Split (3)

train · 24.8k rows

Search is not available for this dataset

article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Rickettsia philipii ( type strain “Rickettsia 364D” ) , the etiologic agent of Pacific Coast tick fever ( PCTF ) , is transmitted to people by the Pacific Coast tick , Dermacentor occidentalis . Following the first confirmed human case of PCTF in 2008 , 13 additional human cases have been reported in California , more ...	Rickettsia philipii , a spotted fever group rickettsia , is the etiologic agent of Pacific Coast tick fever , an emerging tick-borne disease transmitted by the Pacific Coast tick ( Dermacentor occidentalis ) . The Pacific Coast tick’s range , and thus potential for exposure to R . philipii , includes most of California...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dermatology", "invertebrates", "united", "states", "medicine", "and", "health", "sciences", "ixodes", "pathology", "and", "laboratory", "medicine", "pathogens", "california", "geographical", "locations", "microbiology", "rickettsia", "animals", "north", "america", "devel...	2016	The Eco-epidemiology of Pacific Coast Tick Fever in California
Mutations in the CLRN1 gene cause Usher syndrome type 3 ( USH3 ) , a human disease characterized by progressive blindness and deafness . Clarin 1 , the protein product of CLRN1 , is a four-transmembrane protein predicted to be associated with ribbon synapses of photoreceptors and cochlear hair cells , and recently demo...	Usher syndrome ( USH ) is a progressive disease affecting two primary senses: vision and hearing . Often by the third decade of life , affected persons have lost the majority of their rod photoreceptors , which leads to night blindness and peripheral vision loss . Similarly , hearing loss often progresses into the thir...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/neuronal", "and", "glial", "cell", "biology", "genetics", "and", "genomics/animal", "genetics", "ophthalmology/retinal", "disorders", "genetics", "and", "genomics/gene", "expression", "ophthalmology", "neurological", "disorders/neuro-ophthalmology", "and", "n...	2009	CLRN1 Is Nonessential in the Mouse Retina but Is Required for Cochlear Hair Cell Development
Non-intermingling , adjacent populations of cells define compartment boundaries; such boundaries are often essential for the positioning and the maintenance of tissue-organizers during growth . In the developing wing primordium of Drosophila melanogaster , signaling by the secreted protein Hedgehog ( Hh ) is required f...	In developing animal tissues , cells can often re-arrange locally and mix relatively freely . However , in some stereotypic and crucially important instances during body development , cells will strictly not intermingle , and instead form sharp boundaries along which they will sort out from each other . This mechanism ...	[ "Abstract", "Introduction", "Results/Discussion", "Material", "and", "Methods" ]	[ "morphogens", "biochemical", "simulations", "developmental", "biology", "organism", "development", "biophysic", "al", "simulations", "adhesion", "molecules", "molecular", "development", "signaling", "biology", "computational", "biology", "signaling", "networks", "pattern", ...	2011	Cell-Sorting at the A/P Boundary in the Drosophila Wing Primordium: A Computational Model to Consolidate Observed Non-Local Effects of Hh Signaling
Many factors affect the risks for neurodevelopmental maladies such as autism spectrum disorders ( ASD ) and intellectual disability ( ID ) . To compare environmental , phenotypic , socioeconomic and state-policy factors in a unified geospatial framework , we analyzed the spatial incidence patterns of ASD and ID using a...	Disease clusters are defined as geographically compact areas where a particular disease , such as a cancer , shows a significantly increased rate . It is presently unclear how common such clusters are for neurodevelopmental maladies , such as autism spectrum disorders ( ASD ) and intellectual disability ( ID ) . In thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biological", "data", "management", "population", "modeling", "biology", "genomics", "computational", "biology" ]	2014	Environmental and State-Level Regulatory Factors Affect the Incidence of Autism and Intellectual Disability
Methods for detecting the genomic signatures of natural selection have been heavily studied , and they have been successful in identifying many selective sweeps . For most of these sweeps , the favored allele remains unknown , making it difficult to distinguish carriers of the sweep from non-carriers . In an ongoing se...	Methods for detecting the genomic signatures of natural selection have been heavily studied , and they have been successful in identifying genomic regions under positive selection . However , methods that detect positive selective sweeps do not typically identify the favored allele , or even the haplotypes carrying the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Predicting Carriers of Ongoing Selective Sweeps without Knowledge of the Favored Allele
Melanocyte stem cells ( McSCs ) are the undifferentiated melanocytic cells of the mammalian hair follicle ( HF ) responsible for recurrent generation of a large number of differentiated melanocytes during each HF cycle . HF McSCs reside in both the CD34+ bulge/lower permanent portion ( LPP ) and the CD34- secondary hai...	The hair follicle ( HF ) undergoes three different stages , anagen , catagen , and telogen during each hair cycle . In anagen , melanocyte stem cells ( McSCs ) give rise to differentiated melanocytes which are responsible for coloration of hair . In catagen , melanocytes undergo apoptosis while McSCs are retained . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "hair", "growth", "telogen", "phase", "neuroscience", "cell", "differentiation", "epithelial", "cells", "physiological", "processes", "developmental", "biology", "stem", "cells", "chromatophores", "anagen", "phase", "developmental"...	2019	CD34 defines melanocyte stem cell subpopulations with distinct regenerative properties
BACE-1 is the β-secretase responsible for the initial amyloidogenesis in Alzheimer’s disease , catalyzing hydrolytic cleavage of substrate in a pH-sensitive manner . The catalytic mechanism of BACE-1 requires water-mediated proton transfer from aspartyl dyad to the substrate , as well as structural flexibility in the f...	Formation of insoluble amyloid plaques in the vascular and hippocampal areas of the brain characterizes Alzheimer’s disease , a devastating neurodegenerative disorder causing dementia . Site-specific hydrolytic catalysis of β-secretase , or BACE-1 , is responsible for production of oligomerative amyloid β-peptide . As ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria
Recent evidence shows that mutations in several driver genes can cause aberrant methylation patterns , a hallmark of cancer . In light of these findings , we hypothesized that the landscapes of tumor genomes and epigenomes are tightly interconnected . We measured this relationship using principal component analyses and...	Mutations that alter the function of driver genes by changing DNA nucleotides have been recognized as key players in cancer progression . However , recent evidence has shown that DNA methylation , which can control gene expression , is also highly dysregulated in cancer and contributes to carcinogenesis . Whether methy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "endocrine", "tumors", "carcinomas", "endometrial", "carcinoma", "cancers", "and", "neoplasms", "oncology", "mutation", "methylation", "adenocarcinomas", "head", "and", "neck", "tumors", "epigenetics", "dna", "dna", "methylation"...	2017	Significant associations between driver gene mutations and DNA methylation alterations across many cancer types
NMDA receptors ( NMDARs ) are the major mediator of the postsynaptic response during synaptic neurotransmission . The diversity of roles for NMDARs in influencing synaptic plasticity and neuronal survival is often linked to selective activation of multiple NMDAR subtypes ( NR1/NR2A-NMDARs , NR1/NR2B-NMDARs , and trihet...	Release of glutamate from one neuron onto glutamate receptors on adjacent neurons serves as the primary basis for neuronal communication . Further , different types of glutamate signals produce unique responses within the neuronal network , providing the ability for glutamate receptors to discriminate between alternati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemical", "simulations", "cellular", "neuroscience", "synapses", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience", "neurophysiology" ]	2011	Computational Investigation of the Changing Patterns of Subtype Specific NMDA Receptor Activation during Physiological Glutamatergic Neurotransmission
In an effort to enhance accuracy of diagnosis of Schistosoma haematobium , this study explores day-to-day variability and diagnostic performance of real-time PCR for detection and quantification of Schistosoma DNA compared to other diagnostic tools in an endemic area before and after treatment . Previously collected ur...	Schistosoma haematobium is a blood fluke that causes severe urogenital pathology and affects millions of people , mainly in sub-Sahara Africa . Current diagnosis is based on microscopic examination of urine samples , but this method is not only observer dependent , but also known for its low sensitivity and high day-to...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "helminth", "infections", "medicine", "and", "health", "sciences", "schistosomiasis", "diagnostic", "medicine", "infectious", "disease", "epidemiology", "epidemiology", "global", "health", "neglected", "...	2014	Diagnostic Performance of Schistosoma Real-Time PCR in Urine Samples from Kenyan Children Infected with Schistosoma haematobium: Day-to-day Variation and Follow-up after Praziquantel Treatment
Human myxovirus resistance 2 ( MX2/MXB ) is an interferon-induced post-entry inhibitor of human immunodeficiency virus type-1 ( HIV-1 ) infection . While the precise mechanism of viral inhibition remains unclear , MX2 is localized to the nuclear envelope , and blocks the nuclear import of viral cDNAs . The amino-termin...	The movement of large molecules into the cell nucleus is regulated at specific sites within the nuclear envelope termed nuclear pores . To infect cells productively , human immunodeficiency virus type-1 ( HIV-1 ) must traverse the nuclear envelope to enable integration of the viral DNA into the genomic DNA of host cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "nuclear", "import", "medicine", "and", "health", "sciences", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "hela", "cells", "molecular", "probe", "techniques", "gene", "regulation", "pathogens", "cell", "processes", "biological", "cultures", ...	2018	Multiple components of the nuclear pore complex interact with the amino-terminus of MX2 to facilitate HIV-1 restriction
We recently reported that larval stage Aedes aegypti and several other species of mosquitoes grow when living bacteria are present in the gut but do not grow when living bacteria are absent . We further reported that living bacteria induce a hypoxia signal in the gut , which activates hypoxia-induced transcription fact...	Studies conducted in our laboratory indicate that several species of mosquito larvae require living bacteria in their gut to grow . Previous results also show that living bacteria reduce gut oxygen levels below 5% and that bacteria-induced gut hypoxia functions as a signal that activates several processes in larvae wit...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "neutral", "lipids", "diet", "developmental", "biology", "fungi", "model", "organisms", "nutrition", "experimental", "organism", "systems", "hypoxia", "plants", "saccharomyces", "research", "and", "analysis", "methods", "lipids",...	2018	Both living bacteria and eukaryotes in the mosquito gut promote growth of larvae
