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Many bacterial pathogens hijack macrophages to egress from the port of entry to the lymphatic drainage and/or bloodstream , causing dissemination of life-threatening infections . However , the underlying mechanisms are not well understood . Here , we report that Salmonella infection generates directional electric field...	Bacterial pathogens can invade and survive within macrophages and use them as a vehicle to reach important organs of a human body , resulting in life-threatening infections , but the underlying mechanisms are not well understood . Our current understanding is that macrophages are recruited to the infected site by sensi...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "electronics", "cathodes", "pathogens", "immunology", "electricity", "microbiology", "salmonellosis", "bacterial...	2019	Infection-generated electric field in gut epithelium drives bidirectional migration of macrophages
To regulate shape changes , motility and chemotaxis in eukaryotic cells , signal transduction pathways channel extracellular stimuli to the reorganization of the actin cytoskeleton . The complexity of such networks makes it difficult to understand the roles of individual components , let alone their interactions and mu...	Single cells , such as amoeba and white blood cells , change shape and move in response to environmental stimuli . Their behaviour is a consequence of the intracellular properties balanced by external forces . The internal regulation is modulated by several proteins that interact with one another and with membrane lipi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology", "biophysics" ]	2012	How Cells Integrate Complex Stimuli: The Effect of Feedback from Phosphoinositides and Cell Shape on Cell Polarization and Motility
In plants , innate immune responses are initiated by plasma membrane-located pattern recognition receptors ( PRRs ) upon recognition of elicitors , including exogenous pathogen-associated molecular patterns ( PAMPs ) and endogenous damage-associated molecular patterns ( DAMPs ) . Arabidopsis thaliana produces more than...	Both animals and plants have evolved mechanisms to trigger innate immunity through perception of exogenous and endogenous molecules . In the model plant Arabidopsis thaliana , endogenous molecules such as the peptide elicitor PEP1 activate the immune response by means of cell surface-located receptors . Here we describ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "plant", "science" ]	2014	The Secreted Peptide PIP1 Amplifies Immunity through Receptor-Like Kinase 7
Cells interacting through an extracellular matrix ( ECM ) exhibit emergent behaviors resulting from collective intercellular interaction . In wound healing and tissue development , characteristic compaction of ECM gel is induced by multiple cells that generate tensions in the ECM fibers and coordinate their actions wit...	Collective behaviors of multiple cells interacting through an ECM are prohibitively complex to predict with a mechanistic computational model due to its highly nonlinear dynamics and high dimensional space . We introduce a methodology where nonlinear dynamics of single cells are superposed to predict collective multi-c...	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "cell", "physiology", "focal", "adhesions", "random", "variables", "covariance", "cell", "polarity", "simulation", "and", "modeling", "developmental", "biology", "systems", "science", "mathematics", "molecular", "development", "cellular", "structures", "and", "organelles"...	2019	Multi-Cell ECM compaction is predictable via superposition of nonlinear cell dynamics linearized in augmented state space
The African sleeping sickness parasite Trypanosoma brucei evades the host immune system through antigenic variation of its variant surface glycoprotein ( VSG ) coat . Although the T . brucei genome contains ∼1500 VSGs , only one VSG is expressed at a time from one of about 15 subtelomeric VSG expression sites ( ESs ) ....	Trypanosoma brucei causes African sleeping sickness , endemic to sub-Saharan Africa . Bloodstream form T . brucei is covered with a dense coat of variant surface glycoprotein ( VSG ) . Only one VSG is expressed at a time out of a vast repertoire of ∼1500 VSGs . The active VSG is transcribed in a telomeric VSG expressio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "molecular", "biology", "gene", "expression", "genetics", "epigenetics", "biology", "microbiology", "host-pathogen", "interaction", "chromatin", "genetics", "and", "genomics", "parasitology" ]	2012	Histone H1 Plays a Role in Heterochromatin Formation and VSG Expression Site Silencing in Trypanosoma brucei
Protein kinases C ( PKCs ) and extracellular signal-regulated kinases ( ERKs ) are evolutionary conserved cell signalling enzymes that coordinate cell function . Here we have employed biochemical approaches using ‘smart’ antibodies and functional screening to unravel the importance of these enzymes to Schistosoma manso...	Parasitic blood flukes , also called schistosomes , cause human schistosomiasis , a neglected tropical disease and major public health problem in developing countries , especially sub-Saharan Africa . Sustainable control of schistosomiasis is difficult , mainly because the complex life cycle of the parasite involves a ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "erk", "signaling", "cascade", "protein", "kinase", "signaling", "cascade", "protein", "kinase", "c", "signaling", "signal", "transduction", "infectious", "diseases", "medicine", "and", "health", "sciences", "helminth", "infections", "cell", "biology", "biology", "and...	2014	Protein Kinase C and Extracellular Signal-Regulated Kinase Regulate Movement, Attachment, Pairing and Egg Release in Schistosoma mansoni
Extracellular guidance cues steer axons towards their targets by eliciting morphological changes in the growth cone . A key part of this process is the asymmetric recruitment of the cytoplasmic scaffolding protein MIG-10 ( lamellipodin ) . MIG-10 is thought to asymmetrically promote outgrowth by inducing actin polymeri...	To form neural circuits , axons must navigate through the developing nervous system to reach their correct targets . Axon navigation is led by the growth cone , a structure at the tip of the growing axon that responds to extracellular guidance cues . Many of these guidance cues and their receptors have been identified ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "developmental", "neuroscience", "axon", "guidance", "biology", "morphogenesis", "neuroscience" ]	2012	MIG-10 Functions with ABI-1 to Mediate the UNC-6 and SLT-1 Axon Guidance Signaling Pathways
Mutations in LACERATA ( LCR ) , FIDDLEHEAD ( FDH ) , and BODYGUARD ( BDG ) cause a complex developmental syndrome that is consistent with an important role for these Arabidopsis genes in cuticle biogenesis . The genesis of their pleiotropic phenotypes is , however , poorly understood . We provide evidence that neither ...	As the skin of a plant , the epidermis mediates a broad set of protective functions which includes defense against abiotic environmental stresses and pathogens . The majority of its barrier capacity is localized to the outermost cell wall , which is covered by a waxy cuticle . Several distinct cuticular mutants in the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology/plant-environment", "interactions", "plant", "biology/plant", "growth", "and", "development", "plant", "biology/plant", "biochemistry", "and", "physiology", "plant", "biology/plant", "genetics", "and", "gene",...	2009	Dissection of the Complex Phenotype in Cuticular Mutants of Arabidopsis Reveals a Role of SERRATE as a Mediator
Candida albicans is a human commensal and clinically important fungal pathogen that grows as both yeast and hyphal forms during human , mouse and zebrafish infection . Reactive oxygen species ( ROS ) produced by NADPH oxidases play diverse roles in immunity , including their long-appreciated function as microbicidal ox...	Over 45 years ago chronic granulomatous disease ( CGD ) was ascribed to a failure of neutrophils to mount a respiratory burst , and it is now known to result from primary genetic deficiencies in the phagocyte NADPH oxidase complex . Recent work suggests that reactive oxygen species produced by NADPH oxidases have other...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "Methods" ]	[]	2013	NADPH Oxidase-Driven Phagocyte Recruitment Controls Candida albicans Filamentous Growth and Prevents Mortality
When patterns are set during embryogenesis , it is expected that they are straightly established rather than subsequently modified . The patterning of the three mouse molars is , however , far from straight , likely as a result of mouse evolutionary history . The first-formed tooth signaling centers , called MS and R2 ...	Organs , such as teeth , that form regular patterns are of particular interest to developmental biologists . These patterns are established early in the embryo , and it has generally been thought the organs appear in what is their final position . Recent studies that focus on the dynamics of patterning events challenge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "motility", "medicine", "and", "health", "sciences", "developmental", "biology", "embryos", "morphogenesis", "cellular", "structures", "and", "organelles", "pattern", "formation", "digestive", "system", "embryology", "embryonic", "pattern", "formation", "biologica...	2019	Modeling Edar expression reveals the hidden dynamics of tooth signaling center patterning
A common property of aging in all animals is that chronologically and genetically identical individuals age at different rates . To unveil mechanisms that influence aging variability , we identified markers of remaining lifespan for Caenorhabditis elegans . In transgenic lines , we expressed fluorescent reporter constr...	One of the long-standing mysteries in aging is that some individuals die early whereas others die late . The age at which a specific individual will die is difficult or impossible to predict , and thus a fundamental aspect of aging in all animals is that it is stochastic . Aging stochasticity is particularly interestin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "aging", "physiological", "processes", "developmental", "biology", "organism", "development", "evolutionary", "biology", "physiology", "biology", "anatomy", "and", "physiology" ]	2011	Variable Pathogenicity Determines Individual Lifespan in Caenorhabditis elegans
Dominance hierarchies are group-level properties that emerge from the aggression of individuals . Although individuals can gain critical benefits from their position in a hierarchy , we do not understand how real-world hierarchies form . Nor do we understand what signals and decision-rules individuals use to construct ...	An individual’s success depends critically on socially-constructed properties such as rank . A detailed study of two independent captive parakeet groups reveals how these properties come into being . We show that individuals can use localized patterns in the aggression network to learn the relative ranks of individuals...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Social Feedback and the Emergence of Rank in Animal Society
