic variation , the raw material of evolution by natural selection , It can improve traits and organisms , but can also lead to phenomena like cancerous cells and antibiotic resistant pathogens . Increasing the mutation rate can accelerate evolutionary adapt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Methods"
] | [
"medicine",
"and",
"health",
"sciences",
"genome",
"evolution",
"population",
"genetics",
"oncology",
"mutation",
"nonsense",
"mutation",
"evolutionary",
"adaptation",
"population",
"biology",
"population",
"density",
"molecular",
"evolution",
"evolutionary",
"genetics",
... | 2018 | High mutation rates limit evolutionary adaptation in Escherichia coli |
This study evaluates the diagnostic accuracy and cost-effectiveness of the Kato-Katz and Mini-FLOTAC methods for detection of soil-transmitted helminths ( STH ) in a post-treatment setting in western Kenya . A cost analysis also explores the cost implications of collecting samples during school surveys when compared to... | Accurate methods of diagnosis and optimal strategies to sample the population are essential for the reliable mapping and surveillance of infectious diseases . The current standard for detection of soil-transmitted helminths ( STH ) entails use of the Kato-Katz diagnostic method . Alternative diagnostic methods , such a... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [
"medicine",
"and",
"health",
"sciences",
"cost-effectiveness",
"analysis",
"infectious",
"disease",
"epidemiology",
"economic",
"analysis",
"tropical",
"diseases",
"social",
"sciences",
"parasitic",
"diseases",
"health",
"care",
"research",
"design",
"global",
"health",
... | 2014 | Diagnostic Accuracy and Cost-Effectiveness of Alternative Methods for Detection of Soil-Transmitted Helminths in a Post-Treatment Setting in Western Kenya |
The Kaposi's sarcoma-associated herpesvirus ( KSHV ) protein kinase , encoded by ORF36 , functions to phosphorylate cellular and viral targets important in the KSHV lifecycle and to activate the anti-viral prodrug ganciclovir . Unlike the vast majority of mapped KSHV genes , no viral transcript has been identified with... | Kaposi's sarcoma-associated herpesvirus ( KSHV ) is the etiologic agent of multicentric Castleman's disease , primary effusion lymphoma and Kaposi's sarcoma . KSHV expresses a number of transcripts with the potential to generate multiple proteins , yet relies on the cellular translation machinery that is primed to synt... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"virology",
"viruses",
"and",
"cancer",
"viral",
"enzymes",
"biology",
"microbiology",
"viral",
"replication"
] | 2013 | Dual Short Upstream Open Reading Frames Control Translation of a Herpesviral Polycistronic mRNA |
Given the disposability of somatic tissue , selection can favor a higher mutation rate in the early segregating soma than in germline , as seen in some animals . Although in plants intra-organismic mutation rate heterogeneity is poorly resolved , the same selectionist logic can predict a lower rate in shoot than in roo... | Whereas there has been considerable attention paid to understanding differences in the mutation rate between different species , much less is known about variation in the mutation rate within individuals of multicellular species . In animals , evidence suggests that the segregated germline has a lower mutation rate tha... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"methods"
] | [
"biotechnology",
"plant",
"anatomy",
"engineering",
"and",
"technology",
"cell",
"cycle",
"and",
"cell",
"division",
"cell",
"processes",
"trees",
"mutation",
"substitution",
"mutation",
"plant",
"science",
"peach",
"trees",
"plant",
"genomics",
"plants",
"extraction"... | 2019 | The architecture of intra-organism mutation rate variation in plants |
Increased availability of Next Generation Sequencing ( NGS ) techniques allows , for the first time , to distinguish relapses from reinfections in patients with multiple Buruli ulcer ( BU ) episodes . We compared the number and location of single nucleotide polymorphisms ( SNPs ) identified by genomic screening between... | We compared the whole genomes of four pairs of Mycobacterium ulcerans isolates collected at the time of first diagnosis and at recurrence , derived from a collection of almost 5000 well characterized clinical samples from one BU treatment center in Benin . Our findings suggest that after surgical treatment—without anti... | [
"Abstract",
"Introduction",
"Methods",
"Results",
"Discussion"
] | [] | 2015 | A Genomic Approach to Resolving Relapse versus Reinfection among Four Cases of Buruli Ulcer |