Human immunodeficiency virus type 1 ( HIV-1 ) viral protein R ( Vpr ) has been shown to cause G2 cell cycle arrest in human cells by inducing ATR-mediated inactivation of p34cdc2 , but factors directly engaged in this process remain unknown . We used tandem affinity purification to isolate native Vpr complexes . We fou...	Human immunodeficiency virus type 1 ( HIV-1 ) , the causative agent of AIDS , encodes several proteins termed accessory , which play a critical role in viral pathogenesis . Collectively , HIV-1 accessory proteins Vif , Vpr , Vpu , and Nef have been shown to manipulate host cell biology to promote viral replication , im...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "virology", "in", "vitro", "homo", "(human)", "saccharomyces" ]	2007	HIV-1 Vpr-Mediated G2 Arrest Involves the DDB1-CUL4AVPRBP E3 Ubiquitin Ligase
Normal aging leads to an inexorable decline in motor performance , contributing to medical morbidity and decreased quality of life . While much has been discovered about genetic determinants of lifespan , less is known about modifiers of age-related behavioral decline and whether new gene targets may be found which ext...	As humans and animals age , there is an inevitable decrease in functional capacity . Elderly individuals can suffer from a decline in motor function , or the ability to move . Genetic studies in model organisms have led to the identification of genes that can prolong lifespan . Elongation of lifespan is less appealing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience", "developmental", "biology/aging" ]	2010	Manipulation of Behavioral Decline in Caenorhabditis elegans with the Rag GTPase raga-1
Endomyocardial Fibrosis ( EMF ) is a tropical restrictive cardiomyopathy of unknown etiology with high prevalence in Sub-Saharan Africa , for which it is unclear whether the primary target of injury is the endocardial endothelium , the subendocardial fibroblast , the coronary microcirculation or the myocyte . In an att...	Endomyocardial Fibrosis is a tropical disease in which the heart cannot open properly to receive blood due to a scar that covers its inner layer . It affects mainly children and adolescents , and has a poor prognosis because the cause and mechanisms of scarring are unknown . The conventional treatment is frustrating an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/autoimmunity", "cardiovascular", "disorders/heart", "failure" ]	2010	Presence of Circulating Anti-Myosin Antibodies in Endomyocardial Fibrosis
Plants need abundant nitrogen and phosphorus for higher yield . Improving plant genetics for higher nitrogen and phosphorus use efficiency would save potentially billions of dollars annually on fertilizers and reduce global environmental pollution . This will require knowledge of molecular regulators for maintaining ho...	Higher crop yields require increased use of fertilizers , especially for the prime macronutrients nitrogen and phosphorus . Increasing nitrogen and phosphorus use efficiency in plants would decrease crop production cost and reduce environmental pollution . In an attempt to isolate the regulatory genes for nitrogen and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "systems", "biology", "plant", "science", "plant", "biology", "genetics", "biology", "genomics", "molecular", "cell", "biology", "agricultural", "biotechnology", "genetics", "and", "genomics", "agriculture" ]	2011	Genetic Regulation by NLA and MicroRNA827 for Maintaining Nitrate-Dependent Phosphate Homeostasis in Arabidopsis
Schizophrenia and the affective disorders , here comprising bipolar disorder and major depressive disorder , are psychiatric illnesses that lead to significant morbidity and mortality worldwide . Whilst understanding of their pathobiology remains limited , large case-control studies have recently identified single nucl...	An estimated 21 million people live worldwide with schizophrenia , 60 million with bipolar disorder , and 400 million with major depressive disorder . Recent genome-wide association studies have shed light on the genetic variants linked to these disorders , and increasing evidence suggests that their genetic architectu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "body", "fluids", "bipolar", "disorder", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "mood", "disorders", "research", "and", "analysis", "methods", "genome", "compl...	2018	Identification of expression quantitative trait loci associated with schizophrenia and affective disorders in normal brain tissue
Zoonoses account for the most commonly reported emerging and re-emerging infectious diseases in Sub-Saharan Africa . However , there is limited knowledge on how pastoral communities perceive zoonoses in relation to their livelihoods , culture and their wider ecology . This study was carried out to explore local knowled...	Zoonoses are diseases transmissible between animals and humans . Risk factors include animal slaughter , the handling and preparing food of animal origin and particularly the consumption of such food when raw or undercooked . Pastoralists are daily in contact with their livestock and are likely to be more frequently ex...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion", "Conclusion" ]	[ "livestock", "medicine", "and", "health", "sciences", "body", "fluids", "ruminants", "tropical", "diseases", "diet", "vertebrates", "animals", "mammals", "animal", "products", "bacterial", "diseases", "nutrition", "meat", "veterinary", "science", "infectious", "diseases...	2017	Exploring local knowledge and perceptions on zoonoses among pastoralists in northern and eastern Tanzania
The gene daf-12 has long shown to be involved in the dauer pathway in Caenorhabditis elegans ( C . elegans ) . Due to the similarities of the dauer larvae of C . elegans and infective larvae of certain parasitic nematodes such as Strongyloides spp . , this gene has also been suspected to be involved in the development ...	Strongyloides ratti is a model parasitic nematode of interest for its use in understanding basic biology and the development of novel helminth therapies . However a lack of genetic tools has stymied progress , although CRISPR/Cas9 has recently been reported . After determining whether RNAi might work in S . ratti by pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "caenorhabditis", "gene", "regulation", "parasitic", "diseases", "animals", "nematode", "infections", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "or...	2019	RNAi-mediated knockdown of daf-12 in the model parasitic nematode Strongyloides ratti
Infected hosts differ in their responses to pathogens; some hosts are resilient and recover their original health , whereas others follow a divergent path and die . To quantitate these differences , we propose mapping the routes infected individuals take through “disease space . ” We find that when plotting physiologic...	When we get sick , we long for recovery; thus , a major goal of medicine is to promote resilience—the ability of a host to return to its original health following an infection . While in the laboratory we can study the response to infection with precise knowledge of inoculation time and dose , sick patients in the clin...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "infographics", "medicine", "and", "health", "sciences", "body", "fluids", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "reticulocytes", "bone", "marrow", "cells", "protozoans", "red", "blood", "cells", "bioassays", "an...	2016	Tracking Resilience to Infections by Mapping Disease Space
In this study we generated a novel dual specific phosphatase 4 ( DUSP4 ) deletion mouse using a targeted deletion strategy in order to examine the role of MAP kinase phosphatase-2 ( MKP-2 ) in immune responses . Lipopolysaccharide ( LPS ) induced a rapid , time and concentration-dependent increase in MKP-2 protein expr...	In cells of the immune system are switch-on enzymes called kinases which regulate responses to infectious agents such as Leishmania . However , in the same cells there are switch-off enzymes known as phosphatases which function to turn off the kinases once they have done their work . A lot of studies have focussed on t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "immunology/immunity", "to", "infections", "cell", "biology/cell", "signaling" ]	2010	MAP Kinase Phosphatase-2 Plays a Critical Role in Response to Infection by Leishmania mexicana
In most mouse tissues , long-interspersed elements-1 ( L1s ) are silenced via methylation of their 5′-untranslated regions ( 5′-UTR ) . A gradual loss-of-methylation in pre-implantation embryos coincides with L1 retrotransposition in blastocysts , generating potentially harmful mutations . Here , we show that Dicer- an...	A basal network of gene regulation orchestrates the processes ensuring maintenance of genome integrity . Eukaryotic small RNAs generated by the RNAse-III Dicer have emerged as central players in this network , by mediating gene silencing at the transcriptional or post-transcriptional level via RNA interference ( RNAi )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	RNAi-Dependent and Independent Control of LINE1 Accumulation and Mobility in Mouse Embryonic Stem Cells
Proteomic and lipidomic profiling was performed over a time course of acute hepatitis C virus ( HCV ) infection in cultured Huh-7 . 5 cells to gain new insights into the intracellular processes influenced by this virus . Our proteomic data suggest that HCV induces early perturbations in glycolysis , the pentose phospha...	As parasites , viruses rely on the cells they infect to provide the energy and building blocks required for their survival and propagation . However , relatively little is known about the extent to which viruses modulate host cell metabolism and the consequences of these disruptions . Here we integrate proteomic and li...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "gastroenterology", "and", "hepatology/hepatology", "infectious", "diseases", "computational", "biology" ]	2010	Temporal Proteome and Lipidome Profiles Reveal Hepatitis C Virus-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics
Rosetting , the adhesion of Plasmodium falciparum-infected erythrocytes to uninfected erythrocytes , involves clonal variants of the parasite protein P . falciparum erythrocyte membrane protein 1 ( PfEMP1 ) and soluble serum factors . While rosetting is a well-known phenotypic marker of parasites associated with severe...	Erythrocytes infected by parasites causing severe P . falciparum malaria often form rosettes by binding a number of uninfected erythrocytes . Several of the parasite proteins involved are known , whereas the identity of the corresponding host receptor ( s ) on the surrounding erythrocytes is not . Although formation of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	α2-Macroglobulin Can Crosslink Multiple Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) Molecules and May Facilitate Adhesion of Parasitized Erythrocytes
Higher-order genomic architecture varies according to cell type and changes dramatically during differentiation . One of the remarkable examples of spatial genomic reorganization is the rod photoreceptor cell differentiation in nocturnal mammals . The inverted nuclear architecture found in adult mouse rod cells is form...	The motion and spatial reorganization of sub-nuclear domains have been extensively studied using microscopy , but the underlying mechanisms that promote the reorganization are still poorly understood . We found that dynamic nuclear deformation provides a driving force for long-range migration and aggressive clustering ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "classical", "mechanics", "neuronal", "differentiation", "neuroscience", "cell", "differentiation", "developmental", "biology", "damage", "mechanics", "epigenetics", "mammalian", "genomics", "chromatin", "heterochromatin", "contractile", "proteins", "actins", "chromosome", "b...	2019	Role of dynamic nuclear deformation on genomic architecture reorganization
