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Mosquito salivary proteins ( MSPs ) modulate the host immune response , leading to enhancement of arboviral infections . Identification of proteins in saliva responsible for immunomodulation and counteracting their effects on host immune response is a potential strategy to protect against arboviral disease . We selecte...	West Nile virus ( WNV ) is a mosquito-borne flavivirus found on all continents except Antarctica . Humans and equines are not part of the natural transmission cycle , but when they become infected severe illness or death can result . There is no human vaccine for WNV available , so novel approaches to preventing infect...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "emerging", "viral", "diseases", "immunology", "microbiology", "host-pathogen", "interaction", "immunomodulation", "immunizations", "animal", "models", "of", "infection", "infectious", "diseases", "biology", "public", ...	2012	Immunization of Mice with Recombinant Mosquito Salivary Protein D7 Enhances Mortality from Subsequent West Nile Virus Infection via Mosquito Bite
Service provider costs for vaccine delivery have been well documented; however , vaccine recipients’ costs have drawn less attention . This research explores the private household out-of-pocket and opportunity costs incurred to receive free oral cholera vaccine during a mass vaccination campaign in rural Odisha , India...	The price of vaccine and the costs of its delivery are two important economic measures considered by governments and various international organizations in their decisions on the use of a new vaccine . However , the costs to the vaccine recipients resulting from their travel , time and wage loss are hardly considered a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	An Estimation of Private Household Costs to Receive Free Oral Cholera Vaccine in Odisha, India
Mesenteric infection by the parasitic blood fluke Schistosoma bovis is a common veterinary problem in Africa and the Middle East and occasionally in the Mediterranean Region . The species also has the ability to form interspecific hybrids with the human parasite S . haematobium with natural hybridisation observed in We...	In this article we detail the assembly and functional annotation of the Schistosoma bovis genome . S . bovis is a parasitic flatworm that primarily infects bovines , with important economic consequences in affected countries . However , it is also a close relative of the human carcinogenic parasite Schistosoma haematob...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "helminths", "animals", "invertebrate", "genomics", "genome", "analysis", "mammalian", "genomics", "research", "and", "analysis", "methods", "sequence", "analysis", "genomic", "libraries", "sequence", "alignment", ...	2019	Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium
Support of ageing neurons by endogenous neurotrophic factors such as glial cell line–derived neurotrophic factor ( GDNF ) and brain-derived neurotrophic factor ( BDNF ) may determine whether the neurons resist or succumb to neurodegeneration . GDNF has been tested in clinical trials for the treatment of Parkinson disea...	What does a neuron need to survive ? Our body produces its own survival factors for neurons , so-called neurotrophic factors , which have additional roles in neuron differentiation , growth , and function . Declining production of a neurotrophic factor or impaired signal transduction in ageing neurons may contribute to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "neuroscience", "molecular", "biology", "genetics", "and", "genomics" ]	2007	Absence of Ret Signaling in Mice Causes Progressive and Late Degeneration of the Nigrostriatal System
Although leprosy is efficiently treated by multidrug therapy , resistance to first-line ( dapsone , rifampin ) and to second-line drugs ( fluoroquinolones ) was described worldwide . Since Mycobacterium leprae is not growing in vitro , phenotypic susceptibility testing requires a one year experiment in the mouse model ...	Although leprosy is a curable disease using a combination of antibiotics for one year , the transmission is still active with 230 , 000 new cases in 2010 . Drug resistance has been described and may prevent eradication of the disease . The infectious agent causing leprosy , Mycobacterium leprae , is not growing in vitr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "skin", "infections", "diagnostic", "medicine", "neglected", "tropical", "diseases", "leprosy" ]	2012	Detection of Antibiotic Resistance in Leprosy Using GenoType LepraeDR, a Novel Ready-To-Use Molecular Test
HLA-B5701 is the host factor most strongly associated with slow HIV-1 disease progression , although risk of progression may vary among patients carrying this allele . The interplay between HIV-1 evolutionary rate variation and risk of progression to AIDS in HLA-B5701 subjects was studied using longitudinal viral seq...	The clinical course of HIV-1 infection is characterized by considerable variability in the rate of progression to acquired immunodeficiency syndrome ( AIDS ) among patients with different genetic background . The human leukocyte antigen ( HLA ) B*5701 is the host factor most strongly associated with slow HIV-1 disease ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "phylogenetics", "medicine", "and", "health", "sciences", "aids", "molecular", "evolution", "biology", "and", "life", "sciences", "viral", "diseases", "evolutionary", "biology", "evolutionary", "systematics" ]	2014	Baseline CD4+ T Cell Counts Correlates with HIV-1 Synonymous Rate in HLA-B*5701 Subjects with Different Risk of Disease Progression
Various observations argue for a role of adaptation in recent human evolution , including results from genome-wide studies and analyses of selection signals at candidate genes . Here , we use genome-wide SNP data from the HapMap and CEPH-Human Genome Diversity Panel samples to study the geographic distributions of puta...	Since the beginning of the study of evolution , people have been fascinated by recent human evolution and adaptation . Despite great progress in our understanding of human history , we still know relatively little about the selection pressures and historical factors that have been important over the past 100 , 000 year...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "genetics", "and", "genomics/population", "genetics", "evolutionary", "biology/genomics" ]	2009	The Role of Geography in Human Adaptation
Staphylococcus lugdunensis is a coagulase negative bacterial pathogen that is particularly associated with severe cases of infectious endocarditis . Unique amongst the coagulase-negative staphylococci , S . lugdunensis harbors an iron regulated surface determinant locus ( isd ) . This locus facilitates the acquisition ...	Sometimes changing environmental conditions force bacteria to boost protein expression above the level that can be achieved by transcriptional or translational control . Gene duplication and amplification ( GDA ) represents a simple and effective means to augment protein expression and is frequently associated with the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "heme", "cell", "walls", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "molecular", "biology", "techniques", "hemoglobin", "cellular", "structures", "and", "organelles", "bacterial", "pathogens", "res...	2016	Competing for Iron: Duplication and Amplification of the isd Locus in Staphylococcus lugdunensis HKU09-01 Provides a Competitive Advantage to Overcome Nutritional Limitation
Interferon-inducible transmembrane proteins 1 , 2 , and 3 ( IFITM1 , 2 , and 3 ) are recently identified viral restriction factors that inhibit infection mediated by the influenza A virus ( IAV ) hemagglutinin ( HA ) protein . Here we show that IFITM proteins restricted infection mediated by the entry glycoproteins ( G...	Cells express restriction factors , proteins whose primary activity is to inhibit viral replication . We have recently described a family of restriction factors , interferon-inducible transmembrane ( IFITM ) proteins , that interfere with replication of influenza A virus . The IFITM proteins uniquely inhibit replicatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry", "virology/host", "antiviral", "responses" ]	2011	Distinct Patterns of IFITM-Mediated Restriction of Filoviruses, SARS Coronavirus, and Influenza A Virus
The natural history of schistosome infection in the mammalian host is determined by CD4+ T helper responses mounted against different parasite life cycle stages . A T helper 2 ( TH2 ) response to schistosome eggs is required for host survival and establishment of chronic infection . However , a TH2 cell-derived cytokin...	Schistosomiasis , a neglected tropical disease caused by parasites of the genus Schistosoma , is prevalent throughout the developing world , with more than 230 million people infected . Left untreated , schistosome infection may cause relatively mild disease with some morbidity , or , in a minority of cases , result in...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "t", "helper", "cells", "schistosoma", "invertebrates", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "helminths", "spleen", "immunology", "parasitic", "diseases", "animals", "lymph", "nodes"...	2019	A secreted schistosome cathepsin B1 cysteine protease and acute schistosome infection induce a transient T helper 17 response
Gene expression divergence between closely related species could be attributed to both cis- and trans- DNA sequence changes during evolution , but it is unclear how the evolutionary dynamics of epigenetic marks are regulated . In eutherian mammals , biparental DNA methylation marks are erased and reset during gametogen...	The relationship between methylation of genomic DNA and expression of the genes that it encodes—and how this relationship changes during evolution—has been widely studied in mammals , but remains less well understood for insects . Here we analyze the expressed mRNA transcripts and genomic DNA methylation of the hybrid ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "vertebrates", "animals", "mammals", "invertebrate", "genomics", "developmental", "biology", "epigenetics", "dna", "mammalian", "genomics", "dna", "methylation", "chromatin", "chromosome", "biology", "genomic", "imprinting", "gene", "expression", "chromatin...	2016	Allele-Specific Transcriptome and Methylome Analysis Reveals Stable Inheritance and Cis-Regulation of DNA Methylation in Nasonia
Eradicating HIV-1 infection is difficult because of the reservoir of latently infected cells that gets established soon after infection , remains hidden from antiretroviral drugs and host immune responses , and retains the capacity to reignite infection following the cessation of treatment . Drugs called latency-revers...	HIV-1 infection typically requires lifelong treatment because a class of infected cells called latently infected cells remains hidden from drugs and host immune responses and can reignite infection when treatment is stopped . Massive efforts are ongoing to devise ways to eliminate latently infected cells . The most adv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "dose", "prediction", "methods", "pathogens", "messenger", "rna", "microbiology", "dna", "transcription", "retroviruses", "viruses", "immunodeficiency", "viruses", "simulation", "and", ...	2018	Trade-off between synergy and efficacy in combinations of HIV-1 latency-reversing agents
