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Cancer metabolism has received renewed interest as a potential target for cancer therapy . In this study , we use a multi-scale modeling approach to interrogate the implications of three metabolic scenarios of potential clinical relevance: the Warburg effect , the reverse Warburg effect and glutamine addiction . At the...	Cancer metabolism is an emerging hallmark of cancer . In the past decade , a renewed focus on cancer metabolism has led to several distinct hypotheses describing the role of metabolism in cancer . To complement experimental efforts in this field , a scale-bridging computational framework is needed to allow rapid evalua...	[ "Abstract", "Introduction", "Model", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "chemical", "compounds", "oxygen", "carbohydrates", "cell", "metabolism", "organic", "compounds", "glucose", "metabolism", "glucose", "physiological", "processes", "oxygen", "meta...	2018	Multi-scale computational study of the Warburg effect, reverse Warburg effect and glutamine addiction in solid tumors
There are a number of vaccine candidates under development against a small number of the most common outbreak filoviruses all employing the virus glycoprotein ( GP ) as the vaccine immunogen . However , antibodies induced by such GP vaccines are typically autologous and limited to the other members of the same species ...	Development of an effective vaccine against filovirus outbreaks is an important public health aim . Here , we demonstrate the principle that cellular responses can not only protect two strains of mice against a high lethal virus challenge of 1000 LD50 in the absence of glycoprotein antibodies , but a single epigraph T–...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "viral", "vaccines", "medicine", "and", "health", "sciences", "immune", "cells", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "immune", "physiology", "pathogens", "immunology", "microbiology", "vaccines", "viruses", "f...	2019	Complete protection of the BALB/c and C57BL/6J mice against Ebola and Marburg virus lethal challenges by pan-filovirus T-cell epigraph vaccine
While most models of randomly connected neural networks assume single-neuron models with simple dynamics , neurons in the brain exhibit complex intrinsic dynamics over multiple timescales . We analyze how the dynamical properties of single neurons and recurrent connections interact to shape the effective dynamics in la...	Biological neural networks are formed by a large number of neurons whose interactions can be extremely complex . Such systems have been successfully studied using random network models , in which the interactions among neurons are assumed to be random . However , the dynamics of single units are usually described using...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "resonance", "frequency", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "signaling", "networks", "neuroscience", "research", "design", "mathematics", "algebra", "network", "analysis", "computational", "neuroscience", "white", "noise", "...	2019	How single neuron properties shape chaotic dynamics and signal transmission in random neural networks
Anthocyanin is part of secondary metabolites , which is induced by environmental stimuli and developmental signals , such as high light and sucrose . Anthocyanin accumulation is activated by the MYB-bHLH-WD40 ( MBW ) protein complex in plants . But the evidence of how plants maintain anthocyanin in response to signals ...	Anthocyanins , a class of flavonoids distributed ubiquitously in the plant kingdom , are induced by environmental stimuli and developmental signals , such as high light and sucrose . It is well established that anthocyanin accumulation is regulated by the MYB-bHLH-WD40 ( MBW ) protein complex in plants . But little is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "plant", "anatomy", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "ears", "gene", "regulation", "regulatory", "proteins", "brassica", "dna-binding", "proteins", "dna", "transcription", "plant", "science", "model", "organis...	2019	Regulation of anthocyanin accumulation via MYB75/HAT1/TPL-mediated transcriptional repression
It has long been recognized that the modification of penicillin-binding proteins ( PBPs ) to reduce their affinity for β-lactams is an important mechanism ( target modification ) by which Gram-positive cocci acquire antibiotic resistance . Among Gram-negative rods ( GNR ) , however , this mechanism has been considered ...	Decades after their discovery , β-lactams remain key components of our antimicrobial armamentarium for the treatment of infectious diseases . Nevertheless , resistance to these antibiotics is increasing alarmingly . There are two major bacterial strategies to develop resistance to β-lactam antibiotics: the production o...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "microbiology/microbial", "physiology", "and", "metabolism", "microbiology/microbial", "evolution", "and", "genomics", "microbiology/medical", "microbiology", "microbiology" ]	2009	β-Lactam Resistance Response Triggered by Inactivation of a Nonessential Penicillin-Binding Protein
Plant pathogens and parasites are a major threat to global food security . Plant parasitism has arisen four times independently within the phylum Nematoda , resulting in at least one parasite of every major food crop in the world . Some species within the most economically important order ( Tylenchida ) secrete protein...	Plants and their pathogens/parasites are locked in an evolutionary arms race , with considerable attention directed towards the specific functions of the parasites’ “weapons”: the effectors . While we are beginning to understand these functions , we have very little understanding of how plant parasitic nematodes have b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "chemical", "compounds", "parasite", "evolution", "parasitic", "diseases", "organic", "compounds", "animals", "parasitology", "nematode", "infections", "plant", "scien...	2018	Effector gene birth in plant parasitic nematodes: Neofunctionalization of a housekeeping glutathione synthetase gene
Rift Valley fever ( RVF ) is a zoonotic arbovirosis for which the primary hosts are domestic livestock ( cattle , sheep and goats ) . RVF was first described in South Africa in 1950–1951 . Mechanisms for short and long distance transmission have been hypothesised , but there is little supporting evidence . Here we desc...	The factors explaining Rift Valley fever ( RVF ) spread in domestic livestock during an epidemic are attributed to short and long distance mechanisms , including active vector dispersal , passive vector dispersal and movements of infectious animals . However , because of data scarcity , quantifying and disentangling th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary", "epidemiology", "veterinary", "science" ]	2012	Exploratory Space-Time Analyses of Rift Valley Fever in South Africa in 2008–2011
Infection with Burkholderia pseudomallei or B . thailandensis triggers activation of the NLRP3 and NLRC4 inflammasomes leading to release of IL-1β and IL-18 and death of infected macrophages by pyroptosis , respectively . The non-canonical inflammasome composed of caspase-11 is also activated by these bacteria and prov...	Burkholderia pseudomallei is a bacterium that infect macrophages and other cell types and causes a diseases called melioidosis . Inflammasomes are multiprotein complexes that control activation of the proteases caspase-1 and caspase-11 resulting in production of the inflammatory mediators IL-1β and IL-18 and death of i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "melioidosis", "burkholderia", "infection", "immunology", "epithelial", "cells", "bone", "marrow", "cells", "animal", "models", "bacterial", "diseases", "model", "organisms", "inflammasomes", ...	2018	Caspase-11-dependent pyroptosis of lung epithelial cells protects from melioidosis while caspase-1 mediates macrophage pyroptosis and production of IL-18
Virus-infected cells secrete a broad range of interferon ( IFN ) subtypes which in turn trigger the synthesis of antiviral factors that confer host resistance . IFN-α , IFN-β and other type I IFNs signal through a common universally expressed cell surface receptor , whereas IFN-λ uses a distinct receptor complex for si...	The contribution of IFN-λ to innate immunity against virus-induced diseases has remained unclear to date as appropriate mouse models were not available . We now present evidence that IFN-λ is involved in the antiviral defense . Mice lacking functional IFN-λ receptors were only slightly more susceptible to influenza vir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/respiratory", "infections", "virology/host", "antiviral", "responses", "infectious", "diseases/viral", "infections", "immunology/innate", "immunity" ]	2008	Interferon-λ Contributes to Innate Immunity of Mice against Influenza A Virus but Not against Hepatotropic Viruses
Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals . Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entryway to elucidate genetic interactions and signaling pathways . Towards this end , an atlas ...	Signaling pathways drive biological processes with high specificity . Reductionist approaches such as mutagenesis provide one strategy to identity components of pathways . We used high throughput in situ hybridization to systematically map the spatiotemporal expression pattern of ∼1 , 000 developmental genes in the mou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "mammals", "mus", "(mouse)", "neuroscience", "animals", "genetics", "and", "genomics" ]	2007	Regulatory Pathway Analysis by High-Throughput In Situ Hybridization
Following Schistosoma japonicum ( S . japonicum ) infection , granulomatous responses are induced by parasite eggs trapped in host organs , particular in the liver , during the acute stage of disease . While excessive liver granulomatous responses can lead to more severe fibrosis and circulatory impairment in chronical...	Schistosomiasis is a chronic helminthic disease that affects approximately 200 million people . After S . japonicum infection , parasite eggs are trapped in host liver and granulomas are induced to form around eggs . Severe granuloma subsequently results in serious liver fibrosis and circulatory impairment chronically ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "veterinary", "diseases", "zoonoses", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "tropical", "diseases", "parasitic", "diseases", "veterinary", "science" ]	2014	Follicular Helper T Cells Promote Liver Pathology in Mice during Schistosoma japonicum Infection
In chronic infection , Mycobacterium tuberculosis bacilli are thought to enter a metabolic program that provides sufficient energy for maintenance of the protonmotive force , but is insufficient to meet the demands of cellular growth . We sought to understand this metabolic downshift genetically by targeting succinate ...	This work establishes the principle that Mycobacterium tuberculosis undergoes a metabolic remodeling as oxygen concentrations fall that serves to decrease its rate of oxygen consumption and therefore oxidative phosphorylation . Furthermore , cells can be stimulated to respire , even in low oxygen conditions , by provid...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "oxygen", "metabolism", "medical", "microbiology", "electron", "transport", "chain", "microbial", "pathogens", "biology", "and", "life", "sciences", "bioenergetics", "microbiology", "metabolism" ]	2014	Succinate Dehydrogenase is the Regulator of Respiration in Mycobacterium tuberculosis