Chlamydia trachomatis is the most common cause of bacterial sexually transmitted infection , responsible for millions of infections each year . Despite this high prevalence , the elucidation of the molecular mechanisms of Chlamydia pathogenesis has been difficult due to limitations in genetic tools and its intracellula...	Chlamydia are obligate intracellular bacteria that require the establishment and maintenance of a host vacuole ( the inclusion ) for their developmental growth . Chlamydiae modify the inclusion membrane through the secretion of type III membrane proteins and recruited host factors . These membrane modifications are pre...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2019	Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites
Methionyl-tRNA synthetase of Trypanosoma brucei ( TbMetRS ) is an important target in the development of new antitrypanosomal drugs . The enzyme is essential , highly flexible and displaying a large degree of changes in protein domains and binding pockets in the presence of substrate , product and inhibitors . Targetin...	Infection by the protozoan parasite Trypanosoma brucei causes sleeping sickness , also called human African trypanosomiasis . Without treatment , the disease is fatal yet current therapeutic options are inadequate and better medicines are needed . We have previously reported several potent inhibitors of T . brucei meth...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biomacromolecule-ligand", "interactions", "medicine", "and", "health", "sciences", "medicinal", "chemistry", "african", "trypanosomiasis", "enzymes", "tropical", "diseases", "enzymology", "chemical", "biology", "neglected", "tropical", "diseases", "pharmacology", "enzyme", ...	2014	Structures of Trypanosoma brucei Methionyl-tRNA Synthetase with Urea-Based Inhibitors Provide Guidance for Drug Design against Sleeping Sickness
The HIV-1 gp41 envelope ( Env ) membrane proximal external region ( MPER ) is an important vaccine target that in rare subjects can elicit neutralizing antibodies . One mechanism proposed for rarity of MPER neutralizing antibody generation is lack of reverted unmutated ancestor ( putative naive B cell receptor ) antibo...	Critical to the design of an effective HIV-1 vaccine that will induce long-lasting broadly neutralizing antibodies is to understand why broad neutralizing antibodies are not induced . One hypothesis is that there are “holes” in the naïve B cell repertoires for unmutated B cell receptors that can bind to HIV-1 envelope ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	Envelope Deglycosylation Enhances Antigenicity of HIV-1 gp41 Epitopes for Both Broad Neutralizing Antibodies and Their Unmutated Ancestor Antibodies
Chagas disease , caused by infection with the protozoan Trypanosoma cruzi , remains a serious public health issue in Latin America . Genetically diverse , the species is sub-divided into six lineages , known as TcI–TcVI , which have disparate geographical and ecological distributions . TcII , TcV , and TcVI are associa...	Chagas disease remains a significant public health issue in Latin America . Caused by the single-celled parasite Trypanosoma cruzi , the main route of infection is via contact with contaminated faeces from blood-sucking triatomine bugs , but following successful insecticide spraying campaigns , congenital , food-borne ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "immune", "system", "proteins", "infectious", "diseases", "medicine", "and", "health", "sciences", "chagas", "disease", "proteins", "protozoan", "infections", "neglected", "tropical", "diseases", "biology", "and", "life", "sciences", "immunology", "tropi...	2014	Development of Peptide-Based Lineage-Specific Serology for Chronic Chagas Disease: Geographical and Clinical Distribution of Epitope Recognition
The apolipoprotein B editing complex 3 ( A3 ) cytidine deaminases are among the most highly evolutionarily selected retroviral restriction factors , both in terms of gene copy number and sequence diversity . Primate genomes encode seven A3 genes , and while A3F and 3G are widely recognized as important in the restricti...	APOBEC3 genes are part of the host's arsenal against virus infections . Humans have 7 APOBEC3 genes and determining how each specifically functions to inhibit retroviruses like HIV is complicated , because all 7 can be produced in a given cell type or tissue . This is important , because some viruses make their own fac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "innate", "immune", "system", "medicine", "and", "health", "sciences", "model", "organisms", "pathology", "and", "laboratory", "medicine", "immunity", "host-pathogen", "interactions", "virology", "biology", "and", "life", "sciences", "immunology", ...	2014	Different Modes of Retrovirus Restriction by Human APOBEC3A and APOBEC3G In Vivo
It remains unclear what determines the subcellular localization of hepatitis B virus ( HBV ) core protein ( HBc ) and particles . To address this fundamental issue , we have identified four distinct HBc localization signals in the arginine rich domain ( ARD ) of HBc , using immunofluorescence confocal microscopy and fr...	Chronic infection with hepatitis B virus ( HBV ) could lead to cirrhosis and highly malignant liver cancer . At present , treatment of hepatitis B is not very effective , due to notorious side effects and drug resistance . The virus can synthesize a core protein for its own replication . Clinically , this core protein ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2010	Nuclear Export and Import of Human Hepatitis B Virus Capsid Protein and Particles
Controversy persists about the optimal approach to drug-based control of schistosomiasis in high-risk communities . In a systematic review of published studies , we examined evidence for incremental benefits from repeated praziquantel dosing , given 2 to 8 weeks after an initial dose , in Schistosoma-endemic areas of A...	Infection by Schistosoma worms causes serious disease among people who live in areas of Africa , South America , and Asia where these parasites are regularly transmitted . Although yearly treatment with the drug praziquantel is fairly effective in reducing or eliminating active infection , it does not cure everyone , a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "urology", "public", "health", "and", "epidemiology", "science", "policy", "and", "economics", "bladder", "and", "ureteric", "disorders", "parasitic", "diseases", "preventive", "medicine", "cost-benefit", "analysis", "global", "health", "neglected", "tropica...	2011	Utility of Repeated Praziquantel Dosing in the Treatment of Schistosomiasis in High-Risk Communities in Africa: A Systematic Review
Our understanding of most biological systems is in its infancy . Learning their structure and intricacies is fraught with challenges , and often side-stepped in favour of studying the function of different gene products in isolation from their physiological context . Constructing and inferring global mathematical model...	For most biological signalling and regulatory systems we still lack reliable mechanistic models . And where such models exist , e . g . in the form of differential equations , we typically have only rough estimates for the parameters that characterize the biochemical reactions . In order to improve our knowledge of suc...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "biochemical", "simulations", "mathematics", "statistics", "regulatory", "networks", "synthetic", "biology", "biology", "computational", "biology", "signaling", "networks", "genetics", "and", "genomics" ]	2013	Maximizing the Information Content of Experiments in Systems Biology
Primarily used for metabolic engineering and synthetic biology , genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism . Through a novel integration of flux balance analysis and genetic algorithms , a strategy to curate metabolic networks and facilitate...	Flux balance analysis ( FBA ) is a powerful approach for genome-scale metabolic modeling . It provides metabolic engineers with a tool for manipulating , predicting , and optimizing metabolism for biotechnological and biomedical purposes . However , we posit that it can also be used as tool for fundamental research in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Semi-automated Curation of Metabolic Models via Flux Balance Analysis: A Case Study with Mycoplasma gallisepticum
African trypanosomes of the sub-genus Trypanozoon ) are eukaryotic parasitesthat cause disease in either humans or livestock . The development of genomic resources can be of great use to those interested in studying and controlling the spread of these trypanosomes . Here we present a large comparative analysis of Trypa...	Trypanosomes are a major health threat to the people and livestock of Sub-Saharan Africa . Building genomic resources and understanding the genetic structure of these parasites will aid researchers trying to control their spread . To this end , we compared the genomes from 83 trypanosome strains , identifying 162 , 210...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "biogeography", "ecology", "and", "environmental", "sciences", "population", "genetics", "geographical", "locations", "parasitic", "protozoans", "trypanosoma", "brucei", "phylogenetics", "data", "management", "protozoans", "population", "biology", "africa", "com...	2017	Genomic analyses of African Trypanozoon strains to assess evolutionary relationships and identify markers for strain identification
Grid cells in the medial entorhinal cortex encode space with firing fields that are arranged on the nodes of spatial hexagonal lattices . Potential candidates to read out the space information of this grid code and to combine it with other sensory cues are hippocampal place cells . In this paper , we investigate a popu...	The mammalian brain represents space in the population of hippocampal place cells as well as in the population of medial entorhinal cortex grid cells . Since both populations are active at the same time , space information has to be synchronized between the two . Both brain areas are reciprocally connected , and it is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "coding", "mechanisms" ]	2014	Hippocampal Remapping Is Constrained by Sparseness rather than Capacity
Although functionally related proteins can be reliably predicted from phylogenetic profiles , many functional modules do not seem to evolve cohesively according to case studies and systematic analyses in prokaryotes . In this study we quantify the extent of evolutionary cohesiveness of functional modules in eukaryotes ...	Components of a protein complex or a metabolic pathway strongly cooperate to perform a specific function . Because of this functional interdependence , proteins that form a complex or pathway are expected to be present and absent together in different species . Phylogenetic profiling methods , in which proteins with si...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/bioinformatics", "computational", "biology/systems", "biology", "computational", "biology/genomics" ]	2009	Cohesive versus Flexible Evolution of Functional Modules in Eukaryotes