Type 2 diabetes leads to premature death and reduced quality of life for 8% of Americans . Nutrition management is critical to maintaining glycemic control , yet it is difficult to achieve due to the high individual differences in glycemic response to nutrition . Anticipating glycemic impact of different meals can be c...	Type 2 diabetes is a devastating disease that requires constant patient self-management of glucose , insulin , nutrition and exercise . Nevertheless , glucose and insulin dynamics are complicated , nonstationary , nonlinear , and individual-dependent , making self-management of diabetes a complex task . To help allevia...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "chemical", "compounds", "carbohydrates", "organic", "compounds", "glucose", "diabetes", "mellitus", "hba1c", "endocrine", "disorders", "mathematics", "forecasting", "statistics", "(mathematics)", "nutrition", "he...	2017	Personalized glucose forecasting for type 2 diabetes using data assimilation
The transcription factor Flo8/Som1 controls filamentous growth in Saccharomyces cerevisiae and virulence in the plant pathogen Magnaporthe oryzae . Flo8/Som1 includes a characteristic N-terminal LUG/LUH-Flo8-single-stranded DNA binding ( LUFS ) domain and is activated by the cAMP dependent protein kinase A signaling pa...	Invasive fungal infections affecting immunocompromised patients are emerging worldwide . Among various human fungal pathogens , Aspergillus fumigatus is one of the most common molds causing severe invasive aspergillosis in immunocompromised patients . The conidia , which can evade from innate immunity and adhere to epi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Transcription Factor SomA Is Required for Adhesion, Development and Virulence of the Human Pathogen Aspergillus fumigatus
Many microparasites infect new hosts with specialized life stages , requiring a subset of the parasite population to forgo proliferation and develop into transmission forms . Transmission stage production influences infectivity , host exploitation , and the impact of medical interventions like drug treatment . Predicti...	Malaria parasites are carried from host to host by blood-feeding insects , a process that requires some portion of the parasite population to develop into transmission forms that cannot replicate within the current host . The fraction of parasites specialized for transmission instead of replication ( transmission inves...	[ "Abstract", "Introduction", "Results", "&", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "parasite", "groups", "pathology", "and", "laboratory", "medicine", "plasmodium", "gametocytes", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "germ", "cells", "deve...	2016	Quantifying Transmission Investment in Malaria Parasites
Dynamic models of metabolism can be useful in identifying potential drug targets , especially in unicellular organisms . A model of glycolysis in the causative agent of human African trypanosomiasis , Trypanosoma brucei , has already shown the utility of this approach . Here we add the pentose phosphate pathway ( PPP )...	Mathematical models have been valuable tools for investigating the complex behaviors of metabolism . Due to incomplete knowledge of biological systems , these models contain inevitable uncertainty . This uncertainty is present in the measured or estimated parameter values , but also in the structure of the metabolic ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei
The recent emergence of Zika virus ( ZIKV ) in the Americas coincident with increased caseloads of microcephalic infants and Guillain-Barre syndrome has prompted a flurry of research on ZIKV . Much of the research is difficult to compare or repeat because individual laboratories use different virus isolates , growth co...	The ZIKV scientific field has greatly expanded since the emergence of ZIKV in South and Central America , but a comprehensive comparison of the assays used to examine the phenotypic and replicative properties of ZIKV is limited in the literature . The influence of host , whether insect or mammalian , on viral productio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "vero", "cells", "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "pathogens", "biological", "cultures", "microbiology", "cloning", "animals", "viruses", "rna", "viruses", "molecular", "biol...	2018	Growth and adaptation of Zika virus in mammalian and mosquito cells
The ecological importance of the duplication and diversification of gene clusters that synthesize secondary metabolites in fungi remains poorly understood . Here , we demonstrated that the duplication and subsequent diversification of a gene cluster produced two polyketide synthase gene clusters in the cosmopolitan fun...	In fungi , gene clusters that synthesize secondary metabolites are hotspots for the generation of fungal metabolic diversity through gene duplication , but their ecological importance remains poorly understood . Metarhizium species are adapted to life as insect pathogens , plant symbionts and saprophytes , enabling the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "fungal", "genetics", "fungal", "structure", "fungi", "phylogenetics", "data", "management", "phylogenetic", "analysis", "sequence", "motif", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "metarhizium", "computer", "and", "inf...	2018	Duplication of a Pks gene cluster and subsequent functional diversification facilitate environmental adaptation in Metarhizium species
The Mu transposon system of maize is highly active , with each of the ∼50–100 copies transposing on average once each generation . The approximately one dozen distinct Mu transposons contain highly similar ∼215 bp terminal inverted repeats ( TIRs ) and generate 9-bp target site duplications ( TSDs ) upon insertion . Us...	Genomic insertion sites of Mu transposons were amplified and sequenced via next generation technology , revealing more than 40 , 000 non-redundant Mu insertion sites that are non-uniformly distributed across the maize genome and within genes . Along chromosomes , frequencies of Mu transposon insertions are strongly cor...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genomics", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/bioinformatics" ]	2009	Mu Transposon Insertion Sites and Meiotic Recombination Events Co-Localize with Epigenetic Marks for Open Chromatin across the Maize Genome
Recently developed atrophic non-union models are a good representation of the clinical situation in which many non-unions develop . Based on previous experimental studies with these atrophic non-union models , it was hypothesized that in order to obtain successful fracture healing , blood vessels , growth factors , and...	In light of the ageing population , the occurrence of bone fractures is expected to rise substantially in the near future . In 5 to 10% of these cases , the healing process does not succeed in repairing the bone , leading to the formation of delayed unions or even non-unions . In this study we used a combination of an ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physiology/muscle", "and", "connective", "tissue", "rheumatology/bone", "and", "mineral", "metabolism", "pathology/histopathology", "rheumatology/orthopedics", "and", "sports", "medicine" ]	2010	Occurrence and Treatment of Bone Atrophic Non-Unions Investigated by an Integrative Approach
Like other intracellular eukaryotic phytopathogens , the devastating rice blast fungus Magnaporthe ( Pyricularia ) oryzae first infects living host cells by elaborating invasive hyphae ( IH ) surrounded by a plant-derived membrane . This forms an extended biotrophic interface enclosing an apoplastic compartment into wh...	Plant-associated fungi can form intimate connections with living host cells . Clarifying the molecular drivers of these interactions , and which partner is dominant , might be important in understanding how beneficial plant-fungal relationships can be enhanced to improve crop yields while pathogenic interactions that t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "cell", "death", "plant", "anatomy", "autophagic", "cell", "death", "vacuoles", "plant", "cell", "biology", "tor", "signaling", "cell", "processes", "plant", "vacuoles", "plant", "science", "rice", "experimental", "organism", "systems", "plants...	2018	TOR-autophagy branch signaling via Imp1 dictates plant-microbe biotrophic interface longevity
Infection of the mammalian host by the parasitic helminth Schistosoma mansoni is accompanied by the release of excretory/secretory molecules ( ES ) from cercariae which aid penetration of the skin . These ES molecules are potent stimulants of innate immune cells leading to activation of acquired immunity . At present h...	Schistosomiasis is caused by the parasitic worm Schistosoma with over 200 million people infected across 76 countries . The parasitic larvae ( called cercariae ) infect mammalian hosts via the skin , but the exact mechanisms by which dermal cells interact with molecules released by invading larvae are unclear . A bette...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "microbiology/parasitology", "infectious", "diseases/helminth", "infections", "immunology/innate", "immunity", "dermatology/skin", "infections" ]	2009	Fluorescent Imaging of Antigen Released by a Skin-Invading Helminth Reveals Differential Uptake and Activation Profiles by Antigen Presenting Cells
Soil-transmitted helminth ( STH ) infection leads to malnutrition and anemia , and has been linked to impaired child development . Previous research on this topic is limited and mostly conducted in school-age children . The goal of this study was to determine the effect of the number of detected STH infections between ...	Intestinal worm infections are parasites that can have serious health consequences , including malnutrition . They affect over one billion people in low and middle income countries . It has been proposed that intestinal worm infections can have a negative effect on brain development in young children . This topic , how...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "helminths", "tropical", "diseases", "hookworms", "parasitic", "diseases", "animals", "pediatrics", "ascaris", "nutrition", "neglected", "tropical", "diseases", "pediatric", "infections", "malnutrition", "trichuris",...	2018	A longitudinal cohort study of soil-transmitted helminth infections during the second year of life and associations with reduced long-term cognitive and verbal abilities
The Drosophila eggshell constitutes a remarkable system for the study of epithelial patterning , both experimentally and through computational modeling . Dorsal eggshell appendages arise from specific regions in the anterior follicular epithelium that covers the oocyte: two groups of cells expressing broad ( roof cells...	We propose a modeling approach to Drosophila egg appendage development . Relying on a thorough compilation of published data , our model comprises cellular genetic networks and cell-cell communication . It proves to be extremely robust by faithfully replicating the wild type pattern as well as patterns arising from mut...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "developmental", "biology", "computer", "and", "information", "sciences", "computer", "modeling", "network", "analysis", "regulatory", "networks", "biology", "and", "life", "sciences", "computational", "biology", "morphogenesis", "pattern", "formatio...	2014	A Discrete Model of Drosophila Eggshell Patterning Reveals Cell-Autonomous and Juxtacrine Effects
We hypothesized that during binary economic choice , decision makers use the first option they attend as a default to which they compare the second . To test this idea , we recorded activity of neurons in the dorsal anterior cingulate cortex ( dACC ) of macaques choosing between gambles presented asynchronously . We fi...	How we make decisions based on value and how these computations are implemented in neuronal circuits remain topics of active debate . It also remains unclear how attention shapes how we perceive and process value . The dorsal anterior cingulate cortex has been implicated in both value-based decision-making and attentio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "recreation", "cingulate", "cortex", "medicine", "and", "health", "sciences", "decision", "making", "neuronal", "differentiation", "brain", "social", "sciences", "neuroscience", "cell", "differentiation", "developmental", "biology", "cognitive", "psychology", "mathematics",...	2017	Correlates of decisional dynamics in the dorsal anterior cingulate cortex