A compelling body of literature , based on next generation chromatin immunoprecipitation and RNA sequencing of reward brain regions indicates that the regulation of the epigenetic landscape likely underlies chronic drug abuse and addiction . It is now critical to develop highly innovative computational strategies to re...	The mammalian brain responds to environmental stimuli through changes in gene expression . Over the past decade a robust body of bioinformatics data has shown that in neuronal tissue such gene expression is regulated by changes in the epigenetic landscape , including modifications to chromatin . Further , a small but c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "&", "models", "Data", "access" ]	[ "alkaloids", "medicine", "and", "health", "sciences", "chemical", "compounds", "nucleus", "accumbens", "dna-binding", "proteins", "brain", "invertebrate", "genomics", "histone", "modification", "alternative", "splicing", "behavioral", "pharmacology", "epigenetics", "cocaine...	2017	Histone posttranslational modifications predict specific alternative exon subtypes in mammalian brain
Vector-borne transmission of Chagas disease has become an urban problem in the city of Arequipa , Peru , yet the debilitating symptoms that can occur in the chronic stage of the disease are rarely seen in hospitals in the city . The lack of obvious clinical disease in Arequipa has led to speculation that the local stra...	Chagas disease has become an urban problem in the city of Arequipa , Peru , yet there are very few people exhibiting severe symptoms of the disease . Severe symptoms often do not appear until decades after infection . To determine why so few people were exhibiting severe symptoms , we used a new method , epicenter regr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiological", "methods", "ecology", "epidemiology", "infectious", "disease", "epidemiology", "biology", "population", "ecology", "spatial", "epidemiology" ]	2011	Retracing Micro-Epidemics of Chagas Disease Using Epicenter Regression
Successful maintenance of cellular lineages critically depends on the fate decision dynamics of stem cells ( SCs ) upon division . There are three possible strategies with respect to SC fate decision symmetry: ( a ) asymmetric mode , when each and every SC division produces one SC and one non-SC progeny; ( b ) symmetri...	Stem cells have long been associated with their ability to divide asymmetrically , when one daughter cell retains stem cell properties of the parent cell , while the other daughter cell becomes more mature and loses its stemness . Recent findings , however , point at the existence of an alternative , symmetric division...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Role of Symmetric Stem Cell Divisions in Tissue Homeostasis
SUMOylation is associated with epigenetic regulation of chromatin structure and transcription . Epigenetic modifications of herpesviral genomes accompany the transcriptional switch of latent and lytic genes during the virus life cycle . Here , we report a genome-wide comparison of SUMO paralog modification on the KSHV ...	Establishment of KSHV persistent infection requires a dynamic balance between latency , a phase where most viral genes are silenced , and lytic cycle , a phase when nearly all viral genes are expressed . Disruption of this balance may augment virus clearance . During the latent-to-lytic switch , KSHV genomes are subjec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	K-bZIP Mediated SUMO-2/3 Specific Modification on the KSHV Genome Negatively Regulates Lytic Gene Expression and Viral Reactivation
Pentavalent antimonials ( Sb5 ) are the first-line drugs for treating cutaneous leishmaniasis in Colombia; however , given problems with toxicity , compliance , availability , and cost , it is imperative to look for better therapeutic options . Intravenous amphotericin B ( AmB ) has been used extensively to treat visce...	Cutaneous leishmaniasis is a disease caused by Leishmania parasites and transmitted by sand flies . It is a complex disease and is underresearched disease , that depending on the parasite species , can take multiple forms , which can be less or more aggressive . It manifests as ulcers , nodules or other lesions mostly ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "parasitic", "protozoans", "research", "design", "protozoans", "signs", ...	2018	A phase II study to evaluate the safety and efficacy of topical 3% amphotericin B cream (Anfoleish) for the treatment of uncomplicated cutaneous leishmaniasis in Colombia
Cytoplasmic assembly of ciliary dyneins , a process known as preassembly , requires numerous non-dynein proteins , but the identities and functions of these proteins are not fully elucidated . Here , we show that the classical Chlamydomonas motility mutant pf23 is defective in the Chlamydomonas homolog of DYX1C1 . The ...	Most animal cells have antenna-like organelles called “cilia” . These organelles have various important functions both in motility and sensing the environment . Motile cilia are essential for moving cells as well as moving fluids across a surface . The waveform of motile cilia requires large macromolecular motors; thes...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "molecular", "probe", "techniques", "immunoblotting", "parasitic", "protozoans", "dyneins", "molecular", "motors", "protozoans", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "cellular", "structures", "and", "organelles", "motor", "proteins", "res...	2017	Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms
Mating between different species produces hybrids that are usually asexual and stuck as diploids , but can also lead to the formation of new species . Here , we report the genome sequences of 27 isolates of the pathogenic yeast Candida orthopsilosis . We find that most isolates are diploid hybrids , products of mating ...	The genus Candida is one of the leading causes of fungal morbidity in humans . Many pathogenic Candida species are diploid , and do not have have a full sexual cycle . The evolutionary origin of Candida orthopsilosis is unclear . Here , we use whole genome sequencing of 27 C . orthopsilosis isolates from around the wor...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "heterozygosity", "fungal", "genetics", "population", "genetics", "developmental", "biology", "plant", "science", "phylogenetic", "analysis", "energy-producing", "organelles", "mitochondria", "population", "biology", "bioenergetics", "molecular", "biology", "techniques", "pla...	2016	Multiple Origins of the Pathogenic Yeast Candida orthopsilosis by Separate Hybridizations between Two Parental Species
A range of molecular amplification techniques have been developed for the diagnosis of Human African Trypanosomiasis ( HAT ) ; however , careful evaluation of these tests must precede implementation to ensure their high clinical accuracy . Here , we investigated the diagnostic accuracy of molecular amplification tests ...	A range of molecular amplification techniques has been developed for the diagnosis of HAT , with polymerase chain reaction ( PCR ) at the forefront . As laboratory strengthening in endemic areas increases , it is expected that the applicability of molecular tests will increase . However , careful evaluation of these te...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "diagnostic", "medicine", "biology", "zoology", "public", "health" ]	2012	Diagnostic Accuracy of Molecular Amplification Tests for Human African Trypanosomiasis—Systematic Review
Antimicrobial proteins and peptides ( AMPs ) are important effectors of the innate immune system that play a vital role in the prevention of infections . Recent advances have highlighted the similarity between AMPs and amyloid proteins . Using the Eosinophil Cationic Protein as a model , we have rationalized the struct...	Microbial infections are reported among the worst human diseases and cause millions of deaths per year over the world . Antibiotics are used to treat infections and have saved more lives than any other drug in human history . However , due to extended use , many strains are becoming refractive to common antibiotics . I...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "macromolecular", "assemblies", "microbiology", "chemical", "biology", "escherichia", "coli", "bacterial", "pathogens", "immune", "system", "proteins", "proteins", "microbial", "pathogens", "biology", "pathogenesis", "biophysics", "drug", "discovery", "biochemistry", "gram"...	2012	Exploring New Biological Functions of Amyloids: Bacteria Cell Agglutination Mediated by Host Protein Aggregation
Hypoxia-induced cell injury has been related to multiple pathological conditions . In order to render hypoxia-sensitive cells and tissues resistant to low O2 environment , in this current study , we used Drosophila melanogaster as a model to dissect the mechanisms underlying hypoxia-tolerance . A D . melanogaster strai...	Hypoxia-induced injury has been related to multiple pathological conditions . In order to render mammalian cells and tissues resistant to low O2 environment , we wished to first understand the mechanisms underlying hypoxia-tolerance in resistant animals . Therefore , we generated a D . melanogaster strain that is toler...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "genetics", "and", "genomics/physiogenomics", "genetics", "and", "genomics/gene", "function", "genetics", "and", "genomics" ]	2008	Mechanisms Underlying Hypoxia Tolerance in Drosophila melanogaster: hairy as a Metabolic Switch
We describe a comprehensive and general approach for mapping centromeres and present a detailed characterization of two maize centromeres . Centromeres are difficult to map and analyze because they consist primarily of repetitive DNA sequences , which in maize are the tandem satellite repeat CentC and interspersed cent...	Centromeres tend to be the last regions to be assembled in genome projects , as their mapping is hampered by their characteristically high repeat DNA content and lack of genetic recombination . Using unique markers derived from these repeat-rich regions , we were able to generate and annotate physical maps of two maize...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plant", "biology/plant", "genomes", "and", "evolution", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/plant", "genomes", "and", "evolution", "molecular", "biology/centromeres", "evolutionary", "biology/genomics", "genetics", "and", "genomics...	2009	Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons
With few studies conducted to date , very little is known about the epidemiology of rickettsioses in Bhutan . Due to two previous outbreaks and increasing clinical cases , scrub typhus is better recognized than other rickettsial infections and Q fever . A descriptive cross-sectional serosurvey was conducted from Januar...	Rickettsial infections including scrub typhus and Q fever are not widely recognised in Bhutan although the country is situated in an endemic Asian region . With two recorded outbreaks , scrub typhus is known to occur but other rickettsial infections and Q fever have not been recorded . In this first seroprevalence stud...	[ "Abstract", "Introduction", "Methods", "Results", "Discussions" ]	[ "bhutan", "medicine", "and", "health", "sciences", "typhus", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "geographical", "locations", "microbiology", "rickettsia", "bacterial", "diseases", "age", "groups", "antibodies",...	2017	Seroprevalence of rickettsial infections and Q fever in Bhutan