Phagocytosis is required for proliferation and pathogenesis of Entamoeba histolytica and erythrophagocytosis is considered to be a marker of invasive amoebiasis . Ca2+ has been found to play a central role in the process of phagocytosis . However , the molecular mechanisms and the signalling mediated by Ca2+ still rema...	Entamoeba histolytica is one of the major causes of morbidity and mortality in developing countries . Phagocytosis plays an important role in both survival and virulence and has been used as a virulence marker . Inhibition of phagocytosis leads to a defect in cellular proliferation . Therefore , the molecules that part...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "parastic", "protozoans", "signal", "transduction", "molecular", "cell", "biology", "entamoeba", "histolytica", "parasitology", "protozoology", "biology", "microbiology", "host-pathogen", "interaction" ]	2012	The Calmodulin-like Calcium Binding Protein EhCaBP3 of Entamoeba histolytica Regulates Phagocytosis and Is Involved in Actin Dynamics
The vertebrate gut harbors a vast community of bacterial mutualists , the composition of which is modulated by the host immune system . Many gastrointestinal ( GI ) diseases are expected to be associated with disruptions of host-bacterial interactions , but relatively few comprehensive studies have been reported . We h...	Bacterial mutualists within the gastrointestinal tract aid digestion , promote development of the gut immune system , and provide competitive barriers to pathogen invasion . The host , in return , provides bacteria with safe housing and food during lean times . The composition of the gut microbiota is controlled in par...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "primates", "infectious", "diseases", "pathology", "virology", "microbiology", "computational", "biology", "molecular", "biology", "genetics", "and", "genomics", "eubacteria" ]	2008	The Macaque Gut Microbiome in Health, Lentiviral Infection, and Chronic Enterocolitis
Circadian entrainment is necessary for rhythmic physiological functions to be appropriately timed over the 24-hour day . Disruption of circadian rhythms has been associated with sleep and neuro-behavioral impairments as well as cancer . To date , light is widely accepted to be the most powerful circadian synchronizer ,...	The robust timing , or phase , of the circadian clock is critical in directing and synchronizing molecular , cellular , and organismal behaviors . The clock's failure to maintain precision and adaption is associated with sleeping disorders , depression , and cancer . To better study and control the timing of circadian ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "computational", "biology/transcriptional", "regulation" ]	2008	Circadian Phase Resetting via Single and Multiple Control Targets
Errors throughout gene expression are likely deleterious , hence genomes are under selection to ameliorate their consequences . Additional stop codons ( ASCs ) are in-frame nonsense ‘codons’ downstream of the primary stop which may be read by translational machinery should the primary stop have been accidentally read t...	In all organisms , gene expression is error-prone . One such error , translational read-through , occurs where the primary stop codon of an expressed gene is missed by the translational machinery . Failure to terminate is likely to be costly , hence genomes are under selection to prevent this from happening . One propo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "bacteriology", "3'", "utr", "messenger", "rna", "microbiology", "untranslated", "regions", "bacterial", "genetics", "microbial", "genetics", "bacteria", "microbial", "genomics", "bacterial", "genomics", "gene", "expression", "mollicutes", "comparative", "genomics", "bioc...	2019	In eubacteria, unlike eukaryotes, there is no evidence for selection favouring fail-safe 3’ additional stop codons
Homologous recombination is central to repair DNA double-strand breaks , either accidently arising in mitotic cells or in a programed manner at meiosis . Crossovers resulting from the repair of meiotic breaks are essential for proper chromosome segregation and increase genetic diversity of the progeny . However , mecha...	Homologous recombination is a DNA repair mechanism that is essential to preserve the integrity of genetic information and thus to prevent cancer formation . Homologous recombination is also used during sexual reproduction to generate genetic diversity in the offspring by shuffling parental chromosomes . Here , we ident...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "protein", "interactions", "brassica", "dna-binding", "proteins", "phylogenetics", "data", "management", "model", "organisms", "phylogenetic", "analysis", "experimental", "organism", "systems", "dna", "plants", "homologous", "recombination", "research", "and", ...	2018	FIGL1 and its novel partner FLIP form a conserved complex that regulates homologous recombination
We compared conscious and nonconscious processing of briefly flashed words using a visual masking procedure while recording intracranial electroencephalogram ( iEEG ) in ten patients . Nonconscious processing of masked words was observed in multiple cortical areas , mostly within an early time window ( <300 ms ) , acco...	What is the neural signature of the conscious perception of a visual stimulus ? To address this question , we recorded neural activity directly from the brains of human subjects ( who were undergoing neural surgery for medical reasons ) . This rare opportunity afforded greater spatial and temporal resolution than nonin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2009	Converging Intracranial Markers of Conscious Access
Ebola virus ( EBOV ) , family Filoviridae , emerged in 1976 on the African continent . Since then it caused several outbreaks of viral hemorrhagic fever in humans with case fatality rates up to 90% and remains a serious Public Health concern and biothreat pathogen . The most pathogenic and best-studied species is Zaire...	It is currently believed that Ebola virus ( EBOV ) enters cells via macropinocytosis following which , the cysteine proteases cathepsin B and L ( CatB , CatL ) cleave the viral glycoprotein ( GP ) allowing exposure of its core receptor-binding and fusion domain thus facilitating subsequent infection . We studied the ef...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "emerging", "infectious", "diseases", "virology", "biology", "microbiology", "pathogenesis" ]	2012	Cathepsin B & L Are Not Required for Ebola Virus Replication
Rift Valley fever virus ( RVFV ) causes a viral zoonosis , with discontinuous epizootics and sporadic epidemics , essentially in East Africa . Infection with this virus causes severe illness and abortion in sheep , goats , and cattle as well as other domestic animals . Humans can also be exposed through close contact w...	Rift valley fever virus ( RVFV ) is an arthropod-borne virus that causes serious illness in both animals and humans . RVFV is transmitted by direct contact with infectious tissues or by the bites of infected mosquito species of the Aedes and Culex genuses . Its distribution in tropical forests in central Africa is poor...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "livestock", "medicine", "and", "health", "sciences", "rift", "valley", "fever", "virus", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "immunology", "rna", "extraction", "microbiology", "vertebrates", "...	2016	Rift Valley Fever Virus Circulating among Ruminants, Mosquitoes and Humans in the Central African Republic
The Hedgehog ( Hh ) signaling pathway plays a key role in cell fate specification , proliferation , and survival during mammalian development . Cells require a small organelle , the primary cilium , to respond properly to Hh signals and the key regulators of Hh signal transduction exhibit dynamic localization to this o...	The importance of cilia in development and disease has become broadly appreciated in recent years due in part to their roles in signal transduction . Despite this attention , crucial aspects of ciliary assembly and function , such as the mechanisms controlling ciliary assembly and the signal transduction events occurri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "enzymology", "phosphatases", "developmental", "biology", "regulator", "genes", "mathematics", "statistics", "(mathematics)", "gene", "types", "embryos", "cellul...	2017	Cell Cycle-Related Kinase (CCRK) regulates ciliogenesis and Hedgehog signaling in mice
A large number of highly pathogenic bacteria utilize secretion systems to translocate effector proteins into host cells . Using these effectors , the bacteria subvert host cell processes during infection . Legionella pneumophila translocates effectors via the Icm/Dot type-IV secretion system and to date , approximately...	Many pathogenic bacteria exert their function by translocating a set of proteins , termed effectors , into the cytoplasm of their host cell . These effectors subvert various host cell processes for the benefit of the bacteria . Our goal in this study was to identify novel effectors in a genomic scale , towards a better...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "computational", "biology/systems", "biology", "computational", "biology/genomics", "infectious", "diseases/respiratory", "infections" ]	2009	Genome-Scale Identification of Legionella pneumophila Effectors Using a Machine Learning Approach
Exonuclease-mediated RNA decay in plants is known to be involved primarily in endogenous RNA degradation , and several RNA decay components have been suggested to attenuate RNA silencing possibly through competing for RNA substrates . In this paper , we report that overexpression of key cytoplasmic 5’–3’ RNA decay path...	RNA silencing and RNA decay are two essential pathways that determine the fate of cellular RNA molecules . RNA decay has been suggested to compete with RNA silencing for the RNA substrates and thus to suppress RNA silencing in plants . In this report , we show that the deficiency of key cytoplasmic 5’–3’ RNA decay path...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "rna", "interference", "gene", "regulation", "brassica", "viruses", "plant", "science", "model", "organisms", "rna", "viruses", "genetically", "modified", "plants", "experimental", "organism", "systems", "epigenetics", "molecular", "...	2018	RNA decay is an antiviral defense in plants that is counteracted by viral RNA silencing suppressors
The protein complex known as cohesin binds pericentric regions and other sites of eukaryotic genomes to mediate cohesion of sister chromatids . In budding yeast Saccharomyces cerevisiae , cohesin also binds silent chromatin , a repressive chromatin structure that functionally resembles heterochromatin of higher eukaryo...	Replication of chromosomes in each cell cycle produces pairs of identical sister chromatids that are held together by a protein complex known as cohesin . At mitosis , cohesin is dismantled , permitting segregation of one full set of chromosomes to each daughter cell . Cohesin binds at discrete sites along chromatids ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Targeted Sister Chromatid Cohesion by Sir2
RNA silencing is one of the main defense mechanisms employed by plants to fight viruses . In change , viruses have evolved silencing suppressor proteins to neutralize antiviral silencing . Since the endogenous and antiviral functions of RNA silencing pathway rely on common components , it was suggested that viral suppr...	To better understand the specific effect of p19 viral suppressor of RNA silencing ( VSR ) on antiviral silencing and endogenous small RNA pathways , we generated a N . benthamiana plant ( p19syn ) capable of sustaining the ectopic expression of the Cymbidium ringspot virus ( CymRSV ) p19 upon infection with a suppresso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "anatomy", "rna", "interference", "gene", "regulation", "viruses", "micrornas", "plant", "science", "rna", "viruses", "immunoprecipitation", "genetically", "modified", "plants", "epigenetics", "plants", "flowering", "plants", "genetic", "engineer...	2016	Distinct Effects of p19 RNA Silencing Suppressor on Small RNA Mediated Pathways in Plants