Whole cell responses involve multiple subcellular processes ( SCPs ) . To understand how balance between SCPs controls the dynamics of whole cell responses we studied neurite outgrowth in rat primary cortical neurons in culture . We used a combination of dynamical models and experiments to understand the conditions tha...	Mechanisms that cause a change of state of a cell arise from unique patterns of interactions between multiple subcellular processes ( SCPs ) . Neurite outgrowth ( NOG ) is such a change of cell state where a neuron puts out a long process that eventually becomes the axon . We used a top-down based approach to mathemati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "vesicles", "kinesins", "microtubules", "neurites", "neuroscience", "membrane", "proteins", "molecular", "motors", "tubulins", "cellular", "structures", "and", "organelles", "neuronal", "dendrites", "cytoskeleton", "animal", "cells", "proteins", "cell", "membranes", "cyto...	2019	Dynamic balance between vesicle transport and microtubule growth enables neurite outgrowth
A common characteristic of Trichuris spp . infections in humans and animals is the variable but low efficacy of single-dose benzimidazoles currently used in mass drug administration programmes against human trichuriasis . The bacillary band , a specialised morphological structure of Trichuris spp . , as well as the uni...	The human whipworm , Trichuris trichiura is prevalent in many tropical and subtropical countries and is believed to infect more than 460 million people worldwide . Treatment with single-dose albendazole or mebendazole is the current control strategy for human trichuriasis . This strategy , however , has a poor-to-medio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "chemical", "compounds", "tropical", "diseases", "carbohydrates", "parasitic", "diseases", "animals", "organic", "compounds", "glucose", "glucose", "metabolism", "oral", "glucose", "su...	2016	Glucose Absorption by the Bacillary Band of Trichuris muris
Legionella pneumophila , the causative agent of Legionnaires' disease , evades phago-lysosome fusion in mammalian and protozoan hosts to create a suitable niche for intracellular replication . To modulate vesicle trafficking pathways , L . pneumophila translocates effector proteins into eukaryotic cells through a Type ...	Legionella pneumophila is a Gram-negative bacterial species that causes a severe pneumonia known as Legionnaires' disease . Inhalation of L . pneumophila–contaminated aerosols results in the infection of lung macrophages . Following infection , the bacteria use a Type IVB secretion system to deliver multiple effector p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "evolution", "and", "genomics", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/respiratory", "infections", "infectious", "diseases/protozoal", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "infectio...	2008	Legionella Eukaryotic-Like Type IV Substrates Interfere with Organelle Trafficking
The RNA world is a very likely interim stage of the evolution after the first replicators and before the advent of the genetic code and translated proteins . Ribozymes are known to be able to catalyze many reaction types , including cofactor-aided metabolic transformations . In a metabolically complex RNA world , early...	The RNA world refers to the stage of early evolution when RNA macromolecules were responsible both for storing hereditary information and performing enzymatic activities . Conflict arises between these two functions , however , as enzymatic activities of the ribozymes are in tradeoff with their replication rates . Here...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "systems", "biology", "computer", "and", "information", "sciences", "computer", "modeling", "theoretical", "biology", "biology", "and", "life", "sciences", "evolutionary", "biology" ]	2014	Evolution of the Division of Labor between Genes and Enzymes in the RNA World
Cancer cells often rely on glycolysis to obtain energy and support anabolic growth . Several studies showed that glycolytic cells are susceptible to cell death when subjected to low glucose availability or to lack of glucose . However , some cancer cells , including glycolytic ones , can efficiently acquire higher tole...	Tumor heterogeneity exists in many human cancers , and it has been shown that it can play a role in tumor progression . Indeed , cell diversity may be critically important when tumors experience selective pressures , like nutrient deprivation , hypoxia , chemotherapy . PKA , through incompletely understood mechanisms ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "cell", "death", "autophagic", "cell", "death", "medicine", "and", "health", "sciences", "chemical", "compounds", "cancer", "treatment", "cell", "processes", "carbohydrates", "cell", "metabolism", "organic", "compounds...	2016	Protein Kinase A Activation Promotes Cancer Cell Resistance to Glucose Starvation and Anoikis
Fragile X syndrome , the most frequent form of inherited mental retardation , is due to the absence of Fragile X Mental Retardation Protein ( FMRP ) , an RNA-binding protein involved in several steps of RNA metabolism . To date , two RNA motifs have been found to mediate FMRP/RNA interaction , the G-quartet and the “ki...	The most common form of inherited mental retardation , Fragile X syndrome , is caused by the absence of the Fragile X Mental Retardation Protein ( FMRP ) , which can bind mRNA . In mice devoid of FMRP , several hundreds of mRNAs with altered expression and localization have been reported . The impact of these abnormali...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "chemical", "biology", "neuroscience", "molecular", "biology" ]	2009	A Novel Function for Fragile X Mental Retardation Protein in Translational Activation
Selective dimerization of the basic-region leucine-zipper ( bZIP ) transcription factors presents a vivid example of how a high degree of interaction specificity can be achieved within a family of structurally similar proteins . The coiled-coil motif that mediates homo- or hetero-dimerization of the bZIP proteins has b...	Protein interactions are important for all life processes , and an ability to rationally control or selectively inhibit protein complexes would impact studies of cellular structure , biological information processing , molecular regulatory processes and other phenomena . Rational protein design has applications in deve...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Data-Driven Prediction and Design of bZIP Coiled-Coil Interactions
Mutational robustness is defined as the constancy of a phenotype in the face of deleterious mutations . Whether robustness can be directly favored by natural selection remains controversial . Theory and in silico experiments predict that , at high mutation rates , slow-replicating genotypes can potentially outcompete f...	Understanding the conditions that favor the constancy of phenotypes in the face of deleterious mutation pressure—mutational robustness—is an outstanding question in evolutionary biology . Theoretical and in silico studies utilizing digital organisms predict that slow-replicating populations can outcompete those with hi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "viruses", "genetics", "and", "genomics", "virology" ]	2007	Selection for Robustness in Mutagenized RNA Viruses
The stability of the repeat protein IκBα , a transcriptional inhibitor in mammalian cells , is critical in the functioning of the NF-κB signaling module implicated in an array of cellular processes , including cell growth , disease , immunity and apoptosis . Structurally , IκBα is complex , with both ordered and disord...	It is well recognized that unstructured or disordered proteins play a vital role in the cell . How does this disorder translate into function , and what effect does it have when linked to ordered regions ? We attempt to answer this question by computationally characterizing the repeat protein IκBα , a central player in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	A Disorder-Induced Domino-Like Destabilization Mechanism Governs the Folding and Functional Dynamics of the Repeat Protein IκBα
The transcription of individual genes is determined by combinatorial interactions between DNA–binding transcription factors . The current challenge is to understand how such combinatorial interactions regulate broad genetic programs that underlie cellular functions and disease . The transcription factors Hnf1α and Hnf4...	The transcriptional activity of each gene is typically determined by multiple transcription factors . This concept has been well established in studies of single genes . However , transcription factors do not simply regulate single genes , they also control broad gene programs that underlie cellular function and diseas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "diabetes", "and", "endocrinology", "genetics", "and", "genomics/gene", "expression" ]	2010	Epistasis of Transcriptomes Reveals Synergism between Transcriptional Activators Hnf1α and Hnf4α
Phytopathogenic oomycetes , such as Phytophthora infestans , secrete an arsenal of effector proteins that modulate plant innate immunity to enable infection . We describe CRN8 , a host-translocated effector of P . infestans that has kinase activity in planta . CRN8 is a modular protein of the CRN effector family . The ...	Phytophthora infestans is the causal agent of late blight on potato and tomato . It is now well established that oomycetes , such as P . infestans , secrete an arsenal of effector proteins that modulate plant innate immunity to enable infection . The Crinkler ( CRN ) effector family containing the LFLAK translocation m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "plant", "science", "plant", "biology", "genetics", "immunology", "biology", "genomics", "proteomics", "genetics", "and", "genomics" ]	2012	The Irish Potato Famine Pathogen Phytophthora infestans Translocates the CRN8 Kinase into Host Plant Cells
Humans and other mammals mount vigorous immune assaults against helminth parasites , yet there are intriguing reports that the immune response can enhance rather than impair parasite development . It has been hypothesized that helminths , like many free-living organisms , should optimize their development and reproduct...	Many organisms are able to adapt their development to the severity of their environment based on specific cues , and we have identified such a phenomenon , termed phenotypic plasticity , in the filarial parasite Litomosoides sigmodontis . Filarial nematodes infect about 200 million people worldwide , and much effort is...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/helminth", "infections", "immunology/immunity", "to", "infections", "evolutionary", "biology/developmental", "evolution" ]	2010	Filarial Parasites Develop Faster and Reproduce Earlier in Response to Host Immune Effectors That Determine Filarial Life Expectancy