Primary infection of Toxoplasma gondii during pregnancy can be transmitted to the unborn child and may have serious consequences , including retinochoroiditis , hydrocephaly , cerebral calcifications , encephalitis , splenomegaly , hearing loss , blindness , and death . Austria , a country with moderate seroprevalence ...	Toxoplasma gondii is a widespread parasitic disease . In the event of primary infection during pregnancy , this parasite can be transmitted from mother to unborn child . Clinical presentation of congenital toxoplasmosis varies from asymptomatic to life-threatening risk for the fetus and infant and in later life . Preve...	[ "Abstract", "Introduction", "Method", "Results", "Discussion" ]	[ "children", "cognitive", "neurology", "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "toxoplasma", "gondii", "neuroscience", "parasitic", "protozoans", "parasitic", "diseases", "pediatrics", "age", "groups", "cognitive", ...	2017	Congenital toxoplasmosis in Austria: Prenatal screening for prevention is cost-saving
Initial axial patterning of the neural tube into forebrain , midbrain , and hindbrain primordia occurs during gastrulation . After this patterning phase , further diversification within the brain is thought to proceed largely independently in the different primordia . However , mechanisms that maintain the demarcation ...	The thalamus is the interface between the body and the brain . It connects sensory organs with higher brain areas and modulates processes such as sleep , alertness , and consciousness . Our knowledge about the embryonic development of this central relay station is still fragmented . Here , we show that the transcriptio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "neurogenesis", "gene", "regulation", "cadherins", "neuroscience", "cell", "differentiation", "gene", "function", "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "development", "molecular", "genetics", "signali...	2011	Lhx2 and Lhx9 Determine Neuronal Differentiation and Compartition in the Caudal Forebrain by Regulating Wnt Signaling
Leukotriene B4 ( LTB4 ) is secreted by chemotactic neutrophils , forming a secondary gradient that amplifies the reach of primary chemoattractants . This strategy increases the recruitment range for neutrophils and is important during inflammation . Here , we show that LTB4 and its synthesizing enzymes localize to intr...	Neutrophils represent the first line of attack against infections and inflammatory insults . The ability of neutrophils to reach these sites , a key feature in the resolution of infections , is mediated by their capacity to sense and migrate directionally to the core of the inflammation site . Chemicals released at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Exosomes Mediate LTB4 Release during Neutrophil Chemotaxis
The anthelmintics ivermectin ( IVM ) and moxidectin ( MOX ) display differences in toxicity in several host species . Entrance into the brain is restricted by the P-glycoprotein ( P-gp ) efflux transporter , while toxicity is mediated through the brain GABA ( A ) receptors . This study compared the toxicity of IVM and ...	Ivermectin ( IVM ) is used for onchocerciasis mass drug administration and is important for control of lymphatic filariasis , strongyloidiases and Scarcoptes mange in humans . It is widely used for parasite control in livestock . Moxidectin ( MOX ) is being evaluated against Onchocerca volvulus in humans and is also wi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "veterinary", "science", "veterinary", "diseases", "veterinary", "parasitology", "veterinary", "toxicology", "pharmacology", "biology", "veterinary", "pharmacology", "neuroscience", "toxicokinetics", "toxicology", "neurotoxicology" ]	2012	Relative Neurotoxicity of Ivermectin and Moxidectin in Mdr1ab (−/−) Mice and Effects on Mammalian GABA(A) Channel Activity
The midbrain superior colliculus ( SC ) generates a rapid saccadic eye movement to a sensory stimulus by recruiting a population of cells in its topographically organized motor map . Supra-threshold electrical microstimulation in the SC reveals that the site of stimulation produces a normometric saccade vector with lit...	The midbrain Superior Colliculus ( SC ) is crucial for generating rapid saccadic eye movements . It contains a topographically organized map of visuomotor space , in which a large population of recruited cells determines the metrics and kinematics of saccades . The dynamic spike-counting model explains how this populat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2019	Microstimulation in a spiking neural network model of the midbrain superior colliculus
The classical method for detection of Lassa virus-specific antibodies is the immunofluorescence assay ( IFA ) using virus-infected cells as antigen . However , IFA requires laboratories of biosafety level 4 for assay production and an experienced investigator to interpret the fluorescence signals . Therefore , we aimed...	Lassa fever is endemic in several West African countries . However , only few hospitals and laboratories in the region have the capacity to conduct molecular or serological Lassa fever diagnostics . One reason is that the classical serological technique for Lassa fever—the immunofluorescence assay ( IFA ) —requires bio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "bi...	2018	Development and evaluation of antibody-capture immunoassays for detection of Lassa virus nucleoprotein-specific immunoglobulin M and G
Rabies is a devastating yet preventable disease that causes around 59 , 000 human deaths annually . Almost all human rabies cases are caused by bites from rabies-infected dogs . A large proportion of these cases occur in Sub Saharan Africa ( SSA ) . Annual vaccination of at least 70% of the dog population is recommende...	Rabies is a devastating yet preventable disease that causes around 59 , 000 human deaths annually of which a large proportion occurs in Sub Saharan Africa ( SSA ) . In order to eliminate rabies , annual vaccination of at least 70% of the dog population is recommended . In SSA most rabies vaccination programmes use stat...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "immunology", "tropical", "diseases", "geographical", "locations", "vertebrates", "social", "sciences", "malawi", "dogs", "animals", "mammals", "preventive", "medicine", "r...	2018	Barriers of attendance to dog rabies static point vaccination clinics in Blantyre, Malawi
Urea-induced protein denaturation is widely used to study protein folding and stability; however , the molecular mechanism and driving forces of this process are not yet fully understood . In particular , it is unclear whether either hydrophobic or polar interactions between urea molecules and residues at the protein s...	To perform their physiological function , proteins have to fold into their characteristic three-dimensional structure . While the folded state is stable under physiological conditions , changes in the solvent can destabilize the folded state and even induce denaturation . One of the most commonly used denaturants is ur...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/molecular", "dynamics", "biophysics/theory", "and", "simulation", "biophysics/protein", "folding" ]	2008	Polar or Apolar—The Role of Polarity for Urea-Induced Protein Denaturation
In recent years , comparative genome sequence analysis of African Mycobacterium ulcerans strains isolated from Buruli ulcer ( BU ) lesion specimen has revealed a very limited genetic diversity of closely related isolates and a striking association between genotype and geographical origin of the patients . Here , we com...	Infection with Mycobacterium ulcerans causes the debilitating skin disease Buruli ulcer . Until today , transmission pathways and reservoirs of this emerging pathogen are not well understood . Generally , it is assumed that infection occurs after contact with potential environmental sources of M . ulcerans through punc...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "rivers", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "tropical", "diseases", "genomic", "library", "construction", "bacterial", "diseases", "signs", "...	2016	Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana
Seasonal influenza epidemics cause consistent , considerable , widespread loss annually in terms of economic burden , morbidity , and mortality . With access to accurate and reliable forecasts of a current or upcoming influenza epidemic’s behavior , policy makers can design and implement more effective countermeasures ...	Influenza epidemics occur annually , and incur significant losses in terms of lost productivity , sickness , and death . Policy makers employ countermeasures , such as vaccination campaigns , to combat the occurrence and spread of infectious diseases , but epidemics exhibit a wide range of behavior , which makes design...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Flexible Modeling of Epidemics with an Empirical Bayes Framework
The long-term treatment outcome of visceral leishmaniasis ( VL ) patients with HIV co-infection is complicated by a high rate of relapse , especially when the CD4 count is low . Although use of secondary prophylaxis is recommended , it is not routinely practiced and data on its effectiveness and safety are limited . A ...	Achieving parasitological cure at the end of visceral leishmaniasis ( VL ) treatment in HIV co-infected patients does not assure definitive cure , as the disease will recur within a year in many patients . In this cohort study , the probability of relapse-free survival at one-year was 50% in all patients . The use of m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitology", "retroviruses", "viruses", "immunodeficiency", "viruses", "preventive", "medicine", "research...	2019	Long term outcomes and prognostics of visceral leishmaniasis in HIV infected patients with use of pentamidine as secondary prophylaxis based on CD4 level: a prospective cohort study in Ethiopia
Zinc transporters play a critical role in spatiotemporal regulation of zinc homeostasis . Although disruption of zinc homeostasis has been implicated in disorders such as intestinal inflammation and aberrant epithelial morphology , it is largely unknown which zinc transporters are responsible for the intestinal epithel...	Intestinal epithelium undergoes continuous self-renewal to maintain intestinal homeostasis . Given that dysregulation of zinc flux causes intestinal disorders , appropriate spatiotemporal regulation of zinc in the intracellular compartments should be a prerequisite for the intestinal epithelial self-renewal process . Z...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "paneth", "cells", "cell", "death", "organoids", "medicine", "and", "health", "sciences", "biological", "cultures", "cell", "processes", "endoplasmic", "reticulum", "epithelial", "cells", "physiological", "processes", "homeostasis", "stem", "cells", "organ", "cultures",...	2016	Zinc Transporter SLC39A7/ZIP7 Promotes Intestinal Epithelial Self-Renewal by Resolving ER Stress
An estimated 2 . 7 million new HIV-1 infections occurred in 2010 . `Treatment-for-prevention’ may strongly prevent HIV-1 transmission . The basic idea is that immediate treatment initiation rapidly decreases virus burden , which reduces the number of transmittable viruses and thereby the probability of infection . Howe...	HIV-1 continues to spread globally . Antiviral treatment cannot cure patients , but it slows disease progression and may prevent HIV transmission by decreasing the amount of transmittable viruses in treated individuals . ‘Treatment-for-prevention’ argues for immediate treatment initiation and may reduce transmission by...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Optimal Treatment Strategies in the Context of ‘Treatment for Prevention’ against HIV-1 in Resource-Poor Settings