Because most efforts to understand the molecular mechanisms underpinning fungal pathogenicity have focused on studying the function and role of individual genes , relatively little is known about how transcriptional machineries globally regulate and coordinate the expression of a large group of genes involved in pathog... | Rice blast disease , caused by Magnaporthe oryzae , destroys rice crop enough to feed 60 million people every year and has served as a model pathosystem for understanding host-parasite interactions . However , little is known about how M . oryzae globally regulates and coordinates its gene expression at the whole-genom... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"biology",
"agriculture"
] | 2013 | Global Expression Profiling of Transcription Factor Genes Provides New Insights into Pathogenicity and Stress Responses in the Rice Blast Fungus |
In most eutherian mammals , sex chromosomes synapse and recombine during male meiosis in a small region called pseudoautosomal region . However in some species sex chromosomes do not synapse , and how these chromosomes manage to ensure their proper segregation is under discussion . Here we present a study of the meioti... | Meiosis is a special kind of cell division that leads to the formation of gametes . During meiosis the number of chromosomes must be halved in the daughter cells , and to do this properly , most organisms use an amazing strategy: during the first of the two meiotic divisions , homologous chromosomes associate in pairs ... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"mongolian",
"gerbil",
"(meriones",
"unguiculatus)",
"cell",
"biology"
] | 2007 | Meiotic Pairing and Segregation of Achiasmate Sex Chromosomes in Eutherian Mammals: The Role of SYCP3 Protein |
Entamoeba histolytica is an enteric pathogen responsible for amoebic dysentery and liver abscess . It alternates between the host-restricted trophozoite form and the infective environmentally-stable cyst stage . Throughout its lifecycle E . histolytica experiences stress , in part , from host immune pressure . Conversi... | Entamoeba histolytica is the causative agent of amoebic dysentery and liver abscess and is prevalent in underdeveloped countries that lack proper sanitation . Infection is acquired by ingestion of the cyst form in contaminated food or water . During infection , the parasite experiences stress including demanding growth... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods",
"Statistical",
"analysis"
] | [
"phosphorylation",
"antimicrobials",
"trophozoites",
"parasite",
"groups",
"medicine",
"and",
"health",
"sciences",
"chemical",
"compounds",
"oxidative",
"stress",
"drugs",
"microbiology",
"carbohydrates",
"parasitic",
"protozoans",
"polyribosomes",
"parasitology",
"organic",... | 2016 | Phosphorylation of Eukaryotic Initiation Factor-2α during Stress and Encystation in Entamoeba Species |
Gene regulatory networks ( GRNs ) evolve as a result of the coevolutionary processes acting on transcription factors ( TFs ) and the cis-regulatory modules they bind . The zinc-finger TF zelda ( zld ) is essential for the maternal-to-zygotic transition ( MZT ) in Drosophila melanogaster , where it directly binds over t... | Pioneer transcription factors ( TFs ) are considered the first regulators of chromatin accessibility in fruit flies and vertebrates , modulating the expression of a large number of target genes . In fruit flies , zelda resembles a pioneer TF , being essential during early embryogenesis . However , the evolutionary orig... | [
"Abstract",
"Introduction",
"Results/Discussion",
"Materials",
"&",
"methods"
] | [
"invertebrates",
"medicine",
"and",
"health",
"sciences",
"rna",
"interference",
"legs",
"morphogenic",
"segmentation",
"limbs",
"(anatomy)",
"animals",
"animal",
"models",
"developmental",
"biology",
"drosophila",
"melanogaster",
"model",
"organisms",
"animal",
"anatomy"... | 2017 | Evolution and multiple roles of the Pancrustacea specific transcription factor zelda in insects |
Insertions and deletions ( indels ) are a major source of genetic variation within species and may result in functional changes to coding or regulatory sequences . In this study we report that an indel polymorphism in the 3’ untranslated region ( UTR ) of the metallothionein gene MtnA is associated with gene expression... | Although molecular variation is abundant in natural populations , understanding how this variation affects organismal phenotypes that are subject to natural selection remains a major challenge in the field of evolutionary genetics . Here we show that a deletion mutation in a noncoding region of the Drosophila melanogas... | [
"Abstract",
"Introduction",
"Results",
"Discussion",
"Materials",
"and",
"Methods"
] | [
"invertebrates",
"evolutionary",
"biology",
"3'",
"utr",
"oxidative",
"stress",
"messenger",
"rna",
"geographical",
"locations",
"population",
"genetics",
"reporter",
"genes",
"animals",
"animal",
"models",
"drosophila",
"melanogaster",
"model",
"organisms",
"untranslated... | 2016 | An Indel Polymorphism in the MtnA 3' Untranslated Region Is Associated with Gene Expression Variation and Local Adaptation in Drosophila melanogaster |
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