Fibromuscular dysplasia ( FMD ) is a nonatherosclerotic vascular disease leading to stenosis , dissection and aneurysm affecting mainly the renal and cerebrovascular arteries . FMD is often an underdiagnosed cause of hypertension and stroke , has higher prevalence in females ( ~80% ) but its pathophysiology is unclear ...	Fibromuscular Dysplasia ( FMD ) is a vascular disease characterized by a succession of occlusions and dilatation of medium-sized arteries ( e . g renal , carotid or coronary arteries ) with important health consequences , mainly resistant hypertension and stroke . FMD is an atypical vascular disease because it is not a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "renal", "arteries", "fibroblasts", "genetic", "predisposition", "arteries", "connective", "tissue", "cells", "blood", "vessels", "animal", "cells", "connective", "tissue", "biological", "tissue", "ge...	2016	PHACTR1 Is a Genetic Susceptibility Locus for Fibromuscular Dysplasia Supporting Its Complex Genetic Pattern of Inheritance
The proper biological functioning of proteins often relies on the occurrence of coordinated fluctuations around their native structure , or on their ability to perform wider and sometimes highly elaborated motions . Hence , there is considerable interest in the definition of accurate coarse-grained descriptions of prot...	Decades of experimental evidence have underlined the fact that protein structures can hardly be considered as static objects . To understand how a protein achieves its biological purpose , it is therefore quite often necessary to unravel the complexity of its dynamical behavior . However , the definition of accurate an...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Effective Harmonic Potentials: Insights into the Internal Cooperativity and Sequence-Specificity of Protein Dynamics
Damage tolerance mechanisms mediating damage-bypass and gap-filling are crucial for genome integrity . A major damage tolerance pathway involves recombination and is referred to as template switch . Template switch intermediates were visualized by 2D gel electrophoresis in the proximity of replication forks as X-shaped...	Completion of DNA replication is essential for cellular survival . Both endogenous processes and exogenous DNA damage can lead to lesions that impede DNA replication or result in an accumulation of DNA gaps . Recombination plays an important role in facilitating replication completion under conditions of replication st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics/chromosome", "biology" ]	2010	Replication and Recombination Factors Contributing to Recombination-Dependent Bypass of DNA Lesions by Template Switch
Although increased capillary permeability is the major clinical feature associated with severe dengue infections the mechanisms underlying this phenomenon remain unclear . Dextran clearance methodology has been used to investigate the molecular sieving properties of the microvasculature in clinical situations associate...	Dengue is a potentially serious common viral infection with no specific treatment . Plasma leakage from small blood vessels is the major severe problem , but we do not understand how this occurs . Techniques using controlled infusions of carbohydrate solutions , combined with careful measurement of the rate that the di...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "immune", "physiology", "clinical", "research", "design", "integrative", "physiology", "dengue", "anatomy", "and", "physiology", "immunology", "pediatrics", "critical", "care", "team", "organization", "physiological", "processes", "hemorrhagic", "fever", "with...	2011	Dextran Fractional Clearance Studies in Acute Dengue Infection
Efficient adaptation to iron starvation is an essential virulence determinant of the most common human mold pathogen , Aspergillus fumigatus . Here , we demonstrate that the cytosolic monothiol glutaredoxin GrxD plays an essential role in iron sensing in this fungus . Our studies revealed that ( i ) GrxD is essential f...	Aspergillus fumigatus is a ubiquitous saprophytic mold and the major causative pathogen causing life-threatening aspergillosis . To improve therapy , there is an urgent need for a better understanding of the fungal physiology . We have previously shown that adaptation to iron starvation is an essential virulence attrib...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "aspergillus", "fumigatus", "medicine", "and", "health", "sciences", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "aspergillus", "gene", "regulation", "pathogens", "regulatory", "proteins", "microbiology", "dna-binding", ...	2019	The monothiol glutaredoxin GrxD is essential for sensing iron starvation in Aspergillus fumigatus
Partial duplication of genetic material is prevalent in eukaryotes and provides potential for evolution of new traits . Prokaryotes , which are generally haploid in nature , can evolve new genes by partial chromosome duplication , known as merodiploidy . Little is known about merodiploid formation during genetic exchan...	Merodiploids are defined as cells possessing a partial duplication of their genetic material , which potentially allows evolution of new genes . Historically , some have been observed in studies of natural genetic transformation . Transformation allows the bacteria to take up foreign DNA and incorporate it into their g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Natural Genetic Transformation Generates a Population of Merodiploids in Streptococcus pneumoniae
Spo11 is the topoisomerase-like enzyme responsible for the induction of the meiosis-specific double strand breaks ( DSBs ) , which initiates the recombination events responsible for proper chromosome segregation . Nineteen PCR-induced alleles of SPO11 were identified and characterized genetically and cytologically . Re...	Most eukaryotes depend on the meiotic division to segregate each pair of chromosomes properly into their gametes . Chromosome segregation mistakes happening during meiosis are responsible for most miscarriages as well as many diseases such as Down's and Kleinfelter's syndromes in humans . Proper chromosome segregation ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	High Throughput Sequencing Reveals Alterations in the Recombination Signatures with Diminishing Spo11 Activity
The evolution of drug resistant bacteria is a severe public health problem , both in hospitals and in the community . Currently , some countries aim at concentrating highly specialized services in large hospitals in order to improve patient outcomes . Emergent resistant strains often originate in health care facilities...	The increasing spread of bacteria , which are resistant to antibiotics , is a serious threat to clinical care . Currently , several countries aim at concentrating highly specialized services in large hospitals in order to improve patient outcomes . However , empirical studies have shown that resistance levels correlate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2011	On Being the Right Size: The Impact of Population Size and Stochastic Effects on the Evolution of Drug Resistance in Hospitals and the Community
The β1i , β2i and β5i immunoproteasome subunits have an important role in defining the repertoire of MHC class I-restricted epitopes . However , the impact of combined deficiency of the three immunoproteasome subunits in the development of protective immunity to intracellular pathogens has not been investigated . Here ...	CD8+ t lymphocytes are cells of the immune system that mediate control of intracellular infections by viruses , prokaryote as well as eukaryote pathogens . To confer protection , these lymphocytes need to be elicited by pathogen peptides that are presented in association with MHC class I molecules . The degradation of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "spleen", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "clinical", "medicine", "protozoans", "cytotoxic", "t", "cells", "research", "and", "analy...	2016	The Combined Deficiency of Immunoproteasome Subunits Affects Both the Magnitude and Quality of Pathogen- and Genetic Vaccination-Induced CD8+ T Cell Responses to the Human Protozoan Parasite Trypanosoma cruzi
Decreased bioavailability of nitric oxide ( NO ) is a major contributor to the pathophysiology of severe falciparum malaria . Tetrahydrobiopterin ( BH4 ) is an enzyme cofactor required for NO synthesis from L-arginine . We hypothesized that systemic levels of BH4 would be decreased in children with cerebral malaria , c...	Vascular nitric oxide ( NO ) bioavailability is decreased in severe falciparum malaria and associated with microvascular dysfunction , increased activation of the cells lining blood vessels ( endothelial cells ) and increased parasite biomass . Tetrahydrobiopterin ( BH4 ) is an essential cofactor for nitric oxide synth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Impaired Systemic Tetrahydrobiopterin Bioavailability and Increased Oxidized Biopterins in Pediatric Falciparum Malaria: Association with Disease Severity
While the domestication history of Asian rice has been extensively studied , details of the evolution of African rice remain elusive . The inner Niger delta has been suggested as the center of origin but molecular data to support this hypothesis is lacking . Here , we present a comprehensive analysis of the evolutionar...	For many crops it is not clear how they were domesticated from their wild progenitors . Transition from a wild to domesticated state required a series of genetic changes , and studying the evolutionary origin of these domestication-causing mutations are key to understanding the domestication origins of a crop . Moreove...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "biogeography", "animal", "types", "taxonomy", "ecology", "and", "environmental", "sciences", "niger", "domestic", "animals", "population", "genetics", "geographical", "locations", "animals", "genetic", "mapping", "mutation", "phylogenetics", "data", "management", "rice",...	2019	The complex geography of domestication of the African rice Oryza glaberrima
Developmental patterning involves the progressive subdivision of tissue into different cell types by invoking different genetic programs . In particular , cell-cell signaling is a universally deployed means of specifying distinct cell fates in adjacent cells . For this mechanism to be effective , it is essential that a...	Much of the process of animal development is concerned with giving cells specific instructions as to what type of cell they are to become—their “fate” . Often , it is even necessary to assign very different fates to cells that are adjacent to each other in the tissue . In such cases , cell-to-cell signaling is frequent...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "animals", "notch", "signaling", "dna", "transcription", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "sequence", "motif", "analysis", "morphogenesis", "drosophila...	2018	Lateral inhibition: Two modes of non-autonomous negative autoregulation by neuralized