One of the hallmarks of adaptive immunity is the development of a long-term pathogen specific memory response . While persistent memory T cells certainly impact the immune response during a secondary challenge , their role in unrelated infections is less clear . To address this issue , we utilized lymphocytic choriomen...	Cutaneous leishmaniasis has a wide spectrum of clinical presentations , from mild self-healing lesions to severe chronic infections . Differences in each individual's response are related to pathogen dose and the genetic and physiological status of the host , but exactly what causes the broad spectrum of disease is not...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "medicine", "infectious", "diseases", "bacterial", "diseases", "immune", "cells", "immunity", "leishmaniasis", "t", "cells", "immunity", "to", "infections", "immunology", "neglected", "tropical", "diseases", "biology", "viral", "diseases", "lymphocytic"...	2014	Engagement of NKG2D on Bystander Memory CD8 T Cells Promotes Increased Immunopathology following Leishmania major Infection
In eukaryotes , cyclin-dependent kinases ( CDKs ) control the cell cycle and critical steps in gene expression . The lethal parasite Trypanosoma brucei , member of the phylogenetic order Kinetoplastida , possesses eleven CDKs which , due to high sequence divergence , were generically termed CDC2-related kinases ( CRKs ...	Kinetoplastids are vector-borne , unicellular parasites that cause devastating human diseases in the tropics and subtropics of the world . Interestingly , kinetoplastids express protein-coding genes differently than other eukaryotes by producing polycistronic pre-mRNAs that require processing into individual mRNAs by s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "phosphorylation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "parasitic", "protozoans", "protozoans", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "research", "and", "analysis", ...	2016	Cyclin-Dependent Kinase CRK9, Required for Spliced Leader trans Splicing of Pre-mRNA in Trypanosomes, Functions in a Complex with a New L-Type Cyclin and a Kinetoplastid-Specific Protein
Recent technological improvements in the field of genetic data extraction give rise to the possibility of reconstructing the historical pedigrees of entire populations from the genotypes of individuals living today . Current methods are still not practical for real data scenarios as they have limited accuracy and assum...	Learning the correct relationships between individuals from genetic data is a basic theoretical problem in the field of genetics , and has many practical consequences . A wide variety of statistical methods for genetic analysis assume the relationships between individuals are known , and can manifest relatedness inform...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "biology", "and", "life", "sciences", "population", "genetics", "computational", "biology", "evolutionary", "biology", "human", "genetics" ]	2014	Historical Pedigree Reconstruction from Extant Populations Using PArtitioning of RElatives (PREPARE)
Discovering links between the genotype of an organism and its metabolite levels can increase our understanding of metabolism , its controls , and the indirect effects of metabolism on other quantitative traits . Recent technological advances in both DNA sequencing and metabolite profiling allow the use of broad-spectru...	Understanding how genetic variation can control phenotypic variation is a fundamental goal of modern biology . We combined genome-wide association mapping with metabolomics in the plant Arabidopsis thaliana to explore how species-wide genetic variation controls metabolism . We identified numerous naturally-variable gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/plant", "genomes", "and", "evolution", "genetics", "and", "genomics/complex", "traits", "biochemistry/bioinformatics", "computational", "biology/metabolic", "networks", "plant", "biology/plant", "biochemistry", "and", "physiology", "cell", "biology/plan...	2010	The Complex Genetic Architecture of the Metabolome
Understanding how novel functions evolve ( genetic adaptation ) is a critical goal of evolutionary biology . Among asexual organisms , genetic adaptation involves multiple mutations that frequently interact in a non-linear fashion ( epistasis ) . Non-linear interactions pose a formidable challenge for the computational...	Understanding how new biological activities evolve on the molecular level has critical implications for biotechnology and for human health . Here we collect a database of mutations that contribute to the evolution of β-lactamase resistance to inhibitors and to new β-lactam antibiotics in bacterial pathogens , such as E...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequence", "analysis", "genetic", "mutation", "evolutionary", "biology", "microbial", "evolution", "evolutionary", "modeling", "genetics", "genetics", "and", "genomics", "biology", "computational", "biology", "microbiology", "evolutionary", "genetics", "bacterial", "pathog...	2011	Network Models of TEM β-Lactamase Mutations Coevolving under Antibiotic Selection Show Modular Structure and Anticipate Evolutionary Trajectories
Despite the importance of oxidation of blood-borne long-chain fatty acids ( Fa ) in the cardiomyocytes for contractile energy of the heart , the mechanisms underlying the transfer of Fa from the coronary plasma to the cardiomyocyte is still incompletely understood . To obtain detailed insight into this transfer process...	The energy required for pump work of the heart is generated primarily by oxidation of long-chain fatty acids ( Fa ) , transferred to the heart by plasma albumin . In coronary capillaries , Fa detach from albumin , cross endothelial cells , pericapillary interstitium and cardiomyocyte membrane prior to oxidation . The e...	[ "Abstract", "Introduction", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Modeling Fatty Acid Transfer from Artery to Cardiomyocyte
Sexual dimorphism , including differences in morphology , behavior and physiology between females and males , is widespread in animals and plants and is shaped by gene expression differences between the sexes . Such expression differences may also underlie sex-specific responses of hosts to pathogen infections , most n...	Females and males differ from each other in many traits , including morphology , behavior and physiology . Differences in gene expression between the sexes , known as sex-biased gene expression , contribute to such sexual dimorphism . Here we characterize the responses of females and males of the dioecious plant Silene...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Fungal Infection Induces Sex-Specific Transcriptional Changes and Alters Sexual Dimorphism in the Dioecious Plant Silene latifolia
Mice exposed to sand fly saliva are protected against vector-transmitted Leishmania major . Although protection has been related to IFN- γ producing T cells , the early inflammatory response orchestrating this outcome has not been defined . Mice exposed to uninfected P . duboscqi bites and naïve mice were challenged wi...	Sand flies transmit Leishmania parasites during bloodfeeding . Salivary molecules are deposited alongside parasites and can reshape the host's immune response to infection . Exposure to uninfected sand fly bites or immunization with salivary molecules protects the host against Leishmania infection . Here we show that m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "cells", "immunity", "to", "infections", "immunology", "immunomodulation", "veterinary", "science", "infectious", "diseases", "veterinary", "diseases", "inflammation", "zoonoses", "animal", "cells", "epidemiology", "disea...	2014	Characterization of the Early Inflammatory Infiltrate at the Feeding Site of Infected Sand Flies in Mice Protected from Vector-Transmitted Leishmania major by Exposure to Uninfected Bites
The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data . However , with the increasing use of high-throughput experimental assays , a small number of experimental studies dominate th...	Experiments and observations are the vehicles used by science to understand the world around us . In the field of molecular biology , we are increasingly relying on high-throughput , genome-wide experiments to provide answers about the function of biological macromolecules . However , any experimental assay is essentia...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "computational", "biology" ]	2013	Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space
Co-translational folding ( CTF ) facilitates correct folding in vivo , but its precise mechanism remains elusive . For the CTF of a three-domain protein SufI , it was reported that the translational attenuation is obligatory to acquire the functional state . Here , to gain structural insights on the underlying mechanis...	Proteins are synthesized in vivo by ribosome from their N-termini . When N-terminal fragments of nascent proteins get out of the ribosome exit , they start folding , which is called co-translational folding . It has been suggested that well-scheduled co-translational folding schemes would facilitate correct acquisition...	[ "Abstract", "Introduction", "Results", "and", "Discussions", "Materials", "and", "Methods" ]	[]	2015	How Co-translational Folding of Multi-domain Protein Is Affected by Elongation Schedule: Molecular Simulations
Type VI secretion systems ( T6SS ) function to deliver lethal payloads into target cells . Many studies have shown that protection against a single , lethal T6SS effector protein requires a cognate antidote immunity protein , both of which are often encoded together in a two-gene operon . The T6SS and an effector-immun...	Bacterial type VI secretion systems ( T6SS ) function as contractile nanomachines to puncture target cells and deliver lethal effectors . Little is known about the lifestyle or physiology dictating when bacteria normally express their T6SS . Previously , we have reported that discrimination of self during the multicell...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "bacteriology", "complement", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "operons", "secretion", "systems", "dna", "proteus", "mirabilis", "bacterial",...	2017	Subtle variation within conserved effector operon gene products contributes to T6SS-mediated killing and immunity
A most important property of biochemical systems is robustness . Static robustness , e . g . , homeostasis , is the insensitivity of a state against perturbations , whereas dynamics robustness , e . g . , homeorhesis , is the insensitivity of a dynamic process . In contrast to the extensively studied static robustness ...	Cells use signaling pathways to transmit information received on its membrane to DNA , and many important cellular processes are tied to signaling networks . Past experiments have shown that cells’ internal signaling networks are sophisticated enough to process and encode temporal information such as the length of time...	[ "Abstract", "Introduction", "Results", "Discussion", "Models", "and", "methods" ]	[ "phosphorylation", "enzymes", "enzymology", "signaling", "networks", "phosphatases", "systems", "science", "mathematics", "network", "analysis", "mapk", "signaling", "cascades", "protein", "kinase", "signaling", "cascade", "relaxation", "(physics)", "computer", "and", "in...	2017	Dynamics robustness of cascading systems
The African clawed frog Xenopus laevis is an important model organism for studies in developmental and cell biology , including cell-signaling . However , our knowledge of X . laevis protein post-translational modifications remains scarce . Here , we used a mass spectrometry-based approach to survey the phosphoproteome...	Proteins can be modified during their life-cycle in order to regulate their function . The addition of a phosphate group is one of the most abundant and well understood protein modifications . Recent technological developments are now allowing us to uncover thousands of phosphorylation sites within proteins in a single...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Prediction of Functionally Important Phospho-Regulatory Events in Xenopus laevis Oocytes