Viral surveillance programs or diagnostic labs occasionally obtain infectious samples that fail to be typed by available cell culture , serological , or nucleic acid tests . Five such samples , originating from insect pools , skunk brain , human feces and sewer effluent , collected between 1955 and 1980 , resulted in p...	Viral surveillance programs aim to identify circulating viruses to safeguard the public and livestock from viral outbreaks . Occasionally , samples suspected of harboring a virus cause severe disease in laboratory animals , but the identity of the virus eludes researchers . Here , we applied a simple viral discovery te...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/emerging", "viral", "diseases" ]	2008	Rapid Identification of Known and New RNA Viruses from Animal Tissues
The trimeric CAK complex functions in cell cycle control by phosphorylating and activating Cdks while TFIIH-linked CAK functions in transcription . CAK also associates into a tetramer with Xpd , and our analysis of young Drosophila embryos that do not require transcription now suggests a cell cycle function for this in...	Mutations in human xpd cause three different syndromes—XP ( xeroderma pigmentosum ) , TTD ( trichothiodystrophy ) , and CS ( Cockayne syndrome ) —and various different phenotypes , such as sun-induced hyperpigmentation of the skin , cutaneous abnormalities , neuronal degeneration , and developmental retardation . In ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/cancer", "genetics", "cell", "biology/developmental", "molecular", "mechanisms", "genetics", "and", "genomics/genetics", "of...	2010	Drosophila Xpd Regulates Cdk7 Localization, Mitotic Kinase Activity, Spindle Dynamics, and Chromosome Segregation
Polymicrobial sepsis is the result of an exaggerated host immune response to bacterial pathogens . Animal models and human studies demonstrate that alcohol intoxication is a key risk factor for sepsis-induced mortality . Multiple chemokines , such as CXCL1 , CXCL2 and CXCL5 are critical for neutrophil recruitment and p...	Sepsis is still a leading cause of morbidity and mortality in critically ill patients . Multiple organ failure and mortality in sepsis is caused by uncontrolled activation of the immune system . This results in impaired ability to control bacterial colonization and dissemination along with excessive inflammation-induce...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "peritoneal", "lavage", "trauma", "surgery", "medicine", "and", "health", "sciences", "immune", "cells", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "diet", "organic", "compounds", ...	2017	Diminished neutrophil extracellular trap (NET) formation is a novel innate immune deficiency induced by acute ethanol exposure in polymicrobial sepsis, which can be rescued by CXCL1
DMC1 is a meiosis-specific homolog of bacterial RecA and eukaryotic RAD51 that can catalyze homologous DNA strand invasion and D-loop formation in vitro . DMC1-deficient mice and yeast are sterile due to defective meiotic recombination and chromosome synapsis . The authors identified a male dominant sterile allele of D...	About 10%–15% of couples are infertile due to defects in meiosis ( the process by which egg or sperm cells containing a single copy of each chromosome are produced ) . Because studying the genetics of meiosis in humans is difficult , we performed genetic screens in mice and identified a novel mutation in Dmc1 that caus...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "mammals", "mus", "(mouse)", "molecular", "biology", "genetics", "and", "genomics" ]	2007	A Dominant, Recombination-Defective Allele of Dmc1 Causing Male-Specific Sterility
Both endocarditis and Bartonella infections are neglected public health problems , especially in rural Asia . Bartonella endocarditis has been described from wealthier countries in Asia , Japan , Korea , Thailand and India but there are no reports from poorer countries , such as the Lao PDR ( Laos ) , probably because ...	Infection of heart valves ( endocarditis ) with bacteria is an important condition , especially afflicting those with rheumatic heart disease , and has a high mortality if untreated . Most of the evidence for optimal antibiotic and surgical management comes from wealthy countries . There are no published data from poor...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bartonella", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "medical", "microbiology", "microbial", "pathogens", "pathogens", "biology", "and", "life", "sciences", "microbiology", "bacterial", "pathogens" ]	2014	Bartonella henselae Endocarditis in Laos – ‘The Unsought Will Go Undetected’
Clonorchis sinensis is a liver fluke that can dwell in the bile ducts of mammals . Bile acid transporters function to maintain the homeostasis of bile acids in C . sinensis , as they induce physiological changes or have harmful effects on C . sinensis survival . The organic solute transporter ( OST ) transports mainly ...	Clonorchiasis is a neglected tropical disease caused by the liver fluke , Clonorchis sinensis . C . sinensis is a biological carcinogen , causing cholangiocarcinoma in humans . Juvenile flukes migrate to and grow to adults in the bile ducts . The bile is chemo-attractive to the flukes and stimulates growth and egg prod...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biliary", "system", "invertebrates", "taxonomy", "medicine", "and", "health", "sciences", "liver", "body", "fluids", "helminths", "bile", "animals", "trematodes", "solutions", "clonorchis", "sinensis", "phylogenetics", "data", "management", "materials", "science", "phy...	2018	Characterization of a novel organic solute transporter homologue from Clonorchis sinensis
Common genetic variation at human 8q23 . 3 is significantly associated with colorectal cancer ( CRC ) risk . To elucidate the basis of this association we compared the frequency of common variants at 8q23 . 3 in 1 , 964 CRC cases and 2 , 081 healthy controls . Reporter gene studies showed that the single nucleotide pol...	Common inherited variation on human chromosome 8q23 influences the risk of developing colorectal cancer ( CRC ) . To understand the basis of this association we have compared the frequency of common genetic variants at 8q23 in ∼2 , 000 CRC cases and ∼2 , 000 healthy controls . Functional analyses of variants strongly a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/functional", "genomics", "cell", "biology/cell", "growth", "and", "division", "oncology/gastrointestinal", "cancers", "genetics", "and", "genomics", "genetics", "and", "genomics/medical", "genetics", "genetics", "and", "genomics/cancer", "geneti...	2010	Allelic Variation at the 8q23.3 Colorectal Cancer Risk Locus Functions as a Cis-Acting Regulator of EIF3H
Elongation factor P ( EF-P ) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing . However , previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp . ...	Elongation factor P ( EF-P ) is a well-conserved bacterial protein . Although it can enhance protein synthesis in vitro , it is generally regarded as an ancillary factor required for robust translation of transcripts with stretches of consecutive prolines . In this work we performed ribosome profiling to better underst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacterial", "genomics", "molecular", "machines", "protein", "translation", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "molecular", "genetics", "microbiology", "genomics", "molecular", "biology", "microbial", "genomics" ]	2014	EF-P Dependent Pauses Integrate Proximal and Distal Signals during Translation
Most organisms on earth sense light through the use of chromophore-bearing photoreceptive proteins with distinct and characteristic photocycle lengths , yet the biological significance of this adduct decay length is neither understood nor has been tested . In the filamentous fungus Neurospora crassa VIVID ( VVD ) is a ...	Sensing light from the environment using a variety of photoreceptors is of great adaptive significance for most eukaryotes . A key feature of photoreceptors is the photocycle length , the time taken to decay from the initial signaling light state back to the receptive dark state; however , the significance of photocycl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Biological Significance of Photoreceptor Photocycle Length: VIVID Photocycle Governs the Dynamic VIVID-White Collar Complex Pool Mediating Photo-adaptation and Response to Changes in Light Intensity
Computational protein design has found great success in engineering proteins for thermodynamic stability , binding specificity , or enzymatic activity in a ‘single state’ design ( SSD ) paradigm . Multi-specificity design ( MSD ) , on the other hand , involves considering the stability of multiple protein states simult...	The ability to design a new protein with a desired activity has been a longstanding goal of computational biologists , to create proteins with new binding activity or increased stability . An even more ambitious goal is multi-specificity design , which extends general protein design by creating a sequence that has low ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences
Female gamete production relies on coordinated molecular and cellular processes that occur in the ovary throughout oogenesis . In fish , as in other vertebrates , these processes have been extensively studied both in terms of endocrine/paracrine regulation and protein expression and activity . The role of small non-cod...	The role of small non-coding RNAs in the regulation of animal reproduction remains poorly investigated , despite a growing interest for the importance of miRNAs in a wide variety of biological processes . Here , we analyzed the role of miR-202 , a miRNA predominantly expressed in gonads in vertebrate . We studied its e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "urology", "medicine", "and", "health", "sciences", "reproductive", "system", "gonads", "obstetrics", "and", "gynecology", "gene", "regulation", "reproductive", "physiology", "epithelial", "cells", "germ", "cells", "oocytes", "micrornas", "female", "subfertility", "wome...	2018	MiR-202 controls female fecundity by regulating medaka oogenesis
The Aedes aegypti mosquito is a significant public health threat , as it is the main vector of dengue and chikungunya viruses . Disease control efforts could be enhanced through reproductive manipulation of these vectors . Previous work has revealed a relationship between male seminal fluid proteins transferred to fema...	Female post-mating behavior has important consequences for mosquito populations and their ability to transmit diseases . Male Aedes aegypti seminal fluid substances transferred during mating cause many important changes to female behavior and physiology , including blood feeding behavior , egg development , and oviposi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "immunology", "rna", "extraction", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "genome", "analysis", "insect", "vectors", "extraction", "techniques", "dros...	2016	Mating-Induced Transcriptome Changes in the Reproductive Tract of Female Aedes aegypti
Clonorchis sinensis ( C . sinensis ) is the most widespread human liver fluke in East Asia including China and Korea . Clonorchiasis as a neglected tropical zoonosis , leads to serious economic and public health burden in China . There are considerable evidences for an etiological relation between chronic clonorchiasis...	In China , the morbidity of clonorchiasis resulting from the infection of Clonorchis sinensis ( C . sinensis ) increased every year and 1 . 5 to 2 million patients develop to the late stage—liver fibrosis , cirrhosis or cholangiocarcinoma . Proinflammatory and profibrotic cytokines produced by cells of the innate and a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "t", "helper", "cells", "invertebrates", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "helminths", "immunology", "animals", "liver", "diseases", "trematodes", "clonorch...	2018	Clonorchis sinensis adult-derived proteins elicit Th2 immune responses by regulating dendritic cells via mannose receptor