Most of the Leishmania genome is reported to be constitutively expressed during the life cycle of the parasite , with a few regulated genes . Inter-species comparative transcriptomics evidenced a low number of species-specific differences related to differentially distributed genes or the differential regulation of con...	Leishmania is a group of parasites ( Protozoa , Trypanosomatidae ) responsible for a wide spectrum of clinical forms . Among the factors explaining this phenotypic polymorphism , parasite features are important contributors . One approach to identify them consists in characterizing the gene expression profiles througho...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "microbiology", "parasitology" ]	2011	Comparative Gene Expression Analysis throughout the Life Cycle of Leishmania braziliensis: Diversity of Expression Profiles among Clinical Isolates
Sickle cell disease ( SCD ) is a hematological disorder leading to blood vessel occlusion accompanied by painful episodes and even death . Red blood cells ( RBCs ) of SCD patients have diverse shapes that reveal important biomechanical and bio-rheological characteristics , e . g . their density , fragility , adhesive p...	There are many hematological disorders in the human circulation involving significant alteration of the shape and size of red blood cells ( RBCs ) , e . g . sickle cell disease ( SCD ) , spherocytosis , diabetes , HIV , etc . These morphological alterations reflect subtle multiscale processes taking place at the protei...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results/discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "neural", "networks", "genetic", "diseases", "neuroscience", "factor", "analysis", "mathematics", "red", "blood", "cells", "statistics", "(mathematics)", "artificial", "intelligence", "hemoglobinopathies", "autoso...	2017	A deep convolutional neural network for classification of red blood cells in sickle cell anemia
The flavoenzyme pyranose dehydrogenase ( PDH ) from the litter decomposing fungus Agaricus meleagris oxidizes many different carbohydrates occurring during lignin degradation . This promiscuous substrate specificity makes PDH a promising catalyst for bioelectrochemical applications . A generalized approach to simulate ...	Generally , enzymes are perceived as being specific for both their substrates and the reaction they catalyze . This standard paradigm started to shift and currently enzyme promiscuity towards various substrates is perceived rather as the rule than the exception . Enzyme promiscuity seems to be vital for proteins to acq...	[ "Abstract", "Introduction", "Methods", "Results/Discussion", "Conclusions" ]	[ "computational", "chemistry", "molecular", "dynamics", "biology", "and", "life", "sciences", "chemistry", "physical", "sciences", "computational", "biology", "biophysics", "biophysical", "simulations" ]	2014	Pyranose Dehydrogenase Ligand Promiscuity: A Generalized Approach to Simulate Monosaccharide Solvation, Binding, and Product Formation
Cryptococcosis is an important fungal infection in immunocompromised individuals , especially those infected with HIV . In Brazil , despite the free availability of antiretroviral therapy ( ART ) in the public health system , the mortality rate due to Cryptococcus neoformans meningitis is still high . To obtain a more ...	The members of the Cryptococcus neoformans / Cryptococcus gattii species complex are the cause of cryptococcosis , a life-threatening human disease responsible for 624 , 000 deaths annually . Infection is acquired through inhalation of dehydrated yeast cells from environmental sources . After reaching the lungs , the f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cryptococcus", "neoformans", "medicine", "and", "health", "sciences", "cryptococcus", "gattii", "cryptococcus", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "genetics", "geographical", "locations", "microbiology", "fungi", "phylogenetic", "analy...	2017	MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil
Invertebrates rely on innate immunity to respond to the entry of foreign microorganisms . One of the important innate immune responses in arthropods is the activation of prophenoloxidase ( proPO ) by a proteolytic cascade finalized by the proPO-activating enzyme ( ppA ) , which leads to melanization and the elimination...	Melanization is an important reaction in most multicellular organisms , both animals and plants . The initiation steps of this reaction in invertebrates are catalyzed by the prophenoloxidase ( proPO ) activating system a proteolytic enzyme cascade , which primary function is to recognize cell wall products from microor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "immunology", "evolutionary", "biology", "evolutionary", "immunology", "immune", "response", "immune", "system" ]	2014	Caspase-1-Like Regulation of the proPO-System and Role of ppA and Caspase-1-Like Cleaved Peptides from proPO in Innate Immunity
Human African trypanosomiasis ( HAT ) or sleeping sickness leads to a complex neuropsychiatric syndrome with characteristic sleep alterations . Current division into a first , hemolymphatic stage and second , meningoencephalitic stage is primarily based on the detection of white blood cells and/or trypanosomes in the c...	The clinical picture of the parasitic disease human African trypanosomiasis ( HAT , also called sleeping sickness ) is dominated by sleep alterations . We here used actigraphy to evaluate patients affected by the Gambiense form of HAT . Actigraphy is based on the use of battery-run , wrist-worn devices similar to watch...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "diagnostic", "medicine", "neglected", "tropical", "diseases" ]	2012	Actigraphy in Human African Trypanosomiasis as a Tool for Objective Clinical Evaluation and Monitoring: A Pilot Study
Genetic analyses in Drosophila epithelia have suggested that the phenomenon of “cell competition” could participate in organ homeostasis . It has been speculated that competition between different cell populations within a growing organ might play a role as either tumor promoter or tumor suppressor , depending on the c...	One of the major challenges of developmental biology and cancer research is to get a better understanding of how different signals regulate proper organ growth and prevent tumor formation . Even though there is a strong correlation between tumor progression and Myc family misexpression or Hippo signaling pathway malfun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/cancer", "genetics", "developmental", "biology", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2010	dMyc Functions Downstream of Yorkie to Promote the Supercompetitive Behavior of Hippo Pathway Mutant Cells
The Ypd1 phosphorelay protein is a central constituent of fungal two-component signal transduction pathways . Inhibition of Ypd1 in Saccharomyces cerevisiae and Cryptococcus neoformans is lethal due to the sustained activation of the ‘p38-related’ Hog1 stress-activated protein kinase ( SAPK ) . As two-component signall...	As fungi-attributed human deaths are increasing , there is an urgent need to develop new antifungal treatments . Two-component related proteins , such as the Ypd1 phosphorelay protein , have been heralded as antifungal targets as they are not found in humans and because inactivation of YPD1 in several different fungi c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "phosphorylation", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "immunology", "microbiology", "animal", "models", "fungi", "model", "organi...	2017	Blocking two-component signalling enhances Candida albicans virulence and reveals adaptive mechanisms that counteract sustained SAPK activation
Central questions in regenerative biology include how stem cells are maintained and how they transition from self-renewal to differentiation . Germline stem cells ( GSCs ) in Caeno-rhabditis elegans provide a tractable in vivo model to address these questions . In this system , Notch signaling and PUF RNA binding prote...	Stem cells lie at the heart of metazoan development , regeneration , and tissue homeostasis , but the molecular basis of their regulation is poorly understood in their natural context within an animal . Here we investigate this problem in the nematode gonad , where germline stem cells are maintained by Notch signaling ...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "tumor", "stem", "cells", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "nuclear", "staining", "population", "genetics", "gene", "pool", "cell", "differentiation", "germ", "cells", "developmental", "biology", "stem", "cells", "population...	2017	SYGL-1 and LST-1 link niche signaling to PUF RNA repression for stem cell maintenance in Caenorhabditis elegans
Replicating viruses have broad applications in biomedicine , notably in cancer virotherapy and in the design of attenuated vaccines; however , uncontrolled virus replication in vulnerable tissues can give pathology and often restricts the use of potent strains . Increased knowledge of tissue-selective microRNA expressi...	Attenuated viruses have found important applications in medicine , including their use as vaccines ( notably for measles , mumps , polio , influenza , and chicken pox ) and their experimental development as selective cancer-killing agents , so-called “virotherapy . ” Wild-type versions are often most effective in both ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/applied", "microbiology" ]	2009	Use of Tissue-Specific MicroRNA to Control Pathology of Wild-Type Adenovirus without Attenuation of Its Ability to Kill Cancer Cells
Rodents are reservoirs and hosts for several zoonotic diseases such as plague , leptospirosis , and leishmaniasis . Rapid development of industry and agriculture , as well as climate change throughout the globe , has led to change or increase in occurrence of rodent-borne diseases . Considering the distribution of rode...	This review showed that approximately half of the known rodent-borne diseases have been reported in Iran , half of which were reported both in humans and rodents . Most of the diseases were bacterial and parasitic . Plague , leishmaniasis , and hymenolepiasis were the most frequent diseases among rodent populations . A...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "plagues", "atmospheric", "science", "geographical", "locations", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "bacterial", "diseases", "review", "neglected", "tropical", "diseases", "infect...	2018	Rodent-borne diseases and their public health importance in Iran
Shigella is the leading cause for dysentery worldwide . Together with several virulence factors employed for invasion , the presence and length of the O antigen ( OAg ) of the lipopolysaccharide ( LPS ) plays a key role in pathogenesis . S . flexneri 2a has a bimodal OAg chain length distribution regulated in a growth-...	Shigellosis is a major global health concern . Recently , a shift in the dominance of types of Shigella that cause disease has been observed with S . sonnei increasing in prevalence under improved socio-economic conditions leading to a replacement of S . flexneri . Most of the knowledge of Shigella disease mechanisms h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An O Antigen Capsule Modulates Bacterial Pathogenesis in Shigella sonnei
Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined “conditional cooperativity” . Toxin and antitoxin form heteromers with different stoichiometric ratios , and the complex with the intermediate ratio works best as a transcription repressor . This allows transcripti...	The effectiveness of antibiotics on many pathogenic bacteria is compromised by multidrug tolerance . This is caused by a small sub-population of bacteria that happen to be in a dormant , non-dividing state when antibiotics are applied and thus are protected from being killed . These bacteria are called persisters . Unr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy
The ability of microbial species to consume compounds found in the environment to generate commercially-valuable products has long been exploited by humanity . The untapped , staggering diversity of microbial organisms offers a wealth of potential resources for tackling medical , environmental , and energy challenges ....	The ability of microbial species to consume compounds found in the environment to generate commercially-valuable products has long been exploited by humanity . The vast untapped diversity of microbial species offers a wealth of potential resources . However , little is known about most microbial species . While the met...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "bioengineering", "systems", "biology", "biological", "systems", "engineering", "biology", "computational", "biology", "metabolic", "networks", "genetics", "and", "genomics", "engineering" ]	2012	Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient
Cervical cancer is one of the leading causes of cancer death in women worldwide . The causative agents of cervical cancers , high-risk human papillomaviruses ( HPVs ) , cause cancer through the action of two oncoproteins , E6 and E7 . The E6 oncoprotein cooperates with an E3 ubiquitin ligase ( UBE3A ) to target the p53...	Human papillomaviruses ( HPV ) are the causative agents of cervical cancer , one of the leading causes of cancer death in women worldwide . The E6 oncoprotein encoded by HPV has been implicated in the progression of primary tumors to metastatic disease and we have developed a new model in the fruit fly ( Drosophila mel...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "cell", "processes", "animals", "hormones", "endocrine", "physiology", "animal", "models", "oncology", "developmental", "biology", "drosophila", "melanogaster", "model"...	2016	A Drosophila Model of HPV E6-Induced Malignancy Reveals Essential Roles for Magi and the Insulin Receptor
Endosymbiosis has driven major molecular and cellular innovations . Plasmodium spp . parasites that cause malaria contain an essential , non-photosynthetic plastid—the apicoplast—which originated from a secondary ( eukaryote–eukaryote ) endosymbiosis . To discover organellar pathways with evolutionary and biomedical si...	Plasmodium parasites , which cause malaria , and related apicomplexan parasites evolved from photosynthetic algae that acquired their chloroplast through two successive endosymbioses . Although no longer photosynthetic , the apicomplexan plastid—or apicoplast—was retained in these pathogens and provides critical metabo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "parasite", "groups", "parasite", "replication", "plasmodium", "green", "fluorescent", "protein", "cloning", "parasitic", "protozoans", "parasitology", "apicomplexa", "luminescent", "proteins", "protozoans", "molecular", "biology", "techniques", "research", "and", "analysis...	2019	A mutagenesis screen for essential plastid biogenesis genes in human malaria parasites
Optimal Bayesian models have been highly successful in describing human performance on perceptual decision-making tasks , such as cue combination and visual search . However , recent studies have argued that these models are often overly flexible and therefore lack explanatory power . Moreover , there are indications t...	The main task of perceptual systems is to make truthful inferences about the environment . The sensory input to these systems is often astonishingly imprecise , which makes human perception prone to error . Nevertheless , numerous studies have reported that humans often perform as accurately as is possible given these ...	[ "Abstract", "Introduction", "Methods", "Models", "Results", "Discussion" ]	[]	2019	Imperfect Bayesian inference in visual perception
Active sensing involves the fusion of internally generated motor events with external sensation . For rodents , active somatosensation includes scanning the immediate environment with the mystacial vibrissae . In doing so , the vibrissae may touch an object at any angle in the whisk cycle . The representation of touch ...	Animals interrogate the world around them with actively moving sensory organs , resulting in a blend of sensory inputs: one input is from the object under study , while the second is from self-generated movement of the sensor . The detection of an object thus depends on the ability of the animal to distinguish among in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Vibrissa Self-Motion and Touch Are Reliably Encoded along the Same Somatosensory Pathway from Brainstem through Thalamus
Division of labor and task specialization explain the success of human and insect societies . Social insect colonies are characterized by division of labor , with workers specializing in brood care early and foraging later in life . Theory posits that this task switching requires shifts in responsiveness to task-relate...	In social insects such as ants and bees , workers specialize in different tasks . This specialization is thought to be regulated via response thresholds to task-specific cues , which vary between workers conducting different tasks . Whether a worker takes care of the brood , cares for other workers , or leaves the nest...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "invertebrates", "honey", "bees", "sociology", "social", "sciences", "animals", "social", "systems", "animal", "behavior", "zoology", "animal", "sociality", "bees", "foraging", "lipids", "hymenoptera", "ants", "behavior", "fats", "gene", "expression", "insects", "arth...	2018	Vitellogenin-like A–associated shifts in social cue responsiveness regulate behavioral task specialization in an ant
Transmission of zoonotic cutaneous leishmaniasis ( ZCL ) depends on the presence , density and distribution of Leishmania major rodent reservoir and the development of these rodents is known to have a significant dependence on environmental and climate factors . ZCL in Tunisia is one of the most common forms of leishma...	Zoonotic cutaneous leishmaniasis is a human vector-borne disease caused by the parasite Leishmania major and is well spread in rural areas where human resources in public health and infrastructure are limited . The cycle of transmission of the disease is complex because of the impact of climate change . In this study w...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "atmospheric", "science", "geographical", "locations", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "seasons", "mathematics", "forecasting", "statistics", "(mathematics)", "neglected", "tropic...	2017	Modeling zoonotic cutaneous leishmaniasis incidence in central Tunisia from 2009-2015: Forecasting models using climate variables as predictors
Influenza viruses resistant to antiviral drugs emerge frequently . Not surprisingly , the widespread treatment in many countries of patients infected with 2009 pandemic influenza A ( H1N1 ) viruses with the neuraminidase ( NA ) inhibitors oseltamivir and zanamivir has led to the emergence of pandemic strains resistant ...	Although most of the currently circulating 2009 pandemic influenza A ( H1N1 ) viruses are susceptible to neuraminidase ( NA ) inhibitors ( oseltamivir and zanamivir ) , oseltamivir-resistant mutants have sporadically appeared . Yet , the pathogenicity and transmissibility of these oseltamivir-resistant 2009 H1N1 pandem...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetics", "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/animal", "models", "of", "infection", "virology/antivirals,", "including", "modes",...	2010	Characterization of Oseltamivir-Resistant 2009 H1N1 Pandemic Influenza A Viruses
Heterosis has been widely used in agriculture , but the molecular mechanism for this remains largely elusive . In Arabidopsis hybrids and allopolyploids , increased photosynthetic and metabolic activities are linked to altered expression of circadian clock regulators , including CIRCADIAN CLOCK ASSOCIATED1 ( CCA1 ) . I...	All corn in the USA is grown as hybrids , which grow more vigorously and produce higher yield than their parents , a phenomenon known as heterosis . The molecular basis for heterosis remains elusive . Heterosis is predicted to arise from allelic interactions between parental genomes , leading to altered regulatory netw...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "plant", "anatomy", "chemical", "compounds", "brassica", "carbohydrates", "organic", "compounds", "cereal", "crops", "plant", "science", "model", "organisms", "crops", "plant", "genomics", "chronobiology", "plants", "starches", "arabidopsis", "thaliana", ...	2016	Temporal Shift of Circadian-Mediated Gene Expression and Carbon Fixation Contributes to Biomass Heterosis in Maize Hybrids
Folding of the chromosomal fibre in interphase nuclei is an important element in the regulation of gene expression . For instance , physical contacts between promoters and enhancers are a key element in cell-type–specific transcription . We know remarkably little about the principles that control chromosome folding . H...	Folding of chromosomes in interphase nuclei of higher eukaryotes is a key element in regulating gene expression . The mechanisms that control chromatin folding are largely unknown . We have shown earlier that looping is a fundamental aspect of large-scale chromatin structure . Two abundant looping proteins are known: C...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "imaging", "techniques", "cell", "biology", "computational", "techniques", "microscopy", "mathematical", "and", "statistical", "techniques", "biology", "and", "life", "sciences", "computational", "biology", "biophysics", "research", "and", "analysis"...	2014	Depletion of the Chromatin Looping Proteins CTCF and Cohesin Causes Chromatin Compaction: Insight into Chromatin Folding by Polymer Modelling
Drosophila melanogaster larvae irradiated with doses of ionizing radiation ( IR ) that kill about half of the cells in larval imaginal discs still develop into viable adults . How surviving cells compensate for IR-induced cell death to produce organs of normal size and appearance remains an active area of investigation...	Like other insects , Drosophila larvae have epithelial structures called imaginal discs that will give rise to most of the external adult structures , such as wings , limbs , or antennae; these organ precursors are formed by a single layer of epithelial cells that folds into a sac . Imaginal discs manage to regenerate ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "invertebrates", "cell", "processes", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "organism", "development", "stat", "proteins", "embryos", "morphogenesis", "drosophila", "research", "and"...	2016	Drosophila Wnt and STAT Define Apoptosis-Resistant Epithelial Cells for Tissue Regeneration after Irradiation
Receptors of the signalling lymphocyte-activation molecules ( SLAM ) family are involved in the functional regulation of a variety of immune cells upon engagement through homotypic or heterotypic interactions amongst them . Here we show that murine cytomegalovirus ( MCMV ) dampens the surface expression of several SLAM...	Cytomegalovirus ( CMV ) has developed diverse tactics to elude the host immune response and guarantee its survival . The signalling lymphocyte-activation molecules ( SLAM ) family of receptors encompasses a number of adhesion molecules expressed on the surface of leukocytes that play critical roles in both innate and a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viral", "immune", "evasion", "virology", "immunology", "host-pathogen", "interaction", "biology", "microbiology", "immunomodulation" ]	2014	Cytomegalovirus m154 Hinders CD48 Cell-Surface Expression and Promotes Viral Escape from Host Natural Killer Cell Control