Wolbachia are maternally inherited bacteria that infect arthropod species worldwide and are deployed in vector control to curb arboviral spread using cytoplasmic incompatibility ( CI ) . CI kills embryos when an infected male mates with an uninfected female , but the lethality is rescued if the female and her embryos a...	Releases of Wolbachia-infected mosquitos are underway worldwide because Wolbachia block replication of Zika and Dengue viruses and spread themselves maternally through arthropod populations via cytoplasmic incompatibility ( CI ) . The CI drive system depends on a Wolbachia-induced sperm modification that results in emb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "invertebrates", "medicine", "and", "health", "sciences", "bacteriophages", "vector-borne", "diseases", "microbiology", "animals", "wolbachia", "animal", "models", "viruses", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "ex...	2019	Two-By-One model of cytoplasmic incompatibility: Synthetic recapitulation by transgenic expression of cifA and cifB in Drosophila
Flaviviruses deliver their genome into the cell by fusing the viral lipid membrane to an endosomal membrane . The sequence and kinetics of the steps required for nucleocapsid delivery into the cytoplasm remain unclear . Here we dissect the cell entry pathway of virions and virus-like particles from two flaviviruses usi...	Many viruses package their genetic material into a lipid envelope . In order to deliver their genome into the host-cell cytoplasm , where it can be replicated , viruses must fuse their envelope with a cellular lipid membrane . This fusion event is therefore a critical step in the entry of an enveloped virus into the ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "transmission", "and", "infection", "flavivirus", "emerging", "viral", "diseases", "immunology", "microbiology", "viral", "structure", "viruslike", "particles", "neglected", "tropical", "diseases", "japanese", "encephalitis", "infectious", "diseases", ...	2013	Viral Membrane Fusion and Nucleocapsid Delivery into the Cytoplasm are Distinct Events in Some Flaviviruses
Mathematical methods of information theory appear to provide a useful language to describe how stimuli are encoded in activities of signaling effectors . Exploring the information-theoretic perspective , however , remains conceptually , experimentally and computationally challenging . Specifically , existing computatio...	In light of single-cell , live-imaging experiments understanding of how cells transmit information about identity and quantity of stimuli is incomplete . When exposed to the same stimulus individual cells exhibit substantial cell-to-cell heterogeneity . Besides , stimuli have been shown to regulate temporal profiles of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "applied", "mathematics", "cell", "processes", "social", "sciences", "neuroscience", "biologists", "simulation", "and", "modeling", "algorithms", "optimization", "scientists", "probability", "distribution", "mathematics", "cognitive", "psychology", "science", "and", "techno...	2019	Information-theoretic analysis of multivariate single-cell signaling responses
Chagas' disease , produced by Trypanosoma cruzi , affects more than 8 million people , producing approximately 10 , 000 deaths each year in Latin America . Migration of people from endemic regions to developed countries has expanded the risk of infection , transforming this disease into a globally emerging problem . PG...	Chagas' disease is an infection produced by the parasite Trypanosoma cruzi . This pathology is endemic in Latin America and has become a public health issue in some non-endemic countries like the USA , Spain and Australia . There is no curative treatment against Chagas' disease . NSAIDs , like aspirin , have been assay...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "chagas", "disease", "neglected", "tropical", "diseases", "host-pathogen", "interaction", "biology", "microbiology", "parasitic", "diseases", "parasitology" ]	2013	Protective Role of Acetylsalicylic Acid in Experimental Trypanosoma cruzi Infection: Evidence of a 15-epi-Lipoxin A4-Mediated Effect
In auditory cortex , temporal information within a sound is represented by two complementary neural codes: a temporal representation based on stimulus-locked firing and a rate representation , where discharge rate co-varies with the timing between acoustic events but lacks a stimulus-synchronized response . Using a com...	How does our auditory system represent time within a sound ? Previous work has demonstrated that both the firing rate of neurons ( rate code ) and the timing of their stimulus-evoked responses ( temporal code ) can be used by auditory cortical neurons to represent temporal information . We investigated the underlying m...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Role of Inhibition in a Computational Model of an Auditory Cortical Neuron during the Encoding of Temporal Information
Type IV secretion systems ( T4SS ) are used by Gram-negative bacteria to translocate protein and DNA substrates across the cell envelope and into target cells . Translocation across the outer membrane is achieved via a ringed tetradecameric outer membrane complex made up of a small VirB7 lipoprotein ( normally 30 to 45...	Many aspects of bacterial life require that they translocate proteins to the cell exterior . To do this , different macromolecular secretion systems of varying complexity have evolved ( Type I–VI secretion systems ) . These secretion systems are often at the front lines of pathogen-host interactions and are important f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "macromolecular", "assemblies", "microbiology", "host-pathogen", "interaction", "protein", "structure", "bacterial", "pathogens", "proteins", "lipoproteins", "biology", "recombinant", "proteins", "biophysics", "biochemistry", "gram", "negative", "lipoprotein", "structure" ]	2011	A Component of the Xanthomonadaceae Type IV Secretion System Combines a VirB7 Motif with a N0 Domain Found in Outer Membrane Transport Proteins
Animals have many ways of protecting themselves against stress; for example , they can induce animal-wide , stress-protective pathways and they can kill damaged cells via apoptosis . We have discovered an unexpected regulatory relationship between these two types of stress responses . We find that C . elegans mutations...	As an animal interacts with its environment , it invariably encounters stressful conditions such as extreme temperatures , drought , UV exposure and harmful xenobiotics . Since the ability to respond appropriately to stressful stimuli is paramount to survival , organisms have developed sophisticated stress response pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Shift to Organismal Stress Resistance in Programmed Cell Death Mutants
Notch signalling is a fundamental pathway that shapes the developing embryo and sustains adult tissues by direct communication between ligand and receptor molecules on adjacent cells . Among the ligands are two Delta paralogues , DLL1 and DLL4 , that are conserved in mammals and share a similar structure and sequence ....	Notch signalling relies on binding of a ligand to a Notch receptor , both residing on the surfaces of neighbouring cells . This interaction forwards a signal into the receptor-expressing cell , this way coordinating cells in many biological processes such as the segmentation of the axial skeleton . Mammals possess four...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Context-Dependent Functional Divergence of the Notch Ligands DLL1 and DLL4 In Vivo
Ethylene has been regarded as a stress hormone to regulate myriad stress responses . Salinity stress is one of the most serious abiotic stresses limiting plant growth and development . But how ethylene signaling is involved in plant response to salt stress is poorly understood . Here we showed that Arabidopsis plants p...	High salinity , as a world-wide abiotic stress , restricts root water uptake , damages cell physiology , and limits the productivity of agricultural crops . Ethylene is a major phytohormone that regulates plant development in response to adverse environments , including high salt stress . However , the molecular mechan...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "plant", "biochemistry", "plant", "defenses", "plant", "science", "plant", "hormones", "ethylene", "biology", "and", "life", "sciences", "plant", "physiology", "hormones" ]	2014	Salt-Induced Stabilization of EIN3/EIL1 Confers Salinity Tolerance by Deterring ROS Accumulation in Arabidopsis
Chagas disease is one of the most important neglected tropical diseases in the Americas . Vectorborne transmission of Chagas disease has been historically rare in urban settings . However , in marginal communities near the city of Arequipa , Peru , urban transmission cycles have become established . We examined the his...	Chagas disease affects 8–10 million people in the Americas . Although transmission was previously limited to the rural poor , Chagas increasingly affects urban populations , especially near the city of Arequipa , Peru . We interviewed residents of five communities to learn about why and when they migrated to the city a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health", "public", "health", "and", "epidemiology/infectious", "diseases" ]	2009	Chagas Disease, Migration and Community Settlement Patterns in Arequipa, Peru
Virus infections can result in a range of cellular injuries and commonly this involves both the plasma and intracellular membranes , resulting in enhanced permeability . Viroporins are a group of proteins that interact with plasma membranes modifying permeability and can promote the release of viral particles . While t...	Most non-enveloped viruses exit their host cells following cell lysis , which involves breakdown of the cell membrane and death of the host cell , and which is presumably the final result of an increase in plasma membrane permeability . JC virus ( JCV ) is the causative agent of progressive multifocal leukoencephalopat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "infectious", "diseases", "infectious", "diseases/viral", "infections" ]	2010	The Human Polyoma JC Virus Agnoprotein Acts as a Viroporin
Leishmaniasis is a tropical disease threatening 350 million people from endemic regions . The available drugs for treatment are inadequate , with limitations such as serious side effects , parasite resistance or high cost . Driven by this need for new drugs , we developed a high-content , high-throughput image-based sc...	Leishmaniasis , one of the most neglected tropical diseases , affects over 2 million people each year . Visceral leishmaniasis ( VL ) , also known as Kala-azar , is caused by the protozoan parasites Leishmania donovani and Leishmania infantum and is fatal if left untreated . Because existing treatments are often ineffe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parastic", "protozoans", "protozoology", "biology", "microbiology" ]	2012	An Image-Based High-Content Screening Assay for Compounds Targeting Intracellular Leishmania donovani Amastigotes in Human Macrophages