Postsynaptic scaffolding proteins regulate coordinated neurotransmission by anchoring and clustering receptors and adhesion molecules . Gephyrin is the major instructive molecule at inhibitory synapses , where it clusters glycine as well as major subsets of GABA type A receptors ( GABAARs ) . Here , we identified palmi...	Efficient signal transmission at synapses is essential for higher brain functions . Inhibitory signaling in the brain takes place primarily at GABA ( γ-aminobutyric acid ) -ergic synapses . GABA type A receptors ( GABAARs ) are clustered at the postsynaptic side by a scaffold composed of the peripheral membrane protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "developmental", "neuroscience", "cellular", "neuroscience", "synaptic", "plasticity", "anatomy", "synapses", "neurophysiology", "neurotransmission", "nervous", "system", "biology", "and", "life", "sciences", "neuroscience", "neuronal", "plasticit...	2014	Palmitoylation of Gephyrin Controls Receptor Clustering and Plasticity of GABAergic Synapses
The study of object manipulation has been largely confined to discrete tasks , where accuracy , mechanical effort , or smoothness were examined to explain subjects' preferred movements . This study investigated a rhythmic manipulation task , which involved continuous interaction with a nonlinear object that led to unpr...	Daily actions frequently involve manipulation of tools and objects , such as stirring soup with a spoon or carrying a cup of coffee . Carrying the cup of coffee without spilling can be challenging as the coffee can only be indirectly controlled via moving the cup . Interaction forces between the cup and the coffee can ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "computer", "and", "information", "sciences", "behavioral", "neuroscience", "systems", "science", "mathematics", "anatomy", "computational", "neuroscience", "nervous", "system", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology", "non...	2014	Rhythmic Manipulation of Objects with Complex Dynamics: Predictability over Chaos
The majority of melanomas have been shown to harbor somatic mutations in the RAS-RAF-MEK-MAPK and PI3K-AKT pathways , which play a major role in regulation of proliferation and survival . The prevalence of these mutations makes these kinase signal transduction pathways an attractive target for cancer therapy . However ...	Signal transduction pathways can be described as static routes , transmitting extrinsic signals to the nucleus to induce a transcriptional response . In contrast to this reductionist view , the emerging paradigm is that signaling networks undergo dynamic crosstalk , both in disease and physiological conditions . To und...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "cancer", "genetics", "mechanisms", "of", "signal", "transduction", "cancer", "treatment", "cell", "processes", "signaling", "networks", "cancers", "and", "neoplasms", "fuzzy", "logic", "oncology", "cell", "signaling", "phospho...	2014	Data-Derived Modeling Characterizes Plasticity of MAPK Signaling in Melanoma
The morphological , molecular , and functional heterogeneity of astrocytes is under intense scrutiny , but how this diversity is ontogenetically achieved remains largely unknown . Here , by quantitative in vivo clonal analyses and proliferation studies , we demonstrate that the major cerebellar astrocyte types emerge a...	Astrocytes are abundant cells of the brain essential to support and shape neuronal activity . They can be grouped in different subclasses based on their remarkable variety of morphologies , molecular profiles , and specialized functions . Although different astrocyte types likely display specialized interactions with d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "astrocytes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "precursor", "cells", "brain", "cloning", "neuroscience", "macroglial", "cells", "cell", "differentiation", "developmental", "b...	2018	Multiple origins and modularity in the spatiotemporal emergence of cerebellar astrocyte heterogeneity
Neutrophils are rapidly and massively recruited to sites of microbial infection , where they can influence the recruitment of dendritic cells . Here , we have analyzed the role of neutrophil released chemokines in the early recruitment of dendritic cells ( DCs ) in an experimental model of Leishmania major infection . ...	When infectious agents enter our body , neutrophils are the first cells recruited to the scene . In addition to their capacity to kill microbes , neutrophils secrete molecules that attract other cells also involved in immune defense , such as dendritic cells ( DCs ) . Here , we investigate the secretion of DC-attractin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immunity", "to", "infections", "infectious", "diseases/protozoal", "infections", "immunology/innate", "immunity" ]	2010	Neutrophil-Derived CCL3 Is Essential for the Rapid Recruitment of Dendritic Cells to the Site of Leishmania major Inoculation in Resistant Mice
Tumor therapy with replication competent viruses is an exciting approach to cancer eradication where viruses are engineered to specifically infect , replicate , spread and kill tumor cells . The outcome of tumor virotherapy is complex due to the variable interactions between the cancer cell and virus populations as wel...	Tumor therapy with replicating oncolytic viruses is based on the premise that if the tumor specific virus infects and is amplified by the tumor population and spreads sufficiently within the tumor , it will lead to eradication of the cancer . The outcome of this approach is an exercise in population dynamics , and , as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "models" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "cancer", "treatment", "cell", "processes", "biological", "cultures", "microbiology", "oncolytic", "viruses", "viral", "structure", "s...	2019	In vitro and in silico multidimensional modeling of oncolytic tumor virotherapy dynamics
Molecular and cellular studies have begun to unravel a neurobiological basis of olfactory processing , which appears conserved among vertebrate and invertebrate species . Studies have shown clearly that experience-dependent coding of odor identity occurs in “associative” olfactory centers ( the piriform cortex in mamma...	Considerable progress has been made in understanding how olfaction works as the receptor proteins , sensory neurons , and brain circuitry responsible have become increasingly well-characterized . However , olfactory processing in higher brain centers , where neuronal activity is assembled into the perception of odor qu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "neuroscience", "genetics", "and", "genomics" ]	2007	Segregation of Odor Identity and Intensity during Odor Discrimination in Drosophila Mushroom Body
One mechanism by which bacteria survive environmental stress is through the formation of bacterial persisters , a sub-population of genetically identical quiescent cells that exhibit multidrug tolerance and are highly enriched in bacterial toxins . Recently , the Escherichia coli gene mqsR ( b3022 ) was identified as t...	Most bacteria live in biofilms , microbial communities that cause more than 80% of human infections . Biofilms have a genetically identical sub-population of dormant cells , named persister cells , which are the well-recognized source of antibiotic resistance . Recently , it was demonstrated that toxins are highly upre...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "cell", "biology/cell", "signaling", "cell", "biology/cellular", "death", "and", "stress", "responses", "microbiology/microbial", "physiology", "and", "metabolism", "biophysics/experimental", ...	2009	Three Dimensional Structure of the MqsR:MqsA Complex: A Novel TA Pair Comprised of a Toxin Homologous to RelE and an Antitoxin with Unique Properties
A central question in Leishmania research is why most species cause cutaneous infections but others cause fatal visceral disease . Interestingly , L . donovani causes both visceral and cutaneous leishmaniasis in Sri Lanka . L . donovani clinical isolates were therefore obtained from cutaneous leishmaniasis ( CL-SL ) an...	Visceral leishmaniasis is one of the most lethal parasitic diseases , and the mechanisms that govern its survival in visceral organs are not understood . Here , we obtained an atypical cutaneous Leishmania donovani clinical isolate from Sri Lanka and compared it to a typical visceral disease causing clinical isolate . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Genetic Analysis of Leishmania donovani Tropism Using a Naturally Attenuated Cutaneous Strain
A common problem in genomics is to test for associations between two or more genomic features , typically represented as intervals interspersed across the genome . Existing methodologies can test for significant pairwise associations between two genomic intervals; however , they cannot test for associations involving m...	The age of genomics has made a large number of datasets available for the wider scientific community . Many of these datasets come in the form of genomics tracks , represented as features associated with a collections of genomic intervals along chromosomes . A common talk in genomics is to identify putative association...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[]	2017	GINOM: A statistical framework for assessing interval overlap of multiple genomic features
Invasion of mosquito salivary glands ( SGs ) by Plasmodium falciparum sporozoites is an essential step in the malaria life cycle . How infection modulates gene expression , and affects hematophagy remains unclear . Using Affimetrix chip microarray , we found that at least 43 genes are differentially expressed in the gl...	Malaria is transmitted by Plasmodium falciparum-infected Anopheles gambiae mosquitoes . Salivary gland contributes to the development of the parasite by creating a favorable environment for the infection and facilitating blood feeding and reproduction of the vector . However , the molecular mechanism by which the vecto...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Plasmodium falciparum Infection Induces Expression of a Mosquito Salivary Protein (Agaphelin) That Targets Neutrophil Function and Inhibits Thrombosis without Impairing Hemostasis
The cleavage-furrow tip adjacent to the actomyosin contractile ring is believed to be the predominant site for plasma-membrane insertion through exocyst-tethered vesicles during cytokinesis . Here we found that most secretory vesicles are delivered by myosin-V on linear actin cables in fission yeast cytokinesis . Surpr...	Cytokinesis partitions a mother cell into two daughter cells at the end of each cell-division cycle . A significant amount of new plasma membrane is needed at the cleavage furrow during cytokinesis in many cell types . Membrane expansion is achieved through the balance of exocytosis and endocytosis . It is poorly under...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "vesicles", "cell", "cycle", "and", "cell", "division", "cell", "processes", "focal", "planes", "fungi", "model", "organisms", "cytokinesis", "mitochondria", "bioenergetics", "cellular", "structures", "and", "organelles", "optics", "schizosaccharomyces", "research", "an...	2016	Roles of the TRAPP-II Complex and the Exocyst in Membrane Deposition during Fission Yeast Cytokinesis