The six C . elegans vulval precursor cells ( VPCs ) are induced to form the 3°-3°-2°-1°-2°-3° pattern of cell fates with high fidelity . In response to EGF signal , the LET-60/Ras-LIN-45/Raf-MEK-2/MEK-MPK-1/ERK canonical MAP kinase cascade is necessary to induce 1° fate and synthesis of DSL ligands for the lateral Notc...	Developmental signals are increasingly conceptualized in the context of networks rather than linear pathways . Patterning of C . elegans vulval fates is mostly governed by two major signaling cascades that operate antagonistically to induce two cell identities . An additional pair of minor cascades support each of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "deletion", "mutation", "animal", "genetics", "rna", "interference", "caenorhabditis", "signaling", "networks", "animals", "akt", "signaling", "cascade", "animal", "models", "mutation", "guanine", "nucleotide", "exchange", "factors", "caenorhabditis", "el...	2019	Developmental fidelity is imposed by genetically separable RalGEF activities that mediate opposing signals
The single mitochondrion of apicomplexan protozoa is thought to be critical for all stages of the life cycle , and is a validated drug target against these important human and veterinary parasites . In contrast to other eukaryotes , replication of the mitochondrion is tightly linked to the cell cycle . A key step in mi...	Mitochondria fission is mediated by an elaborate “fission complex” of dynamin and receptor proteins , best studied in organisms such as yeast and mammalian cells . Little is known about this process in apicomplexan parasites , unicellular eukaryotes characterised by a single , lasso-shaped mitochondrion . Here , we ana...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "parasite", "groups", "vacuoles", "toxoplasma", "gondii", "enzymes", "enzymology", "parasitic", "protozoans", "parasitology", "apicomplexa", "protozoans", "toxoplasma", "mitochondria", "bioenergetics", "immunologic", "techniques", "cellular", "structures", "and", "organelles"...	2019	A unique dynamin-related protein is essential for mitochondrial fission in Toxoplasma gondii
Ixodes ricinus is the main tick vector of the microbes that cause Lyme disease and tick-borne encephalitis in Europe . Pathogens transmitted by ticks have to overcome innate immunity barriers present in tick tissues , including midgut , salivary glands epithelia and the hemocoel . Molecularly , invertebrate immunity is...	Ixodes ricinus transmits Lyme disease and tick-borne encephalitis in Europe . Tick-borne pathogens ingested with a blood meal persist in the tick gut and , during the next feeding stage , disseminate through the haemolymph to pass into a vertebrate host via the salivary glands . Invertebrate immunity is initiated when ...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results/Discussion", "Conclusions" ]	[]	2015	Deep Sequencing Analysis of the Ixodes ricinus Haemocytome
Current thinking emphasizes the primacy of CD14 in facilitating recognition of microbes by certain TLRs to initiate pro-inflammatory signaling events and the importance of p38-MAPK in augmenting such responses . Herein , this paradigm is challenged by demonstrating that recognition of live Borrelia burgdorferi not only...	Macrophages express CD14 which partners with Toll-like receptor 2/1 to recognize bacterial lipoproteins such as those of Borrelia burgdorferi , the causative agent of Lyme disease . In vitro evidence demonstrates that blocking CD14 recognition of bacterial components ablates innate host cell inflammatory responses . Si...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immunomodulation", "immunology/innate", "immunity", "immunology/leukocyte", "signaling", "and", "gene", "expression", "immunology/immunity", "to", "infections", "immunology/leukocyte", "activation" ]	2009	CD14 Signaling Restrains Chronic Inflammation through Induction of p38-MAPK/SOCS-Dependent Tolerance
Viral capsid proteins assemble into large , symmetrical architectures that are not found in complexes formed by their cellular counterparts . Given the prevalence of the signature jelly-roll topology in viral capsid proteins , we are interested in whether these functionally unique capsid proteins are also structurally ...	Viruses are increasingly viewed not as pathogens that parasitize all domains of life , but as useful nanoplatforms for synthetic maneuvers in a wide range of biomedical and materials science applications . One of the most well-known examples of virus-based nanotools developed so far features viral capsules as therapeut...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "physics", "chemistry", "biology" ]	2013	Viral Capsid Proteins Are Segregated in Structural Fold Space
Tuberculosis exerts a tremendous burden on global health , with ∼9 million new infections and ∼2 million deaths annually . The Mycobacterium tuberculosis complex ( MTC ) was initially regarded as a highly homogeneous population; however , recent data suggest the causative agents of tuberculosis are more genetically and...	Genetic polymorphisms among bacterial pathogens are exploited by epidemiologists to monitor disease outbreaks and transmission of specific strains . Genetic variations occur under selective pressures imposed by the human host , leading to variation amongst clinical isolates . Tuberculosis ( TB ) is an ancient disease c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "microbiology", "genetics", "and", "genomics", "microbiology/medical", "microbiology" ]	2010	Functional Genetic Diversity among Mycobacterium tuberculosis Complex Clinical Isolates: Delineation of Conserved Core and Lineage-Specific Transcriptomes during Intracellular Survival
Microbes usually exist in communities consisting of myriad different but interacting species . These interactions are typically mediated through environmental modifications; microbes change the environment by taking up resources and excreting metabolites , which affects the growth of both themselves and also other micr...	Microbes typically live alongside many other species in complex communities . These microbial communities are very important for us because they also live in and on our bodies and can determine our health and well-being . The composition and function of these communities , such as who is part of such a community and wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protons", "medicine", "and", "health", "sciences", "urea", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "phosphates", "pathogens", "microbiology", "carbohydrates", "organic", "compounds", "glucose",...	2018	Modifying and reacting to the environmental pH can drive bacterial interactions
Extracellular vesicles ( EVs ) are structures with phospholipid bilayer membranes and 100–1000 nm diameters . These vesicles are released from cells upon activation of surface receptors and/or apoptosis . The production of EVs by dendritic cells , mast cells , macrophages , and B and T lymphocytes has been extensively ...	Leishmaniases are a group of diseases—each one individually called leishmaniasis—that are caused by the protozoan Leishmania . They affect millions of people and thousands of dogs in tropical and mediterranean countries . Macrophages are the main cellular hosts of Leishmania in the mammalian host , where it is an oblig...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "protozoans", "leishmania", "pathology", "and", "laboratory", "medicine", "immunity", "host-pathogen", "interactions", "immune", "activation", "biology", "and", "life", "sciences", "immunology", "pathogenesis", "parasitic", "protoz...	2014	Extracellular Vesicles from Leishmania-Infected Macrophages Confer an Anti-infection Cytokine-Production Profile to Naïve Macrophages
The homeostatic mechanisms that regulate the maintenance of immunological memory to the multiple pathogen encounters over time are unknown . We found that a single malaria episode caused significant dysregulation of pre-established Influenza A virus-specific long-lived plasma cells ( LLPCs ) resulting in the loss of In...	Antibody responses to infectious pathogens are critical in host survival , recovery and protection from reinfection; they also correlate with the success of vaccination . It is currently thought that antibody serum titers are maintained at protective levels over long periods of time by specialized long-lived antibody-s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	Recovery of an Antiviral Antibody Response following Attrition Caused by Unrelated Infection
Functionally analogous enzymes are those that catalyze similar reactions on similar substrates but do not share common ancestry , providing a window on the different structural strategies nature has used to evolve required catalysts . Identification and use of this information to improve reaction classification and com...	When species evolve , their genes duplicate and diverge to allow for adaptation of their functional repertoires to the changing environment . In this scenario , unrelated genes can convergently evolve to produce proteins with the same molecular function , termed “functionally analogous . ” A quantitative determination ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biochemistry/molecular", "evolution", "biochemistry/biocatalysis", "genetics", "and", "genomics/functional", "genomics", "biochemistry/chemical", "biology", "of", "the", "cell", "biochemistry/macromolecular", "chemistry", "computational", "biology/evolutionary", "modeling", "bioph...	2010	Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function
Cellular memory , which allows cells to retain information from their environment , is important for a variety of cellular functions , such as adaptation to external stimuli , cell differentiation , and synaptic plasticity . Although posttranslational modifications have received much attention as a source of cellular m...	Cellular memory exists in a wide range of organisms from prokaryotes to eukaryotes and can persist , in some cases , for days at a time . Mounting evidence supports the notion that cells indeed can retain information associated with previous environmental exposures via posttranslational modifications . Molecules with m...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "physics", "systems", "biology", "theoretical", "biology", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology", "biophysics" ]	2014	Kinetic Memory Based on the Enzyme-Limited Competition
Long noncoding RNAs ( lncRNAs ) have been implicated in various biological functions including the regulation of gene expression , however , the functionality of lncRNAs is not clearly understood and conflicting conclusions have often been reached when comparing different methods to investigate them . Moreover , little...	Long noncoding RNAs ( lncRNAs ) have been implicated in various biological functions including regulation of gene expression . However , the mechanism through which they regulate gene expression is not clearly understood . Here we show that a transcriptional co activator—Psip1 specifically regulates the expression of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "gene", "regulation", "long", "non-coding", "rnas", "dna", "transcription", "developmental", "biology", "mammalian", "genomics", "embryos", "embryology", "proteins", "gene", "expression", "genetic", "loci", "animal", "genomics", "homeobox", "biochemistry", "rna", "nucle...	2017	Psip1/p52 regulates posterior Hoxa genes through activation of lncRNA Hottip