During B cell development , the precursor B cell receptor ( pre-BCR ) checkpoint is thought to increase immunoglobulin κ light chain ( Igκ ) locus accessibility to the V ( D ) J recombinase . Accordingly , pre-B cells lacking the pre-BCR signaling molecules Btk or Slp65 showed reduced germline Vκ transcription . To inv...	B lymphocyte development involves the generation of a functional antigen receptor , comprising two heavy chains and two light chains arranged in a characteristic “Y” shape . To do this , the receptor genes must first be assembled by ordered genomic recombination events , starting with the immunoglobulin heavy chain ( I...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "humoral", "immunity", "medicine", "immune", "cells", "immunology", "cell", "differentiation", "developmental", "biology", "molecular", "development", "epigenetics", "chromatin", "chromosome", "biology", "gene", "expression", "biology", "genetics", "of", "the", "immune", ...	2014	Pre-B Cell Receptor Signaling Induces Immunoglobulin κ Locus Accessibility by Functional Redistribution of Enhancer-Mediated Chromatin Interactions
Many microbes are studied by examining colony morphology via two-dimensional top-down images . The quantification of such images typically requires each pixel to be labelled as belonging to either the colony or background , producing a binary image . While this may be achieved manually for a single colony , this proces...	Many microbes are studied by examining the colony morphology via a two-dimensional top-down image . In order to quantify such images , we typically need to label each pixel as belonging either to the colony or the background , creating a binary image . This task is laborious when performed manually and proves infeasibl...	[ "Abstract", "Introduction", "Design", "and", "implementation", "Results", "and", "discussion", "Availability", "and", "future", "directions" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "signal", "processing", "pathogens", "applied", "mathematics", "salts", "microbiology", "simulation", "and", "modeling", "...	2018	TAMMiCol: Tool for analysis of the morphology of microbial colonies
An essential feature of meiosis is Spo11 catalysis of programmed DNA double strand breaks ( DSBs ) . Evidence suggests that the number of DSBs generated per meiosis is genetically determined and that this ability to maintain a pre-determined DSB level , or “DSB homeostasis” , might be a property of the meiotic program ...	Meiosis is a specialized cell division that underpins sexual reproduction . It begins with a diploid cell carrying both parental copies of each chromosome , and ends with four haploid cells , each containing only one copy . An essential feature of meiosis is meiotic recombination , during which the programmed generatio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "genetics", "biology" ]	2013	Budding Yeast ATM/ATR Control Meiotic Double-Strand Break (DSB) Levels by Down-Regulating Rec114, an Essential Component of the DSB-machinery
Chikungunya virus ( CHIKV ) has dispersed in the Americas since 2013 , and its range of distribution has overlapped large forested areas . Herein , we assess vector competence of two sylvatic Neotropical mosquito species , Haemagogus leucocelaenus and Aedes terrens , to evaluate the risk of CHIKV to initiate a sylvatic...	Chikungunya is a mosquito-borne-viral disease of African origin that has spread in the Americas since its first detection in 2013 . The vector of Chikungunya virus ( CHIKV ) in the Americas is the mosquito Aedes aegypti . Due to this vector domestic behavior , CHIKV transmission is limited between this mosquito species...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "viral", "transmission", "and", "infection", "pathogens", ...	2017	High risk for chikungunya virus to initiate an enzootic sylvatic cycle in the tropical Americas
Dosage compensation equates between the sexes the gene dose of sex chromosomes that carry substantially different gene content . In Drosophila , the single male X chromosome is hypertranscribed by approximately two-fold to effect this correction . The key genes are male lethal and appear not to be required in females ,...	When substantially different , sex chromosomes present the challenge of not only gene dose inequity between the sexes , in the heterogametic sex where one chromosome ( frequently the Y ) carries few genes , but also an inequity relative to the autosomes which are diploid . Dosage compensation refers to the process whic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/molecular", "development", "molecular", "biology/transcription", "initiation", "and", "activation" ]	2010	Requirement of Male-Specific Dosage Compensation in Drosophila Females—Implications of Early X Chromosome Gene Expression
An epidemic of Zika virus ( ZIKV ) illness that occurred in July 2007 on Yap Island in the Federated States of Micronesia prompted entomological studies to identify both the primary vector ( s ) involved in transmission and the ecological parameters contributing to the outbreak . Larval and pupal surveys were performed...	Arthropod-borne viruses ( arboviruses ) cause significant human morbidity and mortality throughout the world . Zika virus , which is reported to be transmitted by Aedes ( Stegomyia ) species mosquitoes , caused an outbreak on the island of Yap , in the Federated States of Micronesia in 2007 . This was the first describ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "tropical", "diseases", "medicine", "and", "health", "sciences" ]	2014	Aedes hensilli as a Potential Vector of Chikungunya and Zika Viruses
Deedu ( DU ) Mongolians , who migrated from the Mongolian steppes to the Qinghai-Tibetan Plateau approximately 500 years ago , are challenged by environmental conditions similar to native Tibetan highlanders . Identification of adaptive genetic factors in this population could provide insight into coordinated physiolog...	Throughout history , Mongolians have survived the harsh conditions of northern latitudes , including seasonal cold , drought , and a restricted diet . Approximately 500 years ago , nomadic Deedu ( DU; “at high altitude” ) Mongolians migrated from the Mongolian steppes to the northeastern highlands of the Qinghai-Tibeta...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "natural", "selection", "genetics", "population", "genetics", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "evolutionary", "genetics" ]	2013	Genomic Analysis of Natural Selection and Phenotypic Variation in High-Altitude Mongolians
Burkholderia pseudomallei is a water and soil bacterium and the causative agent of melioidosis . A characteristic feature of this bacterium is the formation of different colony morphologies which can be isolated from environmental samples as well as from clinical samples , but can also be induced in vitro . Previous st...	Melioidosis is a common disease in Northern Australia and East Asia , with regional mortality rates of up to 40% . Clinical manifestations range from soft tissue infections to severe sepsis . It is caused by the Gram negative saprophytic water and soil bacterium Burkholderia pseudomallei , which forms a variety of colo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "burkholderia", "pseudomallei", "pathogens", "microbiology", "carbohydrates", "glucose", "metabolism", ...	2016	Burkholderia pseudomallei Colony Morphotypes Show a Synchronized Metabolic Pattern after Acute Infection
Hepatitis A virus ( HAV ) , the prototype of genus Hepatovirus , has several unique biological characteristics that distinguish it from other members of the Picornaviridae family . Among these , the need for an intact eIF4G factor for the initiation of translation results in an inability to shut down host protein synth...	Each organism has a specific codon usage signature . Translational selection i . e . , selection for the codon adaptation to the tRNA pools , is one of the driving forces of codon bias . In the virus world , this implies an adjustment of the virus codon usage to that of the host cell . Hepatitis A virus appears as an e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virus", "evolution", "and", "symbiosis", "virology" ]	2010	Fine-Tuning Translation Kinetics Selection as the Driving Force of Codon Usage Bias in the Hepatitis A Virus Capsid
Learning causal networks from large-scale genomic data remains challenging in absence of time series or controlled perturbation experiments . We report an information- theoretic method which learns a large class of causal or non-causal graphical models from purely observational data , while including the effects of uno...	The reconstruction of causal networks from genomic data is an important but challenging problem . Predicting key regulatory interactions or genomic alterations at the origin of human diseases can guide experimental investigation and ultimately inspire innovative therapy . However , causal relationships are difficult to...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "genetic", "networks", "genome", "evolution", "applied", "mathematics", "basic", "cancer", "research", "human", "genomics", "departures", "from", "diploidy", "simulation", "and", "modeling", "algorithms", ...	2017	Learning causal networks with latent variables from multivariate information in genomic data
Staphylococcus aureus virulence has been associated with the production of phenol soluble modulins ( PSM ) . PSM are known to activate , attract and lyse neutrophils . However , the functional characterizations were generally performed in the absence of human serum . Here , we demonstrate that human serum can inhibit a...	Infections with methicillin-resistant Staphylococcus aureus ( MRSA ) are difficult to treat because of resistance against standard antibiotics . In contrast to the traditional healthcare-associated ( HA- ) MRSA strains , community-associated ( CA- ) MRSA strains cause severe infections in otherwise healthy individuals ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "immunology", "biology", "microbiology", "bacterial", "pathogens" ]	2012	Inactivation of Staphylococcal Phenol Soluble Modulins by Serum Lipoprotein Particles
Recent studies have highlighted the ability of HIV to escape from cytotoxic T lymphocyte ( CTL ) responses that concurrently target multiple viral epitopes . Yet , the viral dynamics involved in such escape are incompletely understood . Previous analyses have made several strong assumptions regarding HIV escape from CT...	Since the early 1990s , cytotoxic T lymphocytes ( CTLs ) have been known to play an important role in HIV infection with CTLs targeting HIV epitopes and , in turn , HIV escapes arising through mutations in the targeted epitopes . Over the past decade , studies have shown that CTL responses concurrently target multiple ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Broad CTL Response in Early HIV Infection Drives Multiple Concurrent CTL Escapes
Congenital or neonatal cardiomyopathies are commonly associated with a poor prognosis and have multiple etiologies . In two siblings , a male and female , we identified an undescribed type of lethal congenital restrictive cardiomyopathy affecting the right ventricle . We hypothesized a novel autosomal recessive conditi...	Inborn heart defects can be divided into structural heart defects and diseases affecting the heart muscle , called cardiomyopathies . Congenital or neonatal cardiomyopathies are commonly associated with a poor prognosis and have multiple etiologies . In two siblings , a male and female , we identified an undescribed ty...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cardiomyopathies", "fish", "medicine", "and", "health", "sciences", "cardiovascular", "anatomy", "cardiac", "ventricles", "vertebrates", "animals", "fibroblasts", "animal", "models", "osteichthyes", "organisms", "developmental", "biology", "mutation", "model", "organisms",...	2018	Compound heterozygous loss-of-function mutations in KIF20A are associated with a novel lethal congenital cardiomyopathy in two siblings