Recent studies have shown that systems combining mathematical modeling and Bayesian inference methods can be used to generate real-time forecasts of future infectious disease incidence . Here we develop such a system to study and forecast respiratory syncytial virus ( RSV ) . RSV is the most common cause of acute lower...	Respiratory syncytial virus ( RSV ) is the most common cause of acute lower respiratory infection and bronchiolitis . Prompt treatment of RSV is necessary to prevent damage to lung tissue , complications from prolonged oxygen deprivation , and the potential development of reactive airway disorders . Another respiratory...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "respiratory", "infections", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "microbiology", "census", "pulmonology", "simulation", "and", "modeling", "viruses", "research", "desi...	2016	Retrospective Parameter Estimation and Forecast of Respiratory Syncytial Virus in the United States
Interleukin ( IL ) -10 levels are increased in dengue virus ( DENV ) -infected patients with severe disorders . A hypothetical intrinsic pathway has been proposed for the IL-10 response during antibody-dependent enhancement ( ADE ) of DENV infection; however , the mechanisms of IL-10 regulation remain unclear . We foun...	IL-10 has multiple cellular functions , including anti-inflammatory and immunomodulatory effects . Clinical studies have demonstrated that the serum levels of IL-10 are significantly increased in DENV-infected patients with severe disorders . However , the molecular mechanism underlying DENV-induced IL-10 production is...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	Antibody-Dependent Enhancement Infection Facilitates Dengue Virus-Regulated Signaling of IL-10 Production in Monocytes
DNA methylation directed by 24-nucleotide small RNAs involves the small RNA-binding protein ARGONAUTE4 ( AGO4 ) , and it was previously shown that AGO4 localizes to nucleolus-adjacent Cajal bodies , sites of snRNP complex maturation . Here we demonstrate that AGO4 also localizes to a second class of nuclear bodies , ca...	Argonautes are components of the RNA interference ( RNAi ) pathway that bind small interfering RNAs ( siRNAs ) of 21–24 nucleotide length . In the flowering plant Arabidopsis thaliana , ARGONAUTE4 ( AGO4 ) is involved in gene silencing at the transcriptional level in a process called RNA-directed DNA methylation ( RdDM...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "arabidopsis", "(thale", "cress)", "molecular", "biology", "plant", "biology" ]	2008	Dynamic Regulation of ARGONAUTE4 within Multiple Nuclear Bodies in Arabidopsis thaliana
The primitive heart tube is composed of an outer myocardial and an inner endocardial layer that will give rise to the cardiac valves and septa . Specification and differentiation of these two cell layers are among the earliest events in heart development , but the embryonic origins and genetic regulation of early endoc...	In its earliest functional form , the embryonic heart of all vertebrates is a simple linear tube consisting of two cell types . An outer muscular cell layer called the myocardium surrounds an inner vascular cell layer called the endocardium that connects the heart to the vascular system . The integration of both cell t...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Supporting", "Information" ]	[ "danio", "(zebrafish)", "developmental", "biology", "hematology" ]	2007	Early Endocardial Morphogenesis Requires Scl/Tal1
The 2009 H1N1 influenza pandemic provides a unique opportunity for detailed examination of the spatial dynamics of an emerging pathogen . In the US , the pandemic was characterized by substantial geographical heterogeneity: the 2009 spring wave was limited mainly to northeastern cities while the larger fall wave affect...	The determinants of influenza spatial spread are not fully understood , in part due to the insufficient geographic resolution of incidence data . We address this using a fine-grained private sector electronic health database of insurance claims data from health encounters in the US during 2009 . We used physician diagn...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "population", "modeling", "epidemiology", "disease", "dynamics", "influenza", "population", "dynamics", "biology", "and", "life", "sciences", "population", "biology", "infectious", "disease", "modeling", ...	2014	Spatial Transmission of 2009 Pandemic Influenza in the US
Salmonella enterica subsp . enterica contains more than 2 , 600 serovars of which four are of major medical relevance for humans . While the typhoidal serovars ( Typhi and Paratyphi A ) are human-restricted and cause enteric fever , non-typhoidal Salmonella serovars ( Typhimurium and Enteritidis ) have a broad host ran...	With an estimated 20 million typhoid cases and an even higher number of non-typhoid cases the health burden caused by salmonellosis is huge . Salmonellosis is caused by the bacterial species Salmonella enterica and over 2500 different serovars exist , of which four are of major medical relevance for humans: Typhi and P...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "statistics", "pathogens", "microbiology", "salmonella", "typhi", "multivariate", "analysis", "bacterial", "diseases", "protein", "expression", "mathematics", "enterobacteriaceae", "molec...	2019	Salmonella Typhi, Paratyphi A, Enteritidis and Typhimurium core proteomes reveal differentially expressed proteins linked to the cell surface and pathogenicity
Binding to the CD4 receptor induces conformational changes in the human immunodeficiency virus ( HIV-1 ) gp120 exterior envelope glycoprotein . These changes allow gp120 to bind the coreceptor , either CCR5 or CXCR4 , and prime the gp41 transmembrane envelope glycoprotein to mediate virus–cell membrane fusion and virus...	Human immunodeficiency virus type 1 ( HIV-1 ) is the cause of the global AIDS epidemic . HIV-1 gains entry into its target cells by fusing with the cell membrane , a process that begins with the interaction of the viral envelope glycoproteins with cell-surface receptors . HIV-1 uses two receptors on the target cell: CD...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/immunodeficiency", "viruses", "biophysics/experimental", "biophysical", "methods", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance", "infectious", "diseas...	2009	Soluble CD4 and CD4-Mimetic Compounds Inhibit HIV-1 Infection by Induction of a Short-Lived Activated State
Prion diseases are fatal neurodegenerative disorders causing motor dysfunctions , dementia and neuropathological changes such as spongiosis , astroglyosis and neuronal loss . The chain of events leading to the clinical disease and the role of distinct brain areas are still poorly understood . The role of nervous system...	For almost a century , prion disease symptoms , such as dementia and motor system defects , have been accompanied with neuropathological hallmarks in the central nervous system . In past decades , discrepancies between neuropathological changes and clinical symptoms showed that the processes triggering the disease rema...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/motor", "systems", "infectious", "diseases/prion", "diseases", "biophysics/experimental", "biophysical", "methods", "neurological", "disorders/prion", "diseases", "neuroscience/neurobiology", "of", "disease", "and", "regeneration" ]	2009	Impaired Axonal Transport in Motor Neurons Correlates with Clinical Prion Disease
Upstream open reading frames ( uORFs ) play important roles in regulating the main coding DNA sequences ( CDSs ) via translational repression . Despite their prevalence in the genomes , uORFs are overall discriminated against by natural selection . However , it remains unclear why in the genomes there are so many uORFs...	Upstream open reading frames ( uORFs ) in the 5′ untranslated regions ( UTRs ) of messenger RNAs can potentially inhibit translation of the downstream regions that encode proteins by sequestering protein-making machinery the ribosome . Moreover , mutations that destroy existing uORFs or create new ones are known to cau...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "messenger", "rna", "animals", "invertebrate", "genomics", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "untranslated", "regions", "experimental", "organism", "systems", "embryos", "cellular", "structur...	2018	Genome-wide maps of ribosomal occupancy provide insights into adaptive evolution and regulatory roles of uORFs during Drosophila development
Genetic variation among Aedes aegypti populations can greatly influence their vector competence for human pathogens such as the dengue virus ( DENV ) . While intra-species transcriptome differences remain relatively unstudied when compared to coding sequence polymorphisms , they also affect numerous aspects of mosquito...	Genetic variations among Aedes aegypti mosquito populations can greatly influence their ability to transmit human pathogens such as the dengue virus ( DENV ) . Some of these variations between mosquito populations are represented by differences in the expression of specific genes that control susceptibility to a pathog...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "antivirals", "mosquitoes", "emerging", "infectious", "diseases", "immunity", "vector", "biology", "innate", "immunity", "virology", "emerging", "viral", "diseases", "immunology", "host-pathogen", "interaction", "biology", "microbiology", "viral", "vectors" ]	2013	Transcriptomic Profiling of Diverse Aedes aegypti Strains Reveals Increased Basal-level Immune Activation in Dengue Virus-refractory Populations and Identifies Novel Virus-vector Molecular Interactions
Noma is a gangrenous disease that leads to severe disfigurement of the face with high morbidity and mortality , but its etiology remains unknown . Young children in developing countries are almost exclusively affected . The purpose of the study was to record and compare bacterial diversity in oral samples from children...	Noma is a devastating gangrenous disease that leads to severe facial disfigurement , but its cause remains unknown . It is associated with high morbidity and mortality and affects almost exclusively young children living in remote areas of developing countries , particularly in Africa . Several factors have been linked...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "oral", "medicine", "immunology", "genetics", "and", "genomics", "clinical", "genetics" ]	2012	Bacterial Diversity in Oral Samples of Children in Niger with Acute Noma, Acute Necrotizing Gingivitis, and Healthy Controls
Virus infection leads to the activation of transcription factor IRF3 and subsequent production of type I inteferons , which induce the transcription of various antiviral genes called interferon stimulated genes ( ISGs ) to eliminate viral infection . IRF3 activation requires phosphorylation , dimerization and nuclear t...	Innate immunity is the first line of defense to protect host from infection of invading pathogens . Production of type I inteferons by the innate immune cells is pivotal for the cellular antiviral immune responses . After virus infection , IFN-β transcription requires IRF3 , which is activated through phosphorylation ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TRIM26 Negatively Regulates Interferon-β Production and Antiviral Response through Polyubiquitination and Degradation of Nuclear IRF3
There are both pharmacodynamic and evolutionary reasons to use multiple rather than single antibiotics to treat bacterial infections; in combination antibiotics can be more effective in killing target bacteria as well as in preventing the emergence of resistance . Nevertheless , with few exceptions like tuberculosis , ...	In this study , we combine pharmacodynamic experiments using pathogenic strains of E . coli and S . aureus with mathematical and computer simulation models to explore the relative efficacies of two-drug antibiotic combinations in clearing infections and preventing the emergence of resistance . We develop a pharmacodyna...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "biology", "microbiology", "evolutionary", "biology", "population", "biology" ]	2013	The Pharmaco –, Population and Evolutionary Dynamics of Multi-drug Therapy: Experiments with S. aureus and E. coli and Computer Simulations