Dysregulation of iron metabolism in cancer is well documented and it has been suggested that there is interdependence between excess iron and increased cancer incidence and progression . In an effort to better understand the linkages between iron metabolism and breast cancer , a predictive mathematical model of an expa...	Iron is required for cellular metabolism and growth , but can be toxic due to its ability to cause high oxidative stress and consequently DNA damage . To prevent damage , all organisms that require iron have developed mechanisms to tightly control iron levels . Dysregulation of iron metabolism is detrimental and can co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "heme", "medicine", "and", "health", "sciences", "breast", "tumors", "oxidative", "stress", "cancers", "and", "neoplasms", "oncology", "physiological", "processes", "mathematics", "homeostasis", "algebra", "mitochondria", "bioenergetics", "cellular", "structures", "and", ...	2017	Activated Oncogenic Pathway Modifies Iron Network in Breast Epithelial Cells: A Dynamic Modeling Perspective
Schistosomiasis is a chronic neglected tropical disease that is characterized by continued inflammatory challenges to the exposed population and it has been established as a possible risk factor in the aetiology of bladder cancer . Improved diagnosis of schistosomiasis and its associated pathology is possible through m...	Schistosomiasis , caused by S . haematobium , causes inflammation in the bladder and is common in tropical areas such as Nigeria . Undetected schistosomiasis can lead to inflammation in the bladder which may lead to bladder cancer . Diagnosis of bladder cancer in areas with common urinary schistosomiasis is difficult b...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "helminths", "tropical", "diseases", "dna-binding", "proteins", "biomarkers", "parasitic", "diseases", "animals", "urine", "membrane", "receptor", "signaling", "neglected", "tropica...	2017	Quantitative label-free proteomic analysis of human urine to identify novel candidate protein biomarkers for schistosomiasis
Adaptation in eukaryotes is generally assumed to be mutation-limited because of small effective population sizes . This view is difficult to reconcile , however , with the observation that adaptation to anthropogenic changes , such as the introduction of pesticides , can occur very rapidly . Here we investigate adaptat...	Adaptation in eukaryotes is often assumed to be limited by the waiting time for adaptive mutations . This is because effective population sizes are relatively small , typically on the order of only a few million reproducing individuals or less . It should therefore take hundreds or even thousands of generations until a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "genetics", "and", "genomics/population", "genetics" ]	2010	Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites
Energy parasitism by ATP/ADP transport proteins is an essential , common feature of intracellular bacteria such as chlamydiae and rickettsiae , which are major pathogens of humans . Although several ATP/ADP transport proteins have so far been characterized , some fundamental questions regarding their function remained ...	Diverse members of the bacterial order Chlamydiales cause severe diseases in humans . Chlamydiales cannot survive and reproduce outside of host cells , due to the complete loss of several biosynthetic pathways , but rely on specialized transport systems to import the corresponding metabolites from the host . We perform...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "infectious", "diseases", "microbiology", "eubacteria" ]	2007	Enlightening Energy Parasitism by Analysis of an ATP/ADP Transporter from Chlamydiae
Botulism , characterized by flaccid paralysis , commonly results from botulinum neurotoxin ( BoNT ) absorption across the epithelial barrier from the digestive tract and then dissemination through the blood circulation to target autonomic and motor nerve terminals . The trafficking pathway of BoNT/A passage through the...	Botulism is a severe and often fatal disease in man and animals characterized by flaccid paralysis . Clostridium botulinum produces a potent neurotoxin ( botulinum neurotoxin ) responsible for all the symptoms of botulism . Botulism is most often acquired by ingesting preformed botulinum neurotoxin in contaminated food...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology", "microbiology", "molecular", "cell", "biology", "toxicology" ]	2012	Preferential Entry of Botulinum Neurotoxin A Hc Domain through Intestinal Crypt Cells and Targeting to Cholinergic Neurons of the Mouse Intestine
To understand the brain mechanisms of olfaction we must understand the rules that govern the link between odorant structure and odorant perception . Natural odors are in fact mixtures made of many molecules , and there is currently no method to look at the molecular structure of such odorant-mixtures and predict their ...	One hundred years ago , Alexander Graham Bell asked: “Can you measure the difference between one kind of smell and another ? It is very obvious that we have very many different kinds of smells , all the way from the odor of violets and roses up to asafetida . But until you can measure their likenesses and differences y...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Predicting Odor Perceptual Similarity from Odor Structure
Both Schistosoma mansoni and Schistosoma haematobium cause schistosomiasis in sub-Saharan Africa . We assessed the diagnostic value of selected Schistosoma antigens for the development of a multiplex serological immunoassay for sero-epidemiological surveillance . Diagnostic ability of recombinant antigens from S . mans...	More attention is now shifting towards elimination of some of the neglected tropical diseases , including schistosomiasis . Efficient diagnostics and surveillance tools are the bedrock of planning , implementation , monitoring and evaluation of such disease interventions . We had developed a multiplex immunoassay syste...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Species-Specific Serological Detection for Schistosomiasis by Serine Protease Inhibitor (SERPIN) in Multiplex Assay
In order to complete their life cycle , papillomaviruses have evolved to manipulate a plethora of cellular pathways . The products of the human Alphapapillomavirus E6 proteins specifically interact with and target PDZ containing proteins for degradation . This viral phenotype has been suggested to play a role in viral ...	It is thought that the ability to degrade PDZ domain containing proteins is a hallmark of oncogenic papillomaviruses . However , since papillomaviruses did not evolve to be oncogenic , this hypothesis does not address the evolutionary importance of this phenotype . The present manuscript attempts to address whether HPV...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Degradation of Human PDZ-Proteins by Human Alphapapillomaviruses Represents an Evolutionary Adaptation to a Novel Cellular Niche
The development of biomedical interventions to reduce acquisition of HIV-1 infection remains a global priority , however their potential effectiveness is challenged by very high HIV-1 envelope diversity . Two large prophylactic trials in high incidence , clade C epidemic regions in southern Africa are imminent; passive...	Vaccine and passive immunization prophylactic trials that rely on antibody-mediated protection are planned for HIV-1 clade C epidemic regions of southern Africa , which have amongst the highest HIV-1 incidences globally . This includes a phase 2b trial of passively administered monoclonal antibody , VRC01; as well as a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "viral", "vaccines", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "retroviruses", "viruses...	2016	Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization
How non-coding DNA gives rise to new protein-coding genes ( de novo genes ) is not well understood . Recent work has revealed the origins and functions of a few de novo genes , but common principles governing the evolution or biological roles of these genes are unknown . To better define these principles , we performed...	De novo genes are protein-coding genes with no clear homology to previously existing protein-coding genes . Since their discovery in Drosophila and other species including humans , their existence has been controversial , with some doubt as to how they would arise , whether they produce proteins , and whether they coul...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences
This study was conducted to ( i ) determine the prevalence of African Animal Trypanosomosis ( AAT ) in tsetse challenged areas , ( ii ) compare conventional with qPCR detection systems and ( iii ) evaluate the host genetic background and biology as risk factors . AAT prevalence studies are often confronted with low lev...	African Animal Trypanosomosis ( AAT ) is a neglected tropical disease heavily impacting on the poor . Sensitive diagnostic tools are needed since actual parasitaemia levels can be very low , particularly in chronically infected or trypanotolerant animals . Hence , we present a novel real-time PCR ( qPCR ) assay for the...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "veterinary", "epidemiology", "veterinary", "parasitology", "genetics", "biology", "evolutionary", "biology", "evolutionary", "genetics", "veterinary", "science" ]	2013	A Novel qPCR Assay for the Detection of African Animal Trypanosomosis in Trypanotolerant and Trypanosusceptible Cattle Breeds
Long noncoding RNAs ( lncRNAs ) have emerged as critical factors in many biological processes , but little is known about how their regulatory functions evolved . One of the best-studied lncRNAs is TER , the essential RNA template for telomerase reverse transcriptase . We previously showed that Arabidopsis thaliana har...	Telomerase is a highly regulated enzyme whose activity is essential for long-term cellular proliferation . In the presence of DNA double-strand breaks ( DSBs ) , telomerase activity must be curtailed to promote faithful DNA repair . We previously showed that the flowering plant Arabidopsis thaliana rapidly down-regulat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Transposable Element within the Non-canonical Telomerase RNA of Arabidopsis thaliana Modulates Telomerase in Response to DNA Damage
Biological protein interactions networks such as signal transduction or gene transcription networks are often treated as modular , allowing motifs to be analyzed in isolation from the rest of the network . Modularity is also a key assumption in synthetic biology , where it is similarly expected that when network motifs...	Cells rely on complex networks of protein-protein interactions in order to carry out life functions . Scientists believe that these networks are organized in a modular fashion; that is they are made up of functionally distinct parts like an electronic circuit . Modularity implies that just as we put together electronic...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biochemistry", "signal", "transduction", "biochemical", "simulations", "computer", "and", "information", "sciences", "cell", "biology", "theoretical", "biology", "network", "analysis", "synthetic", "biology", "biology", "and", "life", "sciences", ...	2014	Loads Bias Genetic and Signaling Switches in Synthetic and Natural Systems