Innate recognition of invading intracellular pathogens is essential for regulating robust and rapid CD4+ T cell effector function , which is critical for host-mediated immunity . The intracellular apicomplexan parasite , Toxoplasma gondii , is capable of infecting almost any nucleated cell of warm-blooded animals , inc...	It is currently estimated that one third of the world’s population is seropositive for the parasite Toxoplasma gondii and this parasite can lead to serious illness and death in immunocompromised patients , and is one of the leading causes of foodborne-related deaths in the United States . Host immunity against the para...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "toxoplasma", "gondii", "spleen", "immunology", "cell-mediated", "immunity", "parasitic", "diseases", "parasitic", "protozoan...	2019	TLR11-independent inflammasome activation is critical for CD4+ T cell-derived IFN-γ production and host resistance to Toxoplasma gondii
Mosquito-borne alphaviruses such as chikungunya virus and Ross River virus ( RRV ) are emerging pathogens capable of causing large-scale epidemics of virus-induced arthritis and myositis . The pathology of RRV-induced disease in both humans and mice is associated with induction of the host inflammatory response within ...	Arthritogenic alphaviruses such as Ross River virus ( RRV ) and chikungunya virus are transmitted to humans by mosquitoes and cause epidemics of debilitating infectious arthritis and myositis in various areas around the world . Studies in humans and mice indicate that the host inflammatory response is critical for deve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2012	Mannose Binding Lectin Is Required for Alphavirus-Induced Arthritis/Myositis
We use the qualitative insight of a planar neuronal phase portrait to detect an excitability switch in arbitrary conductance-based models from a simple mathematical condition . The condition expresses a balance between ion channels that provide a negative feedback at resting potential ( restorative channels ) and those...	Understanding the changing electrophysiological signatures of neurons in different physiological and pharmacological conditions is a central focus of experimental electrophysiology because a key component of cell signaling in the nervous system . Computational modeling may assist experimentalists in this quest by ident...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "systems", "biology", "mathematics", "computational", "neuroscience", "biology", "computational", "biology", "nonlinear", "dynamics", "biophysics", "neuroscience" ]	2013	A Balance Equation Determines a Switch in Neuronal Excitability
The H1N1 influenza pandemic of 2009 has claimed over 18 , 000 lives . During this pandemic , development of drug resistance further complicated efforts to control and treat the widespread illness . This research utilizes traditional Chinese medicine Database@Taiwan ( TCM Database@Taiwan ) to screen for compounds that s...	The influenza A subtype H1N1 ( H1N1/09 ) pandemic raised public concerns due to drug resistance strains . Drug resistance occurs from conformational changes causing the original drug to lose binding ability and exhibit biological effects . The world's largest TCM Database@Taiwan was employed to screen for potential lea...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "medicine", "physics", "computer", "science", "computer", "modeling", "drug", "research", "and", "development", "drugs", "and", "devices", "pharmacology", "biology", "computational", "biology", "biophysics", "simulations", "biophysics", "drug", "discovery...	2011	Two Birds with One Stone? Possible Dual-Targeting H1N1 Inhibitors from Traditional Chinese Medicine
Bluetongue virus ( BTV ) is the causative agent of a major disease of livestock ( bluetongue ) . For over two decades , it has been widely accepted that the 10 segments of the dsRNA genome of BTV encode for 7 structural and 3 non-structural proteins . The non-structural proteins ( NS1 , NS2 , NS3/NS3a ) play different ...	Bluetongue is a major infectious disease of ruminants caused by bluetongue virus ( BTV ) , an “arbovirus” transmitted from infected to susceptible hosts by biting midges . Historically , bluetongue has been endemic almost exclusively in temperate and tropical areas of the world . However , in the last decade BTV has sp...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "virology", "biology", "microbiology", "veterinary", "science" ]	2011	Identification and Characterization of a Novel Non-Structural Protein of Bluetongue Virus
Non-coding RNA ( ncRNA ) play an important and varied role in cellular function . A significant amount of research has been devoted to computational prediction of these genes from genomic sequence , but the ability to do so has remained elusive due to a lack of apparent genomic features . In this work , thermodynamic s...	Recent advances in DNA sequence technology have made it possible to sequence entire genomes . Once a genome is sequenced , it becomes necessary to identify the set of genes and other functional elements within the genome . This is particularly challenging as much of the genomic sequence does not appear to perform any f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "computational", "biology/genomics" ]	2009	Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae
The mosquito immune system is involved in pathogen-elicited defense responses . The NF-κB factors REL1 and REL2 are downstream transcription activators of Toll and IMD immune pathways , respectively . We have used genome-wide microarray analyses to characterize fat-body-specific gene transcript repertoires activated by...	Mosquito-borne diseases cause tremendous morbidity and mortality worldwide . New approaches to control vector-borne diseases include interruption of the association between pathogens and vectors by genetic manipulation of vectors and the development of transmission-blocking vaccines . Potential success of these approac...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "vector", "biology", "biology", "microbiology" ]	2011	Transcriptome Analysis of Aedes aegypti Transgenic Mosquitoes with Altered Immunity
Hepatitis B virus ( HBV ) persistence is facilitated by exhaustion of CD8 T cells that express the inhibitory receptor programmed cell death-1 ( PD-1 ) . Improvement of the HBV-specific T cell function has been obtained in vitro by inhibiting the PD-1/PD-ligand 1 ( PD-L1 ) interaction . In this study , we examined whet...	Chronic hepatitis B virus ( HBV ) infection is still one of the major public health problems . Two billion people worldwide have been infected with HBV , of whom more than 360 million developed chronic infection . Every year , approximately one million of these individuals will die from HBV-associated liver diseases su...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	Enhancing Virus-Specific Immunity In Vivo by Combining Therapeutic Vaccination and PD-L1 Blockade in Chronic Hepadnaviral Infection
Gammaherpesvirus cyclins have expanded biochemical features relative to mammalian cyclins , and promote infection and pathogenesis including acute lung infection , viral persistence , and reactivation from latency . To define the essential features of the viral cyclin , we generated a panel of knock-in viruses expressi...	Many viruses encode homologs of human oncogenes , including the gammaherpesvirus viral cyclin genes . These viruses cause lifelong infection associated with chronic diseases , including malignancies , which are exacerbated in immune deficiency . The conserved viral cyclins were first recognized nearly two decades ago ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "division", "cell", "biology", "virology", "biology", "microbiology" ]	2012	Viral Cyclins Mediate Separate Phases of Infection by Integrating Functions of Distinct Mammalian Cyclins
The Epstein-Barr virus ( EBV ) infects and transforms B-lymphocytes with high efficiency . This process requires expression of the viral latent proteins and of the 3 miR-BHRF1 microRNAs . Here we show that B-cells infected by a virus that lacks these non-coding RNAs ( Δ123 ) grew more slowly between day 5 and day 20 , ...	This paper explains some of the molecular mechanisms used by the Epstein-Barr virus ( EBV ) BHRF1 microRNA cluster to enhance transformation of B-cells after infection . We find that B-cells exposed to a virus that lacks the BHRF1 microRNAs ( Δ123 ) undergo more apoptosis and grow more slowly between the second and the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	A Viral microRNA Cluster Regulates the Expression of PTEN, p27 and of a bcl-2 Homolog
In a wide range of studies , the emergence of orientation selectivity in primary visual cortex has been attributed to a complex interaction between feed-forward thalamic input and inhibitory mechanisms at the level of cortex . Although it is well known that layer 4 cortical neurons are highly sensitive to the timing of...	While the visual system is selective for a wide range of different inputs , orientation selectivity has been considered the preeminent property of the mammalian visual cortex . Existing models of this selectivity rely on varying relative importance of feedforward thalamic input and intracortical influence . Recently , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "circuit", "models", "visual", "system", "computational", "neuroscience", "sensory", "systems", "biology", "neuroscience", "coding", "mechanisms" ]	2014	The Role of Thalamic Population Synchrony in the Emergence of Cortical Feature Selectivity
Bacterial superantigens ( SAgs ) cause Vβ-dependent T-cell proliferation leading to immune dysregulation associated with the pathogenesis of life-threatening infections such as toxic shock syndrome , and necrotizing pneumonia . Previously , we demonstrated that staphylococcal enterotoxin-like toxin X ( SElX ) from Stap...	Staphylococcus aureus is a bacterial pathogen responsible for an array of disease types in healthcare and community settings . One of the keys to the success of this pathogen is its ability to subvert the immune system of the host . Here we demonstrate that the superantigen ( SAg ) staphylococcal enterotoxin-like toxin...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell", "processes", "microbiology", "rabbits", "vertebrates", "staphylococcus", "aureus"...	2017	The Staphylococcus aureus superantigen SElX is a bifunctional toxin that inhibits neutrophil function
Ethiopia is one of the few African countries where Plasmodium vivax is co-endemic with P . falciparum . Malaria transmission is seasonal and transmission intensity varies mainly by landscape and climate . Although the recent emergence of drug resistant parasites presents a major issue to malaria control in Ethiopia , l...	Sub-Saharan Africa is home to nearly 90% of malaria cases . In Ethiopia , two-thirds of the population lives in areas at risk of malaria infection . Malaria spread via human migrations and emergence of drug resistant parasites are major issues to malaria control in this country . Our study used microsatellite markers t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "parasite", "groups", "medicine", "and", "health", "sciences", "plasmodium", "drugs", "population", "genetics", "geographical", "locations", "microbiology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "antimalarials", "apicomp...	2017	Transmission dynamics of co-endemic Plasmodium vivax and P. falciparum in Ethiopia and prevalence of antimalarial resistant genotypes