Skin pigment patterns are important , being under strong selection for multiple roles including camouflage and UV protection . Pigment cells underlying these patterns form from adult pigment stem cells ( APSCs ) . In zebrafish , APSCs derive from embryonic neural crest cells , but sit dormant until activated to produce...	Pigment patterns are crucial for the many aspects of animal biology , for example , providing camouflage , enabling mate selection and protecting against UV irradiation . These patterns are generated by one or more pigment cell-types , localised in the skin , but derived from specialised stem cells ( adult pigment stem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "cardiovascular", "anatomy", "vertebrates", "pigments", "neuroscience", "animals", "epithelial", "cells", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "stem", "cells", "materials", ...	2019	Endothelin receptor Aa regulates proliferation and differentiation of Erb-dependent pigment progenitors in zebrafish
Rift Valley fever ( RVF ) is an emerging neglected mosquito-borne viral zoonotic disease of domestic animals and humans , with potential for global expansion . The objectives of this study were: to assess perceived relative burden and seasonality of RVF in nomadic cattle herds and validate the burden with sero-prevalen...	Rift Valley fever ( RVF ) , is a neglected vector-borne zoonotic disease , commonly occurring in Africa and the Arabian Peninsula . It causes severe socio-economic and public health impacts on livestock , humans and environment , placing further economic demands on pastoralist communities already experiencing high leve...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "social", "sciences", "animals", "viruses", "rift", "valley", ...	2018	Participatory survey of Rift Valley fever in nomadic pastoral communities of North-central Nigeria: The associated risk pathways and factors
Bacterial infection of plants often begins with colonization of the plant surface , followed by entry into the plant through wounds and natural openings ( such as stomata ) , multiplication in the intercellular space ( apoplast ) of the infected tissues , and dissemination of bacteria to other plants . Historically , m...	Pathogen entry into host tissue is a critical first step in causing infection . For foliar bacterial plant pathogens , natural surface openings , such as stomata , are important entry sites into the leaf apoplast ( internal intercellular spaces ) . Recent studies have shown that plants respond to surface-inoculated bac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology", "microbiology", "host-pathogen", "interaction", "signaling", "in", "selected", "disciplines", "gene", "function", "plant", "science", "model", "organisms", "plant", "pathology", "molecular", "genetics", "bacterial", "pathogens", "arabidopsis", "thalian...	2011	A Genetic Screen Reveals Arabidopsis Stomatal and/or Apoplastic Defenses against Pseudomonas syringae pv. tomato DC3000
Elastase-mediated cleavage of cyclin E generates low molecular weight cyclin E ( LMW-E ) isoforms exhibiting enhanced CDK2–associated kinase activity and resistance to inhibition by CDK inhibitors p21 and p27 . Approximately 27% of breast cancers express high LMW-E protein levels , which significantly correlates with p...	Effective cancer treatment should include targeting not only drivers of tumorigenicity but also the downstream signaling pathways that these drivers activate . Special attention has to be given to the model systems that identify these targets and interrogating if these targets are poor prognostic indicators in patients...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "medicine", "obstetrics", "and", "gynecology", "cancers", "and", "neoplasms" ]	2012	LMW-E/CDK2 Deregulates Acinar Morphogenesis, Induces Tumorigenesis, and Associates with the Activated b-Raf-ERK1/2-mTOR Pathway in Breast Cancer Patients
Mutations in PINK1 , a mitochondrially targeted serine/threonine kinase , cause autosomal recessive Parkinson's disease ( PD ) . Substantial evidence indicates that PINK1 acts with another PD gene , parkin , to regulate mitochondrial morphology and mitophagy . However , loss of PINK1 also causes complex I ( CI ) defici...	Two genes linked to heritable forms of the neurodegenerative movement disorder Parkinson's disease ( PD ) , PINK1 and parkin , play important roles in mitochondrial homeostasis through mechanisms which include the degradation of dysfunctional mitochondria , termed mitophagy , and the maintenance of complex I ( CI ) act...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "cell", "biology", "neurology", "neurodegenerative", "diseases", "biology", "and", "life", "sciences", "molecular", "cell", "biology", "neuroscience" ]	2014	The Complex I Subunit NDUFA10 Selectively Rescues Drosophila pink1 Mutants through a Mechanism Independent of Mitophagy
A novel human oral challenge model with wild-type Salmonella Typhi ( S . Typhi ) was recently established by the Oxford Vaccine Group . In this model , 104 CFU of Salmonella resulted in 65% of participants developing typhoid fever ( referred here as typhoid diagnosis -TD- ) 6–9 days post-challenge . TD was diagnosed in...	Typhoid fever continues to be a public health problem and novel more effective vaccines are needed . To gain new insights into the host-pathogen interactions , which could aid in novel vaccine design , an improved human oral challenge model with wild-type Salmonella Typhi ( S . Typhi ) was recently developed . In this ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "phosphorylation", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "cloning", "salmonella", "typhi", "bacterial", "diseases", "...	2016	Oral Challenge with Wild-Type Salmonella Typhi Induces Distinct Changes in B Cell Subsets in Individuals Who Develop Typhoid Disease
The Src family of tyrosine kinases ( SFKs ) regulate numerous aspects of cell growth and differentiation and are under the principal control of the C-terminal Src Kinase ( Csk ) . Csk and SFKs share a modular design with the kinase domain downstream of the N-terminal SH2 and SH3 domains that regulate catalytic function...	The Src family of protein kinases ( SFKs ) are integral in many cellular signaling pathways . Aberrant SFK activity correlates with the development of various cancers and autoimmune diseases . Csk regulates these kinases via phosphorylation of a tyrosine residue on the C-terminal tail of SFKs , leading to suppression o...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[]	2013	Distal Loop Flexibility of a Regulatory Domain Modulates Dynamics and Activity of C-Terminal Src Kinase (Csk)
Lactate has long been considered a “waste” by-product of cell metabolism , and it accumulates at sites of inflammation . Recent findings have identified lactate as an active metabolite in cell signalling , although its effects on immune cells during inflammation are largely unexplored . Here we ask whether lactate is r...	Acidity is a feature of inflammatory sites such as arthritic synovia , atherosclerotic plaques , and tumor microenvironments and results in part from the accumulation of lactate as a product of glycolysis under hypoxic conditions . Recently it has emerged that lactate may be more than just a bystander and might act to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Lactate Regulates Metabolic and Pro-inflammatory Circuits in Control of T Cell Migration and Effector Functions
Unlike their model membrane counterparts , biological membranes are richly decorated with a heterogeneous assembly of membrane proteins . These proteins are so tightly packed that their excluded area interactions can alter the free energy landscape controlling the conformational transitions suffered by such proteins . ...	Biological membranes are a complex array of lipids and proteins . The typical bacterial membrane is made up of hundreds of copies of different species of membrane proteins embedded in a sea of different types of lipids . One of the distinguishing features of biological matter is the high degree of “crowding” to which t...	[ "Abstract", "Introduction", "Results", "Models", "Discussion" ]	[ "physics", "biochemistry", "proteins", "biology", "biophysics" ]	2012	Entropic Tension in Crowded Membranes
Gene regulatory networks give important insights into the mechanisms underlying physiology and pathophysiology . The derivation of gene regulatory networks from high-throughput expression data via machine learning strategies is problematic as the reliability of these models is often compromised by limited and highly va...	The identification of gene regulatory networks can provide vital information on biological processes . Despite numerous advancements in developing machine learning strategies , the stochastic nature of such biological systems complicates the construction of robust and reliable network structures . In recent years , the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "gene", "networks", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "mathematics", "molecular", "genetics", "gene", "expression", "regulatory", "networks", "biology", "mouse", "probability", "theory", "microarrays", "computer", "science", "computer...	2011	Interspecies Translation of Disease Networks Increases Robustness and Predictive Accuracy
The early inflammatory response to influenza virus infection contributes to severe lung disease and continues to pose a serious threat to human health . The mechanisms by which neutrophils gain entry to the respiratory tract and their role during pathogenesis remain unclear . Here , we report that neutrophils significa...	Influenza-associated morbidity and mortality due to yearly epidemics and sporadic , devastating pandemics are a significant health and economic burden . Severe complications arising from highly virulent viruses are associated with rapid , massive inflammatory cell infiltration . Although neutrophils are the predominant...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "immunologic", "subspecialties", "virology", "immunology", "biology", "microbiology" ]	2012	Matrix Metalloprotease 9 Mediates Neutrophil Migration into the Airways in Response to Influenza Virus-Induced Toll-Like Receptor Signaling
Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins . Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism . The identifica...	Small protein domains as Src Homology 3 often act as docking sites and serve as regulatory elements . To understand their role in the regulation of a protein’s activity , one needs to understand how their backbone and sidechain dynamics are affected when binding to peptides . We have therefore computationally analyzed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "chemical", "characterization", "chemical", "compounds", "aliphatic", "amino", "acids", "calorimetry", "split-decomposition", "method", "organic", "compounds", "multiple", "alignment", "calculation", "amino", "acids", "molecular", "biology", "tec...	2016	From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors
The DNA damage checkpoint response is controlled by the phosphatidylinositol 3-kinase-related kinases ( PIKK ) , including ataxia telangiectasia-mutated ( ATM ) and ATM and Rad3-related ( ATR ) . ATR forms a complex with its partner ATRIP . In budding yeast , ATR and ATRIP correspond to Mec1 and Ddc2 , respectively . A...	The ATR-ATRIP complex is recruited to sites of DNA damage by replication protein A-bound single-stranded DNA ( RPA-ssDNA ) , and controls cellular responses to various types of DNA damage . The recruitment of ATR-ATRIP to RPA-ssDNA is not sufficient for the kinase activation . The activation of ATR-ATRIP requires activ...	[ "Abstract", "Introduction", "Results", "Discussion", "Experimental", "procedures" ]	[ "phosphorylation", "molecular", "probe", "techniques", "cell", "cycle", "and", "cell", "division", "cell", "processes", "immunoblotting", "nucleotides", "dna", "damage", "mutation", "molecular", "biology", "techniques", "dna", "synthesis", "phase", "research", "and", ...	2019	Ddc2ATRIP promotes Mec1ATR activation at RPA-ssDNA tracts