Filarial nematodes , including Brugia malayi , the causative agent of lymphatic filariasis , undergo molting in both arthropod and mammalian hosts to complete their life cycles . An understanding of how these parasites cross developmental checkpoints may reveal potential targets for intervention . Pharmacological evide...	Filarial parasites such as Brugia malayi and Onchocerca volvulus are the causative agents of the tropical diseases lymphatic filariasis and onchocerciasis , which infect 150 million people , mainly in Africa and Southeast Asia . Filarial nematodes have a complex life cycle that involves transmission and development wit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/gene", "function", "biochemistry", "developmental", "biology/developmental", "molecular", "mechanisms" ]	2010	Molecular Evidence for a Functional Ecdysone Signaling System in Brugia malayi
The heparan sulfate ( HS ) chains of proteoglycans are a key regulatory component of the extracellular matrices of animal cells , including the pericellular matrix around the plasma membrane . In these matrices they regulate transport , gradient formation , and effector functions of over 400 proteins central to cell co...	The development , homeostasis , and repair of animal tissues requires communication between cells mediated by effector proteins , which are released from source cells and must move through the surrounding extracellular matrix to reach their receptors on target cells . A major component of the extracellular matrix is th...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biology", "molecular", "cell", "biology", "biophysics" ]	2012	Transport of Fibroblast Growth Factor 2 in the Pericellular Matrix Is Controlled by the Spatial Distribution of Its Binding Sites in Heparan Sulfate
Direct Sanger sequencing of a diploid template containing a heterozygous insertion or deletion results in a difficult-to-interpret mixed trace formed by two allelic traces superimposed onto each other . Existing computational methods for deconvolution of such traces require knowledge of a reference sequence or the avai...	In DNA , information is encoded as a sequence of four types of building blocks–nucleotides . The most common technique for determining such sequences , the Sanger method , outputs a single consensus for a pool of DNA molecules in the analyzed sample . When these are identical , each site in the output contains a single...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/macromolecular", "sequence", "analysis", "computational", "biology/genomics" ]	2008	Decoding of Superimposed Traces Produced by Direct Sequencing of Heterozygous Indels
Retrotransposons are mobile genetic elements that proliferate through an RNA intermediate . Transposons do not encode transcription factors and thus rely on host factors for mRNA expression and survival . Despite information regarding conditions under which elements are upregulated , much remains to be learned about th...	Transposons are present at high copy number in diverse organisms ranging from single-celled bacteria to complex mammals and plants . Transposons are mobile genetic elements that can replicate and move to new locations within the genome . An ongoing debate exists regarding whether transposons are merely genetic parasite...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "schizosaccharomymes", "viruses", "biochemistry", "cell", "biology", "virology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	SREBP Controls Oxygen-Dependent Mobilization of Retrotransposons in Fission Yeast
The most consistent result in more than two decades of experimental evolution is that the fitness of populations adapting to a constant environment does not increase indefinitely , but reaches a plateau . Using experimental evolution with bacteriophage , we show here that the converse is also true . In populations smal...	In any population , two factors determine whether the average fitness of individuals will increase ( adaptation ) or decrease: the size of the population and the distribution of mutational effects ( i . e . , the relative rates and effect sizes of beneficial and deleterious mutations ) . Although it is relatively simpl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "viruses", "microbiology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2007	Understanding the Evolutionary Fate of Finite Populations: The Dynamics of Mutational Effects
Abortive infection , during which an infected bacterial cell commits altruistic suicide to destroy the replicating bacteriophage and protect the clonal population , can be mediated by toxin-antitoxin systems such as the Type III protein–RNA toxin-antitoxin system , ToxIN . A flagellum-dependent bacteriophage of the Myo...	Bacteria are under constant attack by their viral parasites , bacteriophages , which outnumber bacteria by an estimated ten-to-one . The constant selection pressure from this predation promotes the evolution and dissemination of bacterial bacteriophage-resistance mechanisms . One family of protective systems causes the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biochemistry", "microbial", "ecology", "virology", "microbial", "evolution", "genetics", "molecular", "genetics", "biology", "microbiology", "host-pathogen", "interaction", "genetics", "and", "genomics", "viral", "evolution" ]	2012	Viral Evasion of a Bacterial Suicide System by RNA–Based Molecular Mimicry Enables Infectious Altruism
The innate immune response is essential for controlling West Nile virus ( WNV ) infection but how this response is propagated and regulates adaptive immunity in vivo are not defined . Herein , we show that IPS-1 , the central adaptor protein to RIG-I-like receptor ( RLR ) signaling , is essential for triggering of inna...	West Nile virus ( WNV ) is a mosquito-transmitted RNA virus that has emerged in the Western hemisphere and is now the leading cause of arboviral encephalitis in the United States . However , the virus/host interface that controls WNV pathogenesis is not well understood . Previous studies have established that the innat...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "virology", "virology/emerging", "viral", "diseases", "infectious", "diseases/viral", "infections", "virology/host", "antiviral", "responses", "virology/mechanisms", "of", "resistance", "and", ...	2010	IPS-1 Is Essential for the Control of West Nile Virus Infection and Immunity
Hantavirus pulmonary syndrome ( HPS ) , also referred to as hantavirus cardiopulmonary syndrome ( HCPS ) , is a rare but frequently fatal disease caused by New World hantaviruses . In humans HPS is associated with severe pulmonary edema and cardiogenic shock; however , the pathogenesis of this disease remains unclear l...	New World hantaviruses , including Andes virus ( ANDV ) , are rodent-borne pathogens which are associated with hantavirus pulmonary syndrome ( HPS ) and case fatality rates up to 50% . The pathogenesis of HPS remains unclear; however , it is believed to involve a delicate balance of virus infection and deleterious immu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "zoonoses", "hantavirus", "hantavirus", "pulmonary", "syndrome", "viral", "diseases", "infectious", "disease", "modeling" ]	2011	Pathogenesis and Host Response in Syrian Hamsters following Intranasal Infection with Andes Virus
RNA viruses encode various RNA binding proteins that function in many steps of viral infection cycles . These proteins function as RNA helicases , methyltransferases , RNA-dependent RNA polymerases , RNA silencing suppressors , RNA chaperones , movement proteins , and so on . Although many of the proteins bind the vira...	In order to maximize reproduction , RNA viruses often encode multifunctional proteins to perform different activities during replication . We report that the Barley stripe mosaic virus γb VSR protein is recruited to viral replication sites through interactions with the αa replicase subunit protein where it enhances αa ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "rna-binding", "proteins", "nucleic", "acid", "synthesis", "rna", "interference", "enzymes", "plant", "cell", "biology", "rna", "extraction", "microbiology", "enzymology", "chloroplasts", "plant", "science", "epigenetics", "rna", "synthesis", "cellul...	2017	The Barley stripe mosaic virus γb protein promotes chloroplast-targeted replication by enhancing unwinding of RNA duplexes
The cellular prion protein ( PrPC ) is a cell surface glycoprotein attached to the membrane by a glycosylphosphatidylinositol ( GPI ) -anchor and plays a critical role in transmissible , neurodegenerative and fatal prion diseases . Alterations in membrane attachment influence PrPC-associated signaling , and the develop...	The prion protein ( PrPC ) is a glycoprotein attached to the neuronal surface via a GPI-anchor . When misfolded to PrPSc , it leads to fatal neurodegenerative diseases which propagates from host to host . PrPSc is the principal component of the infectious agent of prion diseases , the “prion” . Misfolding occurs at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "disaccharides", "sialic", "acids", "carbohydrates", "organic", "compounds", "animal", "models", "physiological", "processes", "model", "organisms", "experimental", "organism", "systems", "cellular", "struc...	2019	GPI-anchor signal sequence influences PrPC sorting, shedding and signalling, and impacts on different pathomechanistic aspects of prion disease in mice
Shigella flexneri , a Gram-negative enteroinvasive pathogen , causes inflammatory destruction of the human intestinal epithelium . Infection by S . flexneri has been well-studied in vitro and is a paradigm for bacterial interactions with the host immune system . Recent work has revealed that components of the cytoskele...	Shigella are human-adapted Escherichia coli and cause bacillary dysentery via inflammatory destruction of the gut epithelium . In this study , we use a zebrafish ( Danio rerio ) model of Shigella infection to discover new roles for the cytoskeleton in inflammation and infection control . Septins , a poorly understood c...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "vertebrates", "animals", "shigella", "animal", "models", "osteichthyes", "bact...	2017	Septins restrict inflammation and protect zebrafish larvae from Shigella infection
The disruption of the circadian system in humans has been associated with the development of chronic illnesses and the worsening of pre-existing pathologies . Therefore , the assessment of human circadian system function under free living conditions using non-invasive techniques needs further research . Traditionally ,...	Faced with environmental cycles and daily alternation between light and darkness , organisms have evolved a time measuring mechanism , the biological clocks . Besides following circadian rhythms , all physiological variables must be coordinated with one another , like an orchestra led by a conductor; if the appropriate...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/synthetic", "biology", "physiology/pattern", "formation", "physiology", "physiology/integrative", "physiology", "neuroscience", "computational", "biology/systems", "biology" ]	2010	A New Integrated Variable Based on Thermometry, Actimetry and Body Position (TAP) to Evaluate Circadian System Status in Humans
The RNA genomes of picornaviruses are translated into single polyproteins which are subsequently cleaved into structural and non-structural protein products . For genetic economy , proteins and processing intermediates have evolved to perform distinct functions . The picornavirus precursor protein , P3 , is cleaved to ...	Positive-strand RNA viruses are generally typified by a small genome size . To compensate for this limitation they have evolved ways of multiplying the functions achievable from a small genome , thus increasing ‘genetic economy’ . In the picornavirus family of RNA viruses the viral proteins are produced via a series of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "deletion", "mutation", "microbial", "mutation", "microbiology", "dna-binding", "proteins", "plasmid", "construction", "viruses", "mutation", "rna", "viruses", "polymerases", "dna", "construction", "molecular", "biology", "techniques", "research", "and", "...	2017	Genetic economy in picornaviruses: Foot-and-mouth disease virus replication exploits alternative precursor cleavage pathways