Biofilms are dense microbial communities . Although widely distributed and medically important , how biofilm cells interact with one another is poorly understood . Recently , we described a novel process whereby myxobacterial biofilm cells exchange their outer membrane ( OM ) lipoproteins . For the first time we report...	All cells interact with their environment , including other cells , to elicit cellular responses . Cell–cell interactions between eukaryotic cells are widely appreciated as large multicellular organisms coordinate cell behaviors for tissue and organ functions . In bacteria cell–cell interactions are not widely apprecia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "prokaryotic", "models", "model", "organisms", "molecular", "cell", "biology", "genetics", "molecular", "genetics", "biology", "microbiology", "genetics", "and", "genomics" ]	2012	Cell Contact–Dependent Outer Membrane Exchange in Myxobacteria: Genetic Determinants and Mechanism
Kaposi's Sarcoma ( KS ) , the most common tumor of AIDS patients , is a highly vascularized tumor supporting large amounts of angiogenesis . The main cell type of KS tumors is the spindle cell , a cell of endothelial origin , the primary cell type involved in angiogenesis . Kaposi's Sarcoma-associated herpesvirus ( KSH...	Kaposi's Sarcoma ( KS ) is the most common tumor of AIDS patients world-wide and is characterized by very high vascularization . The main KS tumor cell type is the spindle cell , a cell of endothelial origin . Kaposi's Sarcoma-associated herpesvirus ( KSHV ) , the etiologic agent of KS , is found predominantly in the l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viruses", "and", "cancer", "endothelial", "cells", "cancer", "treatment", "microbiology", "basic", "cancer", "research", "cancers", "and", "neoplasms", "cardiovascular", "oncology", "integrins", "tumor", "physiology", "cell", "movement", "signaling", "signa...	2011	Latent KSHV Infection of Endothelial Cells Induces Integrin Beta3 to Activate Angiogenic Phenotypes
An unexpectedly high seroprevalence and pathogenic potential of human parvovirus B19 ( B19V ) have been observed in certain malaria-endemic countries in parallel with local use of chloroquine ( CQ ) as first-line treatment for malaria . The aims of this study were to assess the effect of CQ and other common antimalaria...	Human parvovirus B19 ( B19V ) is typically associated with a childhood febrile illness known as erythema infectiosum . The infection usually resolves without consequence in healthy individuals . However , in patients with immunologic and/or hematologic disorders , B19V can cause a significant pathology . The virus infe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "virology", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology/preventive", "medicine", "hematology/anemias", "microbiology/parasitology", "infectious", "diseases/protozoal", "in...	2010	Chloroquine and Its Derivatives Exacerbate B19V-Associated Anemia by Promoting Viral Replication
Cytosine DNA methylation is a stable epigenetic mark that is frequently associated with the silencing of genes and transposable elements ( TEs ) . In Arabidopsis , the establishment of DNA methylation is through the RNA-directed DNA methylation ( RdDM ) pathway . Here , we report the identification and characterization...	Both plants and animals utilize cytosine DNA methylation as an important epigenetic mark to suppress transposable elements ( TEs ) , repeat sequences and genes , which is crucial for the genome integrity and development . In plants , de novo DNA methylation can be mediated by the RNA-directed DNA methylation ( RdDM ) p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A Pre-mRNA-Splicing Factor Is Required for RNA-Directed DNA Methylation in Arabidopsis
Eukaryotes regulate gene expression and other nuclear processes through the posttranslational modification of histones . In S . cerevisiae , the mono-ubiquitylation of histone H2B on lysine 123 ( H2B K123ub ) affects nucleosome stability , broadly influences gene expression and other DNA-templated processes , and is a ...	Chromatin , a complex of DNA wrapped around histone proteins , impacts all DNA-templated processes , including gene expression . Cells employ various strategies to alter chromatin structure and control access to the genetic material . Nucleosomes , the building blocks of chromatin , are subject to a myriad of modificat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Nucleosome Acidic Patch Regulates the H2B K123 Monoubiquitylation Cascade and Transcription Elongation in Saccharomyces cerevisiae
Tuberculosis is the deadliest infectious disease worldwide . Although the BCG vaccine is widely used , it does not efficiently protect against pulmonary tuberculosis and an improved tuberculosis vaccine is therefore urgently needed . Mycobacterium tuberculosis uses different ESX/Type VII secretion ( T7S ) systems to tr...	One of the major findings of the pioneering Mycobacterium tuberculosis H37Rv genome sequencing project was the identification of the highly abundant PE and PPE proteins , named after their N-terminal motifs Pro–Glu ( PE ) or Pro–Pro–Glu ( PPE ) . Within the 20 years of research since then , many claims were made that P...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "transport", "blood", "cells", "bacteriology", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "processes", "immunology", "microbiology", "vaccines", "physi...	2018	RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection
Metabolic flux is frequently rerouted through cellular metabolism in response to dynamic changes in the intra- and extra-cellular environment . Capturing the mechanisms underlying these metabolic transitions in quantitative and predictive models is a prominent challenge in systems biology . Progress in this regard has ...	Understanding the dynamic response of microorganisms to environmental changes is a major challenge in systems biology . In many cases , these responses manifest themselves through changes in gene transcription , which then propagate to adjust flow through metabolism . Here , we implement a Temporal Expression-based Ana...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "biochemical", "simulations", "genome", "expression", "analysis", "microbial", "metabolism", "systems", "biology", "genomics", "biology", "computational", "biology", "metabolic", "networks", "microbiology", "genetics", "and", "genomics" ]	2012	Temporal Expression-based Analysis of Metabolism
ArtinM , a D-mannose binding lectin from Artocarpus heterophyllus , has immunomodulatory activities through its interaction with N-glycans of immune cells , culminating with the establishment of T helper type 1 ( Th1 ) immunity . This interaction protects mice against intracellular pathogens , including Leishmania majo...	Vaccination is a successful way to eliminate infectious diseases . The generated antibodies neutralize the invading microbe and avoid the establishment of infection . Vaccines are efficient to prevent infections by pathogens living outside rather than inside the host`s cells . This occurs because protection against int...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "cell", "physiology", "cell", "death", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathoge...	2016	Neutrophils Contribute to the Protection Conferred by ArtinM against Intracellular Pathogens: A Study on Leishmania major
Antibodies binding to the surface of virions can lead to virus neutralisation . Different theories have been proposed to determine the number of antibodies that must bind to a virion for neutralisation . Early models are based on chemical binding kinetics . Applying these models lead to very low estimates of the number...	How many antibodies have to bind to a virus particle such that it is prevented from infecting a cell ? This seemingly simple question has not been answered yet . However , this number is crucial to determine whether a vaccine can stimulate the immune system to elicit enough antibodies to neutralise virus before startin...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "theoretical", "biology", "virology", "hiv", "biology", "computational", "biology", "microbiology", "viral", "diseases" ]	2013	Virus Neutralisation: New Insights from Kinetic Neutralisation Curves
M . africanum West African 2 constitutes an ancient lineage of the M . tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M . tuberculosis . In search of candidate genes underlying these differences , the genome of M . africanum West African 2 was seq...	Mycobacterium africanum , a close relative of M . tuberculosis , is studied for the following reasons: M . africanum is commonly isolated from West African patients with tuberculosis yet has not spread beyond this region , it is more common in HIV infected patients , and it is less likely to lead to tuberculosis after ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "genomics", "evolutionary", "biology", "biology", "computational", "biology", "microbiology", "population", "biology" ]	2012	The Genome of Mycobacterium Africanum West African 2 Reveals a Lineage-Specific Locus and Genome Erosion Common to the M. tuberculosis Complex
Influenza A viruses ( IAVs ) inhibit host gene expression by a process known as host shutoff . Host shutoff limits host innate immune responses and may also redirect the translation apparatus to the production of viral proteins . Multiple IAV proteins regulate host shutoff , including PA-X , a ribonuclease that remains...	All viruses depend on host components to convert viral mRNAs into proteins . Several viruses , including influenza A virus , encode factors that trigger RNA destruction . The influenza A virus factor that serves in this capacity is known as PA-X . PA-X limits accumulation of host mRNAs and proteins in infected cells an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "luciferase", "pathology", "and", "laboratory", "medicine", "293t", "cells", "pathogens", "enzymes", "messenger", "rna", "rna", "extraction", "microbiology", "biological", "cultures", "enzymology",...	2016	Selective Degradation of Host RNA Polymerase II Transcripts by Influenza A Virus PA-X Host Shutoff Protein
Identifying modes of species diversification is fundamental to our understanding of how biodiversity changes over evolutionary time . Diversification modes are captured in species phylogenies , but characterizing the landscape of diversification has been limited by the analytical tools available for directly comparing ...	Are there universal laws in the evolution of biodiversity ? Why do some clades go extinct and others flourish ? These questions are fundamental to our understanding of present-day biodiversity . In a meta-analysis of nearly 12 , 000 species spanning ~500 million years of evolution , we find that there are five principa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "taxonomy", "ecology", "and", "environmental", "sciences", "vertebrates", "animals", "mammals", "animal", "phylogenetics", "phylogenetics", "data", "management", "phylogenetic", "analysis", "speciation", "paleontology", "molecular", "biology", "techniques", "paleogenetics", ...	2016	Natural Constraints to Species Diversification
Progress in dengue vaccine development has been hampered by limited understanding of protective immunity against dengue virus infection . Conventional neutralizing antibody titration assays that use FcγR-negative cells do not consider possible infection-enhancement activity . We reasoned that as FcγR-expressing cells a...	Dengue has become a major international public health concern in recent decades . There are four dengue virus serotypes . Recovery from infection with one serotype confers life-long protection to the homologous serotype but only partial protection to subsequent infection with other serotypes . Secondary infection with ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "vaccination", "infectious", "diseases", "clinical", "immunology", "immunity", "immunology", "viral", "diseases" ]	2012	Dengue Virus Infection-Enhancing Activity in Serum Samples with Neutralizing Activity as Determined by Using FcγR-Expressing Cells