During the entry process , the human immunodeficiency virus type 1 ( HIV-1 ) envelope glycoprotein ( Env ) trimer undergoes a sequence of conformational changes triggered by both CD4 and coreceptor engagement . Resolving the conformation of these transient entry intermediates has proven challenging . Here , we fine-map...	The trimeric human immunodeficiency virus type 1 ( HIV-1 ) envelope glycoprotein ( Env ) mediates HIV-1 entry into its target cells . Entry is initiated by sequential triggering of Env upon interaction with its primary receptor CD4 and a coreceptor on target cells . The ensuing structural rearrangements of the Env trim...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "cell", "binding", "flow", "cytometry", "cell", "physiology", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses"...	2019	CD4 occupancy triggers sequential pre-fusion conformational states of the HIV-1 envelope trimer with relevance for broadly neutralizing antibody activity
Active DNA demethylation in plants occurs through base excision repair , beginning with removal of methylated cytosine by the ROS1/DME subfamily of 5-methylcytosine DNA glycosylases . Active DNA demethylation in animals requires the DNA glycosylase TDG or MBD4 , which functions after oxidation or deamination of 5-methy...	DNA cytosine methylation ( 5-methylcytosine , 5-meC ) is an important epigenetic mark , and methylation patterns are coordinately controlled by methylation and demethylation reactions during development and reproduction . In plants , REPRESSOR OF SILENCING ( ROS1 ) is one of the well characterized 5-meC DNA glycosylase...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "developmental", "biology", "base", "excision", "repair", "genomic", "imprinting", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "dna", "dna", "repair", "dna", "modification", "epigenetics", "dna", "methylation" ]	2015	An AP Endonuclease Functions in Active DNA Demethylation and Gene Imprinting in Arabidopsis
The brain's decoding of fast sensory streams is currently impossible to emulate , even approximately , with artificial agents . For example , robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems . In this paper , we propose that recognition can be...	Despite tremendous advances in neuroscience , we cannot yet build machines that recognize the world as effortlessly as we do . One reason might be that there are computational approaches to recognition that have not yet been exploited . Here , we demonstrate that the ability to recognize temporal sequences might play a...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems", "computational", "biology/computational", "neuroscience" ]	2009	Recognizing Sequences of Sequences
We need to find ways of enhancing the potency of existing antibiotics , and , with this in mind , we begin with an unusual question: how low can antibiotic dosages be and yet bacterial clearance still be observed ? Seeking to optimise the simultaneous use of two antibiotics , we use the minimal dose at which clearance ...	So-called “cocktail” treatments are often proposed as a way of enhancing the potency of antibiotics , based on the idea that multiple drugs can synergise when used together as part of a single combined therapy . We investigated whether any other multidrug deployment strategies are as effective as—or perhaps even better...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Using a Sequential Regimen to Eliminate Bacteria at Sublethal Antibiotic Dosages
The common non-steroidal anti-inflammatory drug ibuprofen has been associated with a reduced risk of some age-related pathologies . However , a general pro-longevity role for ibuprofen and its mechanistic basis remains unclear . Here we show that ibuprofen increased the lifespan of Saccharomyces cerevisiae , Caenorhabd...	Aging is the greatest risk factor for many diseases , which together account for the majority of global deaths and healthcare costs . Here we show that the common drug ibuprofen increases the lifespan of yeast , worms and flies , indicative of conserved longevity effects . In budding yeast , an excellent model of cellu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "biochemistry", "cell", "biology", "fungal", "genetics", "genetics", "microbial", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "molecular", "cell", "biology" ]	2014	Enhanced Longevity by Ibuprofen, Conserved in Multiple Species, Occurs in Yeast through Inhibition of Tryptophan Import
Snakebite envenomation is a neglected condition that constitutes a public health problem in tropical and subtropical countries , including Brazil . Interestingly , some animals are resistant to snake envenomation due to the presence of inhibitory glycoproteins in their serum that target toxic venom components . DM64 is...	Snakebite envenomation causes medical emergencies that , depending on the species responsible for the bite , involve different organs and tissues . Envenomation by snakebite is a worldwide problem , and Brazil presents a high incidence of Bothrops bites . Bothrops venoms cause pathological alterations with prominent lo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "molecular", "mass", "pichia", "pastoris", "tropical", "diseases", "vertebrates", "silver", "staining", "animals", "toxicology", "toxic", "agents", "fungi", "reptiles", "n...	2017	Heterologous expression of the antimyotoxic protein DM64 in Pichia pastoris
Two Kato-Katz thick smears ( Kato-Katzs ) from a single stool are currently recommended for diagnosing Schistosoma mansoni infections to map areas for intervention . This ‘gold standard’ has low sensitivity at low infection intensities . The urine point-of-care circulating cathodic antigen test ( POC-CCA ) is potential...	Schistosomiasis is a parasitic disease infecting over 200 million people . It remains a major public health concern despite treatment of over 120 million people in sub-Saharan Africa alone . Accurate diagnostic methods are essential for monitoring drug efficacy and long-term control program success . The World Health O...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "schistosomiasis", "plant", "science", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "epidemiology", "disease", "surveillance", "plant", "pathology", "biology", "and", "life", "sciences", "tropical", "diseases", "neglected", ...	2014	Sensitivity and Specificity of Multiple Kato-Katz Thick Smears and a Circulating Cathodic Antigen Test for Schistosoma mansoni Diagnosis Pre- and Post-repeated-Praziquantel Treatment
Genome-scale metabolic models provide a powerful means to harness information from genomes to deepen biological insights . With exponentially increasing sequencing capacity , there is an enormous need for automated reconstruction techniques that can provide more accurate models in a short time frame . Current methods f...	Genome-scale metabolic modeling is a powerful approach that allows one to computationally simulate a variety of metabolic phenotypes . However , manually constructing accurate metabolic networks is extremely time intensive and it is thus desirable to have automated computational methods for providing high-quality metab...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "computer", "and", "information", "sciences", "network", "analysis", "biology", "and", "life", "sciences", "metabolic", "networks", "computerized", "simulations" ]	2014	Likelihood-Based Gene Annotations for Gap Filling and Quality Assessment in Genome-Scale Metabolic Models
Ebola virus ( EBOV ) infections are characterized by deficient T-lymphocyte responses , T-lymphocyte apoptosis and lymphopenia . We previously showed that disabling of interferon-inhibiting domains ( IIDs ) in the VP24 and VP35 proteins effectively unblocks maturation of dendritic cells ( DCs ) and increases the secret...	The extensive investigation of interferon antagonism mediated by Ebola virus ( EBOV ) over the last 16 years resulted in identification of two interferon inhibiting domains ( IIDs ) located in the VP24 and VP35 proteins of the virus and of multiple mechanisms by which the domains disable the innate immune system and pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "phosphorylation", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "cloning", "developmental", "biology", "molecular", "development", "mol...	2016	The Ebola Interferon Inhibiting Domains Attenuate and Dysregulate Cell-Mediated Immune Responses
The mechanosensitive channel of large conductance ( MscL ) has become a model system in which to understand mechanosensation , a process involved in osmoregulation and many other physiological functions . While a high resolution closed state structure is available , details of the open structure and the gating mechanis...	Cells in biological organisms have to be able to respond to mechanical forces during processes such as touch , hearing , pain sensation and tissue growth . One way this is achieved is through mechanosensitive ion channels , membrane embedded proteins that initiate electrical signalling upon tension within the cell or c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "signal", "transduction", "molecular", "cell", "biology", "membrane", "receptor", "signaling", "biology", "biophysics", "simulations", "biophysics" ]	2012	Structural Investigation of MscL Gating Using Experimental Data and Coarse Grained MD Simulations
Plesiosaurians are an extinct group of highly derived Mesozoic marine reptiles with a global distribution that spans 135 million years from the Early Jurassic to the Late Cretaceous . During their long evolutionary history they maintained a unique body plan with two pairs of large wing-like flippers , but their locomot...	Plesiosaurs are an extinct group of Mesozoic marine reptiles with a global distribution that spans 135 million years . They maintained a unique body plan with two pairs of large wing-like flippers throughout their long evolutionary history , but how plesiosaurs swam has remained a topic of debate for almost 200 years ....	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[]	2015	Computer Simulations Imply Forelimb-Dominated Underwater Flight in Plesiosaurs
The APOBEC3 proteins form a multigene family of cytidine deaminases with inhibitory activity against viruses and retrotransposons . In contrast to APOBEC3G ( A3G ) , APOBEC3A ( A3A ) has no effect on lentiviruses but dramatically inhibits replication of the parvovirus adeno-associated virus ( AAV ) . To study the contr...	The APOBEC3 proteins constitute a family of seven cytidine deaminases . Cytidine deaminases are editing enzymes able to remove the amine group from cytidine in single-strand DNA ( ssDNA ) and RNA , converting it to uracil . APOBEC3 proteins have potent antiviral activity against retroviruses , retrotransposons , and DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry/replication", "and", "repair", "molecular", "biology", "immunology/immunity", "to", "infections", "virology/host", "antiviral", "responses" ]	2009	Deaminase-Independent Inhibition of Parvoviruses by the APOBEC3A Cytidine Deaminase