Systemic iron homeostasis involves a negative feedback circuit in which the expression level of the peptide hormone hepcidin depends on and controls the iron blood levels . Hepcidin expression is regulated by the BMP6/SMAD and IL6/STAT signaling cascades . Deregulation of either pathway causes iron-related diseases suc...	The nutritional iron uptake is tightly regulated because the body has limited capacity of iron excretion . Mammals maintain iron homeostasis by a negative feedback loop , in which the peptide hepcidin senses the iron blood level and controls iron resorption . Molecular perturbations in the homeostasis loop lead to iron...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2014	A Multi-Scale Model of Hepcidin Promoter Regulation Reveals Factors Controlling Systemic Iron Homeostasis
Infertility and adverse gynecological outcomes such as preeclampsia and miscarriage represent significant female reproductive health concerns . The spatiotemporal expression of growth factors indicates that they play an important role in pregnancy . The goal of this study is to define the role of the ERBB family of gro...	Approximately 10% of reproductive aged women are considered infertile . While great strides have been made in assisted reproductive technologies , overall success rates , especially considering the cost , remain low . Studies indicate that due to its sequential nature , nearly 75% of pregnancy failures are due to defec...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "death", "urology", "medicine", "and", "health", "sciences", "rna", "interference", "maternal", "health", "obstetrics", "and", "gynecology", "reproductive", "endocrinology", "cell", "processes", "reproductive", "physiology", "endocrine", "physiology", "miscarriage...	2014	The Epidermal Growth Factor Receptor Critically Regulates Endometrial Function during Early Pregnancy
Prior to receiving visual stimuli , spontaneous , correlated activity in the retina , called retinal waves , drives activity-dependent developmental programs . Early-stage waves mediated by acetylcholine ( ACh ) manifest as slow , spreading bursts of action potentials . They are believed to be initiated by the spontane...	Both within the visual system and more generally , two general processes describe nervous system development: first , genetically determined cues provide a coarse layout of cells and connections and second , neuronal activity removes unwanted cells and refines connections . This activity occurs not just through externa...	[ "Abstract", "Introduction", "Results", "Discussion", "Models" ]	[ "developmental", "neuroscience", "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "neural", "circuit", "formation" ]	2014	A Reaction-Diffusion Model of Cholinergic Retinal Waves
Schistosomiasis is the second-most widespread tropical parasitic disease after malaria . Various research strategies and treatment programs for achieving the objective of eradicating schistosomiasis within a decade have been recommended and supported by the World Health Organization . One of these approaches is based o...	The present paper reports the isolation and the characterization of a new microbial pathogen of the freshwater snail , Biomphalaria glabrata . Genetic analyses revealed that the species has not been previously described and could be classified into the Paenibacillus genus . These bacteria invade most snail tissues and ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Novel Bacterial Pathogen of Biomphalaria glabrata: A Potential Weapon for Schistosomiasis Control?
Dengue is an acute illness caused by the positive-strand RNA dengue virus ( DENV ) . There are four genetically distinct DENVs ( DENV-1–4 ) that cause disease in tropical and subtropical countries . Most patients are viremic when they present with symptoms; therefore , RT-PCR has been increasingly used in dengue diagno...	Significant expansion of the four DENV serotypes ( DENV-1 , -2 , -3 and -4 ) has been reported throughout tropical and sub-tropical regions of the world , with estimates of 390 million cases annually . The need has arisen for expanded diagnostic testing for DENV infections in the United States , as dengue infection has...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "laboratory", "sciences", "diagnostic", "medicine", "travel-associated", "diseases", "neglected", "tropical", "diseases", "infectious", "disease", "control", "viral", "diseases" ]	2013	Analytical and Clinical Performance of the CDC Real Time RT-PCR Assay for Detection and Typing of Dengue Virus
Combining data from genome-wide association studies ( GWAS ) conducted at different locations , using genotype imputation and fixed-effects meta-analysis , has been a powerful approach for dissecting complex disease genetics in populations of European ancestry . Here we investigate the feasibility of applying the same ...	Malaria kills nearly a million people every year , most of whom are young children in Africa . The risk of developing severe malaria is known to be affected by genetics , but so far only a handful of genetic risk factors for malaria have been identified . We studied over a million DNA variants in over 5 , 000 individua...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "plasmodium", "falciparum", "genome-wide", "association", "studies", "medicine", "infectious", "diseases", "genetic", "association", "studies", "genetics", "biology", "human", "genetics", "malaria", "parasitic", "diseases" ]	2013	Imputation-Based Meta-Analysis of Severe Malaria in Three African Populations
Bacterial bloodstream infection ( bBSI ) is one of the leading causes of death in critically ill patients and accurate diagnosis is therefore crucial . We here report a 16S metagenomics approach for diagnosing and understanding bBSI . The proof-of-concept was delivered in 75 children ( median age 15 months ) with sever...	Bacterial bloodstream infection ( bBSI ) is one of the biggest causes of mortality in critically ill patients and standard diagnosis is still done by blood culture methods . Parallel deep sequencing of the 16S ribosomal RNA genes ( 16S metagenomics ) is a new and rapidly evolving research field for profiling bacterial ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "enterobacter", "medicine", "and", "health", "sciences", "body", "fluids", "gut", "bacteria", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "parasitic", "diseases", "escherichia", "coli", "bacterial", "diseases", "pro...	2016	Diagnosis of Bacterial Bloodstream Infections: A 16S Metagenomics Approach
Many disease-associated variants affect gene expression levels ( expression quantitative trait loci , eQTLs ) and expression profiling using next generation sequencing ( NGS ) technology is a powerful way to detect these eQTLs . We analyzed 94 total blood samples from healthy volunteers with DeepSAGE to gain specific i...	Many genetic variants that are associated with diseases also affect gene expression levels . We used a next generation sequencing approach targeting 3′ transcript ends ( DeepSAGE ) to gain specific insight into how genetic variants affect the expression of genes and the usage and length of 3′-untranslated regions . We ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "genome", "analysis", "tools", "biology", "genomics", "computational", "biology", "transcriptomes" ]	2013	DeepSAGE Reveals Genetic Variants Associated with Alternative Polyadenylation and Expression of Coding and Non-coding Transcripts
Abnormal metabolism and uncontrolled angiogenesis are two important characteristics of malignant tumors . The occurrence of both events involves many key molecular changes including miRNA . However , EBV encoded miRNAs are rarely mentioned as capable of regulating tumor metabolism and tumor angiogenesis . Here , we rep...	The Epstein-Barr virus ( EBV ) , the first reported human tumor virus found to encode miRNAs , which closely related to malignant progression of tumors . In our study , we have observed that EBV-miR-BART1-5P , an EBV-BARTs encoded miRNA , promotes glycolysis and induces angiogenesis in NPC . Interestingly , we showed t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "transfection", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "cardiovascular", "physiology", "natural", "antisense", "transcripts", "metabolic", "processes", "gene", "regulation", "carcinomas", "cancers", "and", "neoplasms", "glucose", "metabolism"...	2018	EBV-miR-BART1-5P activates AMPK/mTOR/HIF1 pathway via a PTEN independent manner to promote glycolysis and angiogenesis in nasopharyngeal carcinoma
Penalized Multiple Regression ( PMR ) can be used to discover novel disease associations in GWAS datasets . In practice , proposed PMR methods have not been able to identify well-supported associations in GWAS that are undetectable by standard association tests and thus these methods are not widely applied . Here , we ...	Genome-wide association studies ( GWAS ) have identified hundreds of regions of the human genome that are associated with susceptibility to common diseases . Yet many lines of evidence indicate that many susceptibility loci , which cannot be detected by standard statistical methods , remain to be discovered . We have d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "mathematics", "statistics", "genetics", "biology", "statistical", "methods" ]	2013	PUMA: A Unified Framework for Penalized Multiple Regression Analysis of GWAS Data
Transposable elements ( TEs ) are dynamically expressed at high levels in multiple human tissues , but the function of TE-derived transcripts remains largely unknown . In this study , we identify numerous TE-derived microRNAs ( miRNAs ) by conducting Argonaute2 RNA immunoprecipitation followed by small RNA sequencing (...	Transposable elements ( TEs ) are repetitive sequences , that have contributed to the landscaping of the genome by jumping into new positions and amplifying in number . TEs have been suggested to play a role in gene regulation , but it remains poorly understood how they contribute to this process . In this study , we s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "transfer", "rna", "medicine", "and", "health", "sciences", "natural", "antisense", "transcripts", "gene", "regulation", "blastomas", "cancers", "and", "neoplasms", "oncology", "neurological", "tumors", "micrornas", "genetic", "elements", "mo...	2019	LINE-2 transposable elements are a source of functional human microRNAs and target sites
Cell-to-cell communication is crucial for the development of multicellular organisms , especially during the generation of new tissues and organs . Secondary growth—the lateral expansion of plant growth axes—is a highly dynamic process that depends on the activity of the cambium . The cambium is a stem cell–like tissue...	In contrast to animals , plants have the capacity to grow and form new organs throughout their entire life cycle , thereby building up some of the largest organisms on earth . This remarkable capacity is based on the activity of stem cell–like tissues—the meristems—located at shoot and root apices and , in a large repe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "developmental", "biology/plant", "growth", "and", "development", "developmental", "biology/pattern", "formation", "developmental", "biology/stem", "cells" ]	2011	Characterization of Transcriptome Remodeling during Cambium Formation Identifies MOL1 and RUL1 As Opposing Regulators of Secondary Growth