Chagas disease is a neglected parasitic infection caused by the protozoan Trypanosoma cruzi ( T . cruzi ) that affects more than 6 million people , mainly in Latin America . Benznidazole is still the drug of choice in many countries to treat it in spite of its dosage regimen and adverse side effects such as such as all...	Chagas disease is a neglected parasitic infection caused by the protozoan Trypanosoma cruzi ( T . cruzi ) that affects more than 6 million people , mainly in Latin America . Benznidazole is still the drug of choice in many countries to treat it in spite of its dosage regimen and adverse side effects such as such as all...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animal", "models", "model...	2017	Elucidating the impact of low doses of nano-formulated benznidazole in acute experimental Chagas disease
Pandemic HIV-1 originated from the cross-species transmission of SIVcpz , which infects chimpanzees , while SIVcpz itself emerged following the cross-species transmission and recombination of monkey SIVs , with env contributed by the SIVgsn/mus/mon lineage that infects greater spot-nosed , mustached and mona monkeys . ...	Use of an entry coreceptor , in conjunction with CD4 , is the main determinant of HIV/SIV cell targeting , which in turn may be a central factor determining pathogenicity of infection . Two SIVs that generally do not cause AIDS in their natural hosts , SIVsmm of sooty mangabeys and SIVagm of African green monkeys , exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "pathology", "and", "laboratory", "medicine", "cd", "coreceptors", "enzymes", "pathogens", "immunology", "microbiology", "vertebrates", "enzymology", "animals", "mammals", "retro...	2018	Loss of CXCR6 coreceptor usage characterizes pathogenic lentiviruses
Predicting RNA-binding protein ( RBP ) specificity is important for understanding gene expression regulation and RNA-mediated enzymatic processes . It is widely believed that RBP binding specificity is determined by both the sequence and structural contexts of RNAs . Existing approaches , including traditional machine ...	RNA-binding proteins ( RBPs ) play a key role in modulating various cellular processes , including transcription , alternative splicing , and translational regulation . Identifying protein-RNA interactions and the binding preferences of RBPs are critical to unraveling the mechanism of post-transcriptional gene regulati...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "rna-binding", "proteins", "rna", "sequences", "neural", "networks", "neuroscience", "protein", "structure", "prediction", "protein", "structure", "sequence", "motif", "analysis", "thermodynamics", "research", "and", "analysis", "methods", "sequence", "analysis", "compute...	2019	Integrating thermodynamic and sequence contexts improves protein-RNA binding prediction
School closure policies are among the non-pharmaceutical measures taken into consideration to mitigate influenza epidemics and pandemics spread . However , a systematic review of the effectiveness of alternative closure policies has yet to emerge . Here we perform a model-based analysis of four types of school closure ...	School closure is a non-pharmaceutical intervention , considered for the mitigation of influenza epidemics and pandemics , whose impact and cost-effectiveness are still disputed . We propose the first systematic computational model study assessing the potential impact of different school closure policies . We consider ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2016	Model-Based Comprehensive Analysis of School Closure Policies for Mitigating Influenza Epidemics and Pandemics
Rhizoctonia solani is a soil-borne basidiomycete fungus with a necrotrophic lifestyle which is classified into fourteen reproductively incompatible anastomosis groups ( AGs ) . One of these , AG8 , is a devastating pathogen causing bare patch of cereals , brassicas and legumes . R . solani is a multinucleate heterokary...	The fungus Rhizoctonia solani is divided into several sub-species which cause disease in a range of plant species that includes most major agriculture , forestry and bioenergy species . This study focuses on sub-species AG8 which causes disease of cereals , canola and legumes , and compares its genome to other R . sola...	[ "Abstract", "Introduction", "Results", "&", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "functional", "genomics", "genome", "evolution", "sequence", "assembly", "tools", "genome", "sequencing", "fungi", "plant", "science", "genome", "analysis", "crops", "plant", "pathology", "molecular", "genetics", "molecular", "biology", "tech...	2014	Genome Sequencing and Comparative Genomics of the Broad Host-Range Pathogen Rhizoctonia solani AG8
Translational repression is often accompanied by mRNA degradation . In contrast , many mRNAs in germ cells and neurons are “stored" in the cytoplasm in a repressed but stable form . Unlike repression , the stabilization of these mRNAs is surprisingly little understood . A key player in Caenorhabditis elegans germ cell ...	One of the most striking developmental events is the oocyte-to-embryo transition that , in the absence of Pol II–dependent transcription , depends on regulated translation of maternal mRNAs . Prior to their activation , these maternal mRNAs need to be “stored" in the egg cytoplasm in a repressed but stable form . Surpr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "developmental", "biology", "molecular", "cell", "biology", "nucleic", "acids", "protein", "translation", "gene", "expression", "biology", "rna", "stability", "cell", "differentiation", "molecular", "biology" ]	2012	Genome-Wide Analysis of GLD-1–Mediated mRNA Regulation Suggests a Role in mRNA Storage
Active screening by mobile teams is considered the best method for detecting human African trypanosomiasis ( HAT ) caused by Trypanosoma brucei gambiense but the current funding context in many post-conflict countries limits this approach . As an alternative , non-specialist health care workers ( HCWs ) in peripheral h...	Human African trypanosomiasis ( HAT or sleeping sickness ) is an almost always fatal disease affecting poor people in rural , conflict-affected areas of sub-Saharan Africa . It is difficult to diagnose . Effective treatment exists , but because diagnostic and treatment services are usually based only in hospitals , man...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "health", "screening", "public", "health", "and", "epidemiology", "clinical", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "african", "trypanosomiasis", "neglected", "tropical", "diseases", "infectious", "dis...	2013	Syndromic Algorithms for Detection of Gambiense Human African Trypanosomiasis in South Sudan
Visceral leishmaniasis ( VL ) is characterized by parasite-specific immunosuppression besides an intense pro-inflammatory response . Lipopolisaccharide ( LPS ) has been implicated in the immune activation of T-cell deficient diseases such as HIV/AIDS and idiopathic lymphocytopenia . The source of LPS is gram-negative b...	Visceral leishmaniasis ( VL ) affects organs rich in lymphocytes , being characterized by intense Leishmania-induced T-cell depletion and reduction in other hematopoietic cells . In other infectious and non-infectious diseases in which the immune system is affected , such as HIV-AIDS and inflammatory bowel disease , da...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunology", "biology" ]	2011	Evidence That Lipopolisaccharide May Contribute to the Cytokine Storm and Cellular Activation in Patients with Visceral Leishmaniasis
The conduction of electrical signals through cardiac tissue is essential for maintaining the function of the heart , and conduction abnormalities are known to potentially lead to life-threatening arrhythmias . The properties of cardiac conduction have therefore been the topic of intense study for decades , but a number...	The electrochemical wave traversing the heart during every beat is essential for cardiac pumping function and supply of blood to the body . Understanding the stability of this wave is crucial to understanding how lethal arrhythmias are generated . Despite this importance , our knowledge of the physical determinants of ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "action", "potentials", "nervous", "system", "membrane", "potential", "junctional", "complexes", "electrophysiology", "neuroscience", "sodium", "gap", "junctions", "ion", "channels", "cellular", "structures", ...	2019	Properties of cardiac conduction in a cell-based computational model
Buruli ulcer ( BU ) caused by Mycobacterium ulcerans is a necrotizing skin disease usually starting with a subcutaneous nodule or plaque , which may ulcerate and progress , if untreated , over months and years . During the currently recommended antibiotic treatment with rifampicin/streptomycin plaque lesions tend to ul...	The tropical necrotizing skin disease Buruli ulcer ( BU ) caused by Mycobacterium ulcerans is associated with extensive tissue destruction and local immunosuppression caused by the macrolide exotoxin mycolactone . Chemotherapy with a combination of rifampicin and streptomycin for 8 weeks is the currently recommended tr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "anatomical", "pathology", "infectious", "diseases", "buruli", "ulcer", "histopathology", "diagnostic", "medicine", "pathology", "neglected", "tropical", "diseases" ]	2011	Histopathological Changes and Clinical Responses of Buruli Ulcer Plaque Lesions during Chemotherapy: A Role for Surgical Removal of Necrotic Tissue?
To explore the link between DNA damage and gene silencing , we induced a DNA double-strand break in the genome of Hela or mouse embryonic stem ( ES ) cells using I-SceI restriction endonuclease . The I-SceI site lies within one copy of two inactivated tandem repeated green fluorescent protein ( GFP ) genes ( DR-GFP ) ....	Genomic DNA can be modified by cytosine methylation . This epigenetic modification is layered on the primary genetic information and can silence the affected gene . Epigenetic modification has been implicated in cancer and aging . To date , the primary cause and the mechanism leading to DNA methylation are not known . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "in", "vitro", "mus", "(mouse)", "homo", "(human)", "mammals" ]	2007	DNA Damage, Homology-Directed Repair, and DNA Methylation
Broadly neutralizing antibody ( bnAb ) induction is a high priority for effective HIV-1 vaccination . VRC01-class bnAbs that target the CD4 binding site ( CD4bs ) of trimeric HIV-1 envelope ( Env ) glycoprotein spikes are particularly attractive to elicit because of their extraordinary breadth and potency of neutraliza...	Activation of appropriate naïve B cells is a critical initial step in the elicitation of broadly neutralizing antibodies ( bnAbs ) by HIV-1 vaccines . Germline-reverted forms of bnAbs partially mimic naïve B cell receptors , making them useful for designing and identifying immunogens that can initiate early stages of b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "hek", "293", "cells", "293t", "cells", "pathogens", "immunology", "biological", "cultures", "microbiology", "retrovirus...	2018	HIV-1 envelope glycan modifications that permit neutralization by germline-reverted VRC01-class broadly neutralizing antibodies

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