Understanding the principles governing the dynamic coordination of functional brain networks remains an important unmet goal within neuroscience . How do distributed ensembles of neurons transiently coordinate their activity across a variety of spatial and temporal scales ? While a complete mechanistic account of this ...	How is the functional role of a particular neuron established within an ensemble ? The concept of a neural tuning curve – the mapping from input variables such as movement direction to output firing rate – has proven useful in investigating neural function . However , prior work shows that tuning curves are not fixed b...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computer", "science", "computer", "modeling", "neural", "networks", "computational", "neuroscience", "biology", "computing", "methods", "neuroscience", "neurophysiology", "coding", "mechanisms" ]	2012	Task-Dependent Changes in Cross-Level Coupling between Single Neurons and Oscillatory Activity in Multiscale Networks
A critical determinant in chronic gammaherpesvirus infections is the ability of these viruses to establish latency in a lymphocyte reservoir . The nuclear factor ( NF ) -κB family of transcription factors represent key players in B-cell biology and are targeted by gammaherpesviruses to promote host cell survival , prol...	A central aspect of chronic infection of a host by herpesviruses is the ability of these viruses to establish a quiescent infection ( latent infection ) in some cell type ( s ) in which there is only intermittent production of progeny virus ( virus reactivation ) . The establishment of a latent infection in the antibod...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "mus", "(mouse)", "viruses", "virology" ]	2007	Inhibition of NF-κB Activation In Vivo Impairs Establishment of Gammaherpesvirus Latency
Human T-lymphotropic virus type 1 ( HTLV-1 ) is a retrovirus that persists lifelong in the host . In ∼4% of infected people , HTLV-1 causes a chronic disabling neuroinflammatory disease known as HTLV-1-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . The pathogenesis of HAM/TSP is unknown and treatment ...	Infection with the Human T Lymphotropic virus is widespread in the tropics and subtropics , where it causes a chronic disabling disease of the nervous system abbreviated as HAM/TSP . There is no effective treatment available for HAM/TSP , because it is not understood how the virus causes the neuronal damage that result...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "virology", "immunology", "biology", "microbiology" ]	2012	Systems Biology Approaches Reveal a Specific Interferon-Inducible Signature in HTLV-1 Associated Myelopathy
The formation of gaps in the endothelium is a crucial process underlying both cancer and immune cell extravasation , contributing to the functioning of the immune system during infection , the unfavorable development of chronic inflammation and tumor metastasis . Here , we present a stochastic-mechanical multiscale mod...	Transmigration of immune cells into and out of the blood vessels is a crucial process for the functioning of the immune system during infections and acute inflammations , and aberrant transmigration may contribute to chronic inflammations . Likewise , cancer metastasis critically depends on intra-and extravasation of c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2019	Balance of mechanical forces drives endothelial gap formation and may facilitate cancer and immune-cell extravasation
anzctr . org . au ACTRN12612000814875; anzctr . org . au ACTRN12613000565741; anzctr . org . au ACTRN12613001040752; ClinicalTrials . gov NCT02281344; anzctr . org . au ACTRN12612001096842; anzctr . org . au ACTRN12613001008718 Malaria vaccine research efforts have been directed predominantly at P . falciparum , since ...	The specific immune responses that contribute to protective immunity in humans following Plasmodium infection are yet to be fully characterized . The species P . vivax and P . falciparum account for most human infections , yet little is known about P . vivax specific immune responses and whether they are similar to or ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "parasite", "groups", "medicine", "and", "health", "sciences", "immune", "cells", "plasmodium", "immunology", "plasmodium", "falciparum", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "red", "blood", "...	2016	Plasmodium vivax but Not Plasmodium falciparum Blood-Stage Infection in Humans Is Associated with the Expansion of a CD8+ T Cell Population with Cytotoxic Potential
Identification of regulatory elements within the genome is crucial for understanding the mechanisms that govern cell type–specific gene expression . We generated genome-wide maps of open chromatin sites in 3T3-L1 adipocytes ( on day 0 and day 8 of differentiation ) and NIH-3T3 fibroblasts using formaldehyde-assisted is...	Humans consist of a few hundred types of specialized-function cells . Spatial and temporal transcriptional regulation of genes is essential for manifestation of cellular phenotypes . Identification of regulatory regions in the genome is central to understanding the mechanism of cell type–specific gene regulation . Rece...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "carbohydrate", "metabolism", "diabetic", "endocrinology", "cell", "differentiation", "hormones", "gene", "function", "dna", "transcription", "histone", "modification", "developmental", "biology", "nutrition", "obesity", "epigenetics", "chromatin", "lipid", "met...	2011	Global Mapping of Cell Type–Specific Open Chromatin by FAIRE-seq Reveals the Regulatory Role of the NFI Family in Adipocyte Differentiation
One quadrillion synapses are laid in the first two years of postnatal construction of the human brain , which are then pruned until age 10 to 500 trillion synapses composing the final network . Genetic epilepsies are the most common neurological diseases with onset during pruning , affecting 0 . 5% of 2–10-year-old chi...	Major remodeling of the neuronal synaptic network occurs during childhood . The quadrillion synapses formed till the end of age two are trimmed to 500 trillion by age 10 through a selective process of strengthening of ideal connections , removal of redundant ones , and formation of new contacts . Very little is known a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "neurobiology", "of", "disease", "and", "regeneration", "animal", "genetics", "genetic", "mutation", "genetics", "molecular", "genetics", "biology", "genetics", "of", "disease", "neuroscience", "genetics", "and", "genomics" ]	2011	LGI2 Truncation Causes a Remitting Focal Epilepsy in Dogs
Obg proteins are a family of P-loop GTPases , conserved from bacteria to human . The Obg protein in Escherichia coli ( ObgE ) has been implicated in many diverse cellular functions , with proposed molecular roles in two global processes , ribosome assembly and stringent response . Here , using pre-steady state fast kin...	GTPases commonly act as molecular switches in biological systems . By oscillating between two conformational states , depending on the type of guanine nucleotide bound ( GTP or GDP ) , GTPases are essential regulators of many aspects of cell biology . Additional levels of regulation can be acquired through the synthesi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "interactions", "molecular", "complexes", "enzymes", "regulatory", "proteins", "enzymology", "microbiology", "ribozymes", "developmental", "biology", "protein", "synthesis", "protein", "structure", "microbial", "growth", "and", "development", "microbial", "physio...	2014	Structural and Functional Insights into the Mode of Action of a Universally Conserved Obg GTPase
The blast fungus Magnaporthe oryzae threatens global food security through the widespread destruction of cultivated rice . Foliar infection requires a specialized cell called an appressorium that generates turgor to force a thin penetration hypha through the rice cuticle and into the underlying epidermal cells , where ...	The blast fungus Magnaporthe oryzae destroys rice and wheat harvests and could compromise global food security . Following penetration into the rice cell , M . oryzae elaborates bulbous invasive hyphae that grow in living rice cells for most of the infection cycle without causing disease symptoms . Little is known abou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "plant", "science", "model", "organisms", "biology", "and", "life", "sciences", "microbiology", "research", "and", "analysis", "methods" ]	2014	Evidence for a Transketolase-Mediated Metabolic Checkpoint Governing Biotrophic Growth in Rice Cells by the Blast Fungus Magnaporthe oryzae
Leishmania major parasites reside and multiply in late endosomal compartments of host phagocytic cells . Immune control of Leishmania growth absolutely requires expression of inducible Nitric Oxide Synthase ( iNOS/NOS2 ) and subsequent production of NO . Here , we show that CD11b+ CD11c+ Ly-6C+ MHC-II+ cells are the ma...	Leishmania spp . are protozoan parasites infecting a variety of mammals , including humans and mice . Much information has been gleaned from murine models of Leishmania major infection . The control of L . major infection by resistant C57BL/6 mice requires the secretion of type 1 ( Th1 ) cytokines ( i . e . IFN-γ ) by ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections", "immunology/immune", "response", "immunology/innate", "immunity" ]	2009	iNOS-Producing Inflammatory Dendritic Cells Constitute the Major Infected Cell Type during the Chronic Leishmania major Infection Phase of C57BL/6 Resistant Mice
Although Bcl-XL and Bax are structurally similar , activated Bax forms large oligomers that permeabilize the outer mitochondrial membrane , thereby committing cells to apoptosis , whereas Bcl-XL inhibits this process . Two different models of Bcl-XL function have been proposed . In one , Bcl-XL binds to an activator , ...	During development and under stress , cells can become committed to die via programmed cell death ( apoptosis ) . In most cases , the permeabilization of the outer mitochondrial membrane is a key component of this commitment . The membrane permeablization step is both positively and negatively regulated by members of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry" ]	2008	Bcl-XL Inhibits Membrane Permeabilization by Competing with Bax
Structural classifications of proteins assume the existence of the fold , which is an intrinsic equivalence class of protein domains . Here , we test in which conditions such an equivalence class is compatible with objective similarity measures . We base our analysis on the transitive property of the equivalence relati...	Making order of the fast-growing information on proteins is essential for gaining evolutionary and functional knowledge . The most successful approaches to this task are based on classifications of protein structures , such as SCOP and CATH , which assume a discrete view of the protein structure space as a collection o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "biophysics/structural", "genomics", "biophysics/protein", "folding", "molecular", "biology/molecular", "evolution", "molecular", "biology/bioinformatics", "evolutionary", "biology/bioinformatics" ]	2009	Cross-Over between Discrete and Continuous Protein Structure Space: Insights into Automatic Classification and Networks of Protein Structures

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