Chronic helminth infections typically induce an immunoregulatory environment , with markedly reduced immune responses to both parasite-specific and unrelated bystander antigens . Here we tested whether these changes are also observed in human infections with Mansonella ozzardi , a neglected filarial nematode widely dis...	Helminth infections downregulate immunity and reduce host’s inflammatory responses , but the filarial nematode Mansonella ozzardi , which is widely distributed across Latin America , appears to represent an exception to this rule . We found similar lymphoproliferative responses to filarial and unrelated antigens and co...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "glycosylamines", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "parasitic", "diseases", "nematode", "infections", "developmental", "biology", "molecular", "...	2018	CD39 and immune regulation in a chronic helminth infection: The puzzling case of Mansonella ozzardi
A role for natural selection in reinforcing premating barriers is recognized , but selection for reinforcement of postmating barriers remains controversial . Organisms lacking evolvable premating barriers can theoretically reinforce postmating isolation , but only under restrictive conditions: parental investment in hy...	Although Darwin believed that natural selection could not drive intersterility between species , it is now well established that there is a role for natural selection in the evolution of premating discrimination that reinforces barriers to hybridization . However , natural selection for postmating barriers , like hybri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "fungi", "adaptation", "natural", "selection", "speciation", "biology", "evolutionary", "biology", "hybridization", "microbiology", "evolutionary", "processes" ]	2011	Genetic Architecture of a Reinforced, Postmating, Reproductive Isolation Barrier between Neurospora Species Indicates Evolution via Natural Selection
The Saccharomyces cerevisiae Dun1 protein kinase is a downstream target of the conserved Mec1-Rad53 checkpoint pathway . Dun1 regulates dNTP pools during an unperturbed cell cycle and after DNA damage by modulating the activity of ribonucleotide reductase ( RNR ) by multiple mechanisms , including phosphorylation of RN...	Dun1 is a non-essential protein kinase important for the maintenance of genome stability in budding yeast . Earlier studies found that simultaneous deletion of DUN1 and IXR1 results in lethality , but the reason for this so-called synthetic lethality is not clear . Ixr1 is implicated in DNA repair based on its ability ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "dna", "replication", "nucleic", "acids", "genetics", "molecular", "genetics", "biology", "dna", "dna", "repair", "nucleotides", "molecular", "biology", "genetics", "and", "genomics", "gene", "function" ]	2011	Ixr1 Is Required for the Expression of the Ribonucleotide Reductase Rnr1 and Maintenance of dNTP Pools
In Trypanosoma brucei , glycosylphosphatidylinositol phospholipase C ( GPI-PLC ) is a virulence factor that releases variant surface glycoprotein ( VSG ) from dying cells . In live cells , GPI-PLC is localised to the plasma membrane where it is concentrated on the flagellar membrane , so activity or access must be tigh...	African trypanosomes are unicellular parasites with a single flagellum that maintain a persistent infection through antigenic variation based on changes in a densely packed cell surface coat of variant surface glycoprotein ( VSG ) . The cells also contain an enzyme , GPI-PLC , able to shed the VSG from the cell surface...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "membranes", "and", "sorting", "biology" ]	2013	Determinants of GPI-PLC Localisation to the Flagellum and Access to GPI-Anchored Substrates in Trypanosomes
In recent years , there has been a growing interest in teichoic acids as targets for antibiotic drug design against major clinical pathogens such as Staphylococcus aureus , reflecting the disquieting increase in antibiotic resistance and the historical success of bacterial cell wall components as drug targets . It is n...	Historically , β-lactam class antibiotics such as methicillin have been very successful in the treatment of bacterial infections , effectively destroying bacteria by rupturing their cell walls while posing little harm to the human organism . In recent years , however , the alarming emergence of Methicillin Resistant S ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "condensed", "matter", "physics", "microbiology", "enzymology", "staphylococcus", "aureus", "petroleum", "products", "methicillin-resistant...	2016	Structure and Mechanism of Staphylococcus aureus TarS, the Wall Teichoic Acid β-glycosyltransferase Involved in Methicillin Resistance
Cholera burden in Africa remains unknown , often because of weak national surveillance systems . We analyzed data from the African Cholera Surveillance Network ( www . africhol . org ) . During June 2011–December 2013 , we conducted enhanced surveillance in seven zones and four outbreak sites in Togo , the Democratic R...	Cholera burden in Africa remains unknown , often because of weak national surveillance systems . Reporting is non-exhaustive for various reasons , such as individual and community fears of stigmatization and economic loss . Furthermore , only 3% to 5% of all cases are laboratory confirmed . A variety of case definition...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "guinea", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "tropical", "diseases", "geographical", "locations", "uganda", "bacterial", "diseases", "aquatic", "environments", "bodies", "of", "water", "neglected", "tropical", "diseas...	2016	Cholera Incidence and Mortality in Sub-Saharan African Sites during Multi-country Surveillance
Regulated degradation of proteins by the 26S proteasome plays important roles in maintenance and signalling in eukaryotic cells . Proteins are marked for degradation by the action of E3 ligases that site-specifically modify their substrates by adding chains of ubiquitin . Innate immune signalling in plants is deeply re...	Plants are continuously exposed to different disease agents , including bacteria , fungi , oomycetes and chewing or sucking insects . To protect themselves plants have evolved a sophisticated multi-layered immune system that depends on the reprogramming of large gene repertoires to prioritize the expression of immune g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "immunology", "enzymology", "plant", "physiology", "ubiquitin", "ligases", "plant", "science", "plant", "pathology", "ligases", "proteins", "gene", "expression...	2018	Proteasome-associated HECT-type ubiquitin ligase activity is required for plant immunity
The first decade of Genome Wide Association Studies ( GWAS ) has uncovered a wealth of disease-associated variants . Two important derivations will be the translation of this information into a multiscale understanding of pathogenic variants and leveraging existing data to increase the power of existing and future stud...	For complex human diseases , identifying the genes harboring susceptibility variants has taken on medical importance . Disease-associated genes provide clues for elucidating disease etiology , predicting disease risk , and highlighting therapeutic targets . Here , we develop a method to predict whether a given gene and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
Drosophila harbor substantial genetic variation for antibacterial defense , and investment in immunity is thought to involve a costly trade-off with life history traits , including development , life span , and reproduction . To understand the way in which insects invest in fighting bacterial infection , we selected fo...	The fruit fly is commonly used as a model organism to understand the mechanistic nature of the immune response to bacterial pathogens . The fly is also commonly used to understand what immunity costs hosts in terms of other traits such as life span and reproductive success . Here , we examine these two questions togeth...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "microbiology/innate", "immunity" ]	2009	Effective but Costly, Evolved Mechanisms of Defense against a Virulent Opportunistic Pathogen in Drosophila melanogaster
Brain connectivity studies have revealed that highly connected ‘hub’ regions are particularly vulnerable to Alzheimer pathology: they show marked amyloid-β deposition at an early stage . Recently , excessive local neuronal activity has been shown to increase amyloid deposition . In this study we use a computational mod...	An intriguing recent observation is that deposition of the amyloid-β protein , one of the hallmarks of Alzheimer's disease , mainly occurs in brain regions that are highly connected to other regions . To test the hypothesis that these ‘hub’ regions are more vulnerable due to a higher neuronal activity level , we examin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurobiology", "of", "disease", "and", "regeneration", "neural", "networks", "neuroscience", "mathematics", "computational", "neuroscience", "alzheimer", "disease", "biology", "dementia", "nonlinear", "dynamics", "central", "nervous", "system", "neurological", ...	2012	Activity Dependent Degeneration Explains Hub Vulnerability in Alzheimer's Disease
Brain metastases are prevalent in various types of cancer and are often terminal , given the low efficacy of available therapies . Therefore , preventing them is of utmost clinical relevance , and prophylactic treatments are perhaps the most efficient strategy . Here , we show that systemic prophylactic administration ...	Brain metastases are prevalent and often terminal . Thus , reducing their occurrence could markedly improve cancer outcome . We show that systemic prophylactic and perioperative administration of a TLR9 agonist , CpG-C , reduced metastatic growth in experimental and spontaneous brain metastasis models , employing mouse...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2019	Prophylactic TLR9 stimulation reduces brain metastasis through microglia activation
West Nile Virus ( WNV ) is now endemic throughout North America , with annual recurrence dependent upon successful overwintering when cold temperatures drive mosquito vectors into inactivity and halt transmission . To investigate whether avian hosts may serve as an overwintering mechanism , groups of eight to ten House...	House Sparrows experimentally infected with West Nile virus [WNV] were necropsied at multiple time points from 3 to 18 weeks post infection ( pi ) . The percent of birds with tissues positive for WNV RNA decreased from 100% at 3 wks to 13% at 18 wks pi; infectious virus was recovered from some birds by tissue co-cultiv...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "west", "nile", "fever", "viral", "diseases" ]	2012	Dynamics of West Nile Virus Persistence in House Sparrows (Passer domesticus)
Schistosomiasis remains a significant health burden in many areas of the world . Morbidity control , focused on limiting infection intensity through periodic delivery of anti-schistosomal medicines , is the thrust of current World Health Organization guidelines ( 2006 ) for reduction of Schistosoma-related disease . A ...	Debate persists about how best to prevent disease caused by Schistosoma parasites . Current guidelines focus on suppressing morbidity by limiting average intensity of infection during childhood . However , this may not be sufficient to cure infection or prevent reinfection , leaving risk for sub-clinical morbidities su...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "science", "policy", "and", "economics", "applied", "mathematics", "parasitic", "diseases", "preventive", "medicine", "mathematics", "cost-benefit", "analysis", "neglected", "tropical", "diseases", "urologic", "infect...	2012	Projecting the Long-Term Impact of School- or Community-Based Mass-Treatment Interventions for Control of Schistosoma Infection

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