Y chromosomes often contain amplified genes which can increase dosage of male fertility genes and counteract degeneration via gene conversion . Here we identify genes with increased copy number on both X and Y chromosomes in various species of Drosophila , a pattern that has previously been associated with sex chromoso...	Sex chromosomes are hot spots for genetic conflict , and selfish genetic elements that increase their transmission are prone to originate on sex chromosomes . Previous work has shown that genes that co-amplify on both the X and Y chromosome are involved in sex chromosome drive in mice . Here , we use bioinformatic appr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "x-linked", "traits", "experimental", "organism", "systems", "y-linked", "traits", "drosophila", "resea...	2019	Recurrent gene co-amplification on Drosophila X and Y chromosomes
In Latin America and the Caribbean , around 195 million people live in poverty , a situation that increases the burden of some infectious diseases . Neglected diseases , in particular , are often restricted to poor , marginalized sections of the population . Tools exist to combat these diseases , making it imperative t...	Neglected diseases are often restricted to poor , marginalized sections of the population . Tools exist to combat these diseases , making it imperative to work towards their elimination . In 2009 , the Pan American Health Organization received a mandate to support the countries in the Region in eliminating neglected di...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2011	Elimination of Neglected Diseases in Latin America and the Caribbean: A Mapping of Selected Diseases
The regulatory logic underlying global transcriptional programs controlling development of visceral organs like the pancreas remains undiscovered . Here , we profiled gene expression in 12 purified populations of fetal and adult pancreatic epithelial cells representing crucial progenitor cell subsets , and their endocr...	Discovery of specific pancreas developmental regulators has accelerated in recent years . In contrast , the global regulatory programs controlling pancreas development are poorly understood compared to other organs or tissues like heart or blood . Decoding this regulatory logic may accelerate development of replacement...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "expression", "analysis", "medicine", "and", "health", "sciences", "diabetic", "endocrinology", "cell", "differentiation", "dna", "transcription", "hormones", "gene", "function", "diabetes", "mellitus", "developmental", "biology", "organism", "development", "net...	2014	An Integrated Cell Purification and Genomics Strategy Reveals Multiple Regulators of Pancreas Development
The influenza A virus ( IAV ) HA protein must be activated by host cells proteases in order to prime the molecule for fusion . Consequently , the availability of activating proteases and the susceptibility of HA to protease activity represents key factors in facilitating virus infection . As such , understanding the in...	IAV is associated with significant morbidity and mortality , and represents a challenging public health threat that affects social and economic welfare each year , particularly during IAV pandemics . Although we know that all human strains derive , either directly or via intermediate hosts , from avian viral sources , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "biology", "microbiology" ]	2013	Influenza HA Subtypes Demonstrate Divergent Phenotypes for Cleavage Activation and pH of Fusion: Implications for Host Range and Adaptation
The neuronal processing of visual stimuli in primary visual cortex ( V1 ) can be modified by perceptual training . Training in bisection discrimination , for instance , changes the contextual interactions in V1 elicited by parallel lines . Before training , two parallel lines inhibit their individual V1-responses . Aft...	Neuronal models of perceptual learning often focus on the feedforward information stream extending from the primary sensory area up to the prefrontal cortex . In these models , the stimulus representation in the sensory area remains unchanged during learning while higher cortical areas adapt the read out of the relevan...	[ "Abstract", "Introduction" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2009	Adaptive Gain Modulation in V1 Explains Contextual Modifications during Bisection Learning
Ant colonies regulate activity in response to changing conditions without using centralized control . Desert harvester ant colonies forage for seeds , and regulate foraging to manage a tradeoff between spending and obtaining water . Foragers lose water while outside in the dry air , but ants obtain water by metabolizin...	We investigate the collective behavior that allows colonies of desert harvester ants to regulate foraging activity in response to environmental conditions . We develop an analytical model connecting three processes: 1 ) the interactions between foragers returning to the nest and available foragers waiting inside the ne...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "collective", "animal", "behavior", "invertebrates", "control", "theory", "ecology", "and", "environmental", "sciences", "engineering", "and", "technology", "atmospheric", "science", "social", "sciences", "animals", "simulation", "and", "modeling", "control", "engineering...	2018	Regulation of harvester ant foraging as a closed-loop excitable system
SXT is an integrative and conjugative element ( ICE ) that confers resistance to multiple antibiotics upon many clinical isolates of Vibrio cholerae . In most cells , this ∼100 Kb element is integrated into the host genome in a site-specific fashion; however , SXT can excise to form an extrachromosomal circle that is t...	Integrative and conjugative elements ( ICEs ) are a diverse group of mobile genetic elements found in many bacteria . These elements integrate into the host chromosome as well as excise and transfer to other bacteria . SXT , an ICE that encodes resistances to multiple antibiotics , is currently present in most clinical...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/gene", "discovery", "microbiology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/antimicrobials", "and", "drug", "resistance" ]	2009	A Toxin–Antitoxin System Promotes the Maintenance of an Integrative Conjugative Element
Transmissible spongiform encephalopathies ( TSEs ) are a group of neurodegenerative diseases affecting a wide range of mammalian species . They are caused by prions , a proteinaceous pathogen essentially composed of PrPSc , an abnormal isoform of the host encoded cellular prion protein PrPC . Constrained steric interac...	Prions are infectious pathogens causing irremediably fatal neurodegenerative diseases in human and in farmed or wild animals . They are formed from abnormally folded assemblies ( PrPSc ) of the host-encoded prion protein ( PrPC ) . Different PrPSc conformational variants or ‘strains’ can propagate in the same host , gi...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	Transgenic Rabbits Expressing Ovine PrP Are Susceptible to Scrapie
Eukaryotic cells can move spontaneously without being guided by external cues . For such spontaneous movements , a variety of different modes have been observed , including the amoeboid-like locomotion with protrusion of multiple pseudopods , the keratocyte-like locomotion with a widely spread lamellipodium , cell divi...	Actin is a globular protein , assembling ( polymerizing ) into filaments . This process is called actin polymerization . Cell biologists have revealed that actin polymerization plays a central role in eukaryotic cell locomotion . Stimulated by internal/external molecular signals , actin polymerization occurs just benea...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology/cell", "signaling", "biophysics/theory", "and", "simulation", "cell", "biology/cytoskeleton" ]	2009	Cortical Factor Feedback Model for Cellular Locomotion and Cytofission
The striking differences between the clinical symptoms of tetanus and botulism have been ascribed to the different fate of the parental neurotoxins once internalised in motor neurons . Tetanus toxin ( TeNT ) is known to undergo transcytosis into inhibitory interneurons and block the release of inhibitory neurotransmitt...	Botulinum neurotoxins are the most toxic molecules known to mankind , and as a result , are currently listed among the top bio-threats . However , their ability to bind specifically to neurons and their inhibitory effects on regulated secretion prompted their clinical use in pathologies characterised by increased muscu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "molecular", "neuroscience", "drugs", "and", "devices", "microbiology", "neuroscience", "toxicology", "toxic", "agents", "neurotoxicology", "motor", "systems", "drug", "information", "peripheral", "nervous", "system", "signaling", "pathways", "neurotransmitters"...	2012	Botulinum Neurotoxins A and E Undergo Retrograde Axonal Transport in Primary Motor Neurons
Cutaneous beta human papillomavirus ( HPV ) types appear to be involved in the development of non-melanoma skin cancer ( NMSC ) ; however , it is not entirely clear whether they play a direct role . We have previously shown that E6 and E7 oncoproteins from the beta HPV type 38 display transforming activities in several...	Epidemiological and biological lines of evidence support a possible involvement of a sub-group of human papillomaviruses ( HPV ) , referred to as cutaneous beta HPV types , in the development of non-melanoma skin cancer ( NMSC ) . However , their role in carcinogenesis , in particular whether they synergize with other ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "biology" ]	2011	E6 and E7 from Beta Hpv38 Cooperate with Ultraviolet Light in the Development of Actinic Keratosis-Like Lesions and Squamous Cell Carcinoma in Mice
The var gene encoded hyper-variable Plasmodium falciparum erythrocyte membrane protein 1 ( PfEMP1 ) family mediates cytoadhesion of infected erythrocytes to human endothelium . Antibodies blocking cytoadhesion are important mediators of malaria immunity acquired by endemic populations . The development of a PfEMP1 base...	About one million African children die from malaria every year . The severity of malaria infections in part depends on which type of the parasitic protein PfEMP1 is expressed on the surface of the infected red blood cells . Natural immunity to malaria is mediated through antibodies to PfEMP1 . Therefore hopes for a mal...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "molecular", "biology/recombination", "infectious", "diseases/protozoal", "infections", "cell", "biology/cell", "adhesion", "genetics", "and", "genomics" ]	2010	Plasmodium falciparum Erythrocyte Membrane Protein 1 Diversity in Seven Genomes – Divide and Conquer
Mosaic Variegated Aneuploidy ( MVA ) syndrome is a rare autosomal recessive disorder characterized by inaccurate chromosome segregation and high rates of near-diploid aneuploidy . Children with MVA syndrome die at an early age , are cancer prone , and have progeroid features like facial dysmorphisms , short stature , a...	Aging is the main risk factor for the majority of chronic diseases and the leading cause of death and disability in humans . Humans age at different rates , but the molecular genetic basis underlying this phenomenon remains largely unknown . Efforts to understand how we age have focused on genetic changes that extend l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "aging", "public", "health", "and", "epidemiology", "model", "organisms", "genetics", "population", "genetics", "biology", "population", "biology", "genetics", "and", "genomics" ]	2012	Reduced Life- and Healthspan in Mice Carrying a Mono-Allelic BubR1 MVA Mutation

Subsets and Splits

No community queries yet

The top public SQL queries from the community will appear here once available.