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The helminth Strongyloides stercoralis , which is transmitted through soil , infects 30–100 million people worldwide . S . stercoralis reproduces sexually outside the host as well as asexually within the host , which causes a life-long infection . To understand the population structure and transmission patterns of this...	Strongyloides stercoralis , one of the most neglected helminths causes strongyloidiasis mainly in tropical and subtropical regions worldwide . The parasite’s complex lifecycle includes sexual and asexual reproduction outside and inside the host , respectively . The parasite can also asexually complete a life cycle with...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "heterozygosity", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "parasitic", "diseases", "animals", "invertebrate", "genomics", "parasitology", "developmental", "biology", "phylogenetic", ...	2016	Genome-Wide Analyses of Individual Strongyloides stercoralis (Nematoda: Rhabditoidea) Provide Insights into Population Structure and Reproductive Life Cycles
Control of Aedes aegypti , the mosquito vector of dengue , chikungunya and yellow fever , is a challenging task . Pyrethroid insecticides have emerged as a preferred choice for vector control but are threatened by the emergence of resistance . The present study reports a focus of pyrethroid resistance and presence of t...	Dengue and chikungunya are the two important human arboviral infections in India transmitted mainly by Aedes aegypti . In absence of any specific drug or vaccine for these infections , vector control and personal protection are the only control options available . The success of insecticide-based vector control heavily...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2015	Pyrethroid-Resistance and Presence of Two Knockdown Resistance (kdr) Mutations, F1534C and a Novel Mutation T1520I, in Indian Aedes aegypti
Chagas disease has historically been hyperendemic in the Bolivian Department of Cochabamba . In the early 2000s , an extensive vector control program was implemented; 1 . 34 million dwelling inspections were conducted to ascertain infestation ( 2000–2001/2003–2011 ) , with blanket insecticide spraying in 2003–2005 and ...	Chagas disease is among the most serious public health problems in Latin America; the highest prevalence of infection by its causative agent , the parasite Trypanosoma cruzi , has historically been recorded in some parts of Bolivia . In the early 2000s , a massive insecticide-spraying program was set up to control dwel...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "infectious", "diseases", "medicine", "and", "health", "sciences", "disease", "ecology", "chagas", "disease", "infectious", "disease", "epidemiology", "epidemiology", "neglected", "tropical", "diseases", "tropical", "diseases", ...	2014	Chagas Disease Vector Control in a Hyperendemic Setting: The First 11 Years of Intervention in Cochabamba, Bolivia
In long-term potentiation ( LTP ) , one of the most studied types of neural plasticity , synaptic strength is persistently increased in response to stimulation . Although a number of different proteins have been implicated in the sub-cellular molecular processes underlying induction and maintenance of LTP , the precise...	The brain stores memories by adjusting the strengths of connections between neurons , a phenomenon known as synaptic plasticity . Different types of plasticity mechanisms have either a strengthening or a weakening effect and produce synaptic modifications that last from milliseconds to months or more . One of the most ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "nervous", "system", "enzymes", "messenger", "rna", "cell", "processes", "enzymology", "electrophysiology", "neuroscience", "learning", "and", "memory", "protein", "synthesis", "cognition", "memory", "enzyme", "inhibitors", "chem...	2018	Coupled feedback loops maintain synaptic long-term potentiation: A computational model of PKMzeta synthesis and AMPA receptor trafficking
The human immunodeficiency virus type 1 ( HIV-1 ) envelope glycoprotein gp120 is a vaccine immunogen that can signal via several cell surface receptors . To investigate whether receptor biology could influence immune responses to gp120 , we studied its interaction with human , monocyte-derived dendritic cells ( MDDCs )...	Dendritic cells ( DCs ) initiate immune responses to pathogens or vaccine antigens . The HIV-1 gp120 envelope glycoprotein is an antigen that is a focus of vaccine design strategies . We have studied how gp120 proteins interact with DCs in cell culture . Certain gp120s stimulate DCs from some , but not all , human dono...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "virology" ]	2007	HIV-1 gp120 Mannoses Induce Immunosuppressive Responses from Dendritic Cells
Urinary tract infections are the second most common infectious disease in humans and are predominantly caused by uropathogenic E . coli ( UPEC ) . A majority of UPEC isolates express the type 1 pilus adhesin , FimH , and cell culture and murine studies demonstrate that FimH is involved in invasion and apoptosis of urot...	Urinary tract infections ( UTI ) are the second most common infectious disease in humans and are predominantly caused by uropathogenic E . coli ( UPEC ) . In vitro and in vivo studies have demonstrated that UPEC induce several responses in the bladder , including inflammation , rapid onset of bladder cell death , and b...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/urological", "infections", "urology/urological", "infections", "cell", "biology/cell", "signaling", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenes...	2009	Bacteria-Induced Uroplakin Signaling Mediates Bladder Response to Infection
HMG-box proteins , including Sox/SRY ( Sox ) and TCF/LEF1 ( TCF ) family members , bind DNA via their HMG-box . This binding , however , is relatively weak and both Sox and TCF factors employ distinct mechanisms for enhancing their affinity and specificity for DNA . Here we report that Capicua ( CIC ) , an HMG-box tran...	Transcription factors bind specific sites in the genome via discrete protein domains that recognize their target DNA sequences . One such domain is the HMG-box , which is found in many chromatin and transcriptional regulators across species . Two salient groups of HMG-box proteins are the Sox/SRY and TCF/LEF1 factors ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "chemical", "characterization", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "animals", "animal", "models", "developmental", "biology", "mutation", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", ...	2017	A new mode of DNA binding distinguishes Capicua from other HMG-box factors and explains its mutation patterns in cancer
In this study the function of the two isoforms of creatine kinase ( CK; EC 2 . 7 . 3 . 2 ) in myocardium is investigated . The ‘phosphocreatine shuttle’ hypothesis states that mitochondrial and cytosolic CK plays a pivotal role in the transport of high-energy phosphate ( HEP ) groups from mitochondria to myofibrils in ...	Creatine kinase ( CK ) has several functions in cellular energy metabolism . It catalyzes the reversible transfer of high-energy phosphate from ATP to creatine , facilitating storage of energy in the form of phosphocreatine . In muscle cells , this extra energy buffer plays a pivotal role in maintaining ATP homeostasis...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "systems", "biology", "computer", "science", "biology", "computational", "biology", "computerized", "simulations", "genetics", "and", "genomics" ]	2011	Analyzing the Functional Properties of the Creatine Kinase System with Multiscale ‘Sloppy’ Modeling
New safe and effective treatments for Chagas disease ( CD ) are urgently needed . Current chemotherapy options for CD have significant limitations , including failure to uniformly achieve parasitological cure or prevent the chronic phase of CD , and safety and tolerability concerns . Fexinidazole , a 2-subsituted 5-nit...	This study describes the in vivo activity of fexinidazole against Trypanosoma cruzi , the protozoan parasite causing Chagas disease , using mice infected with parasite strains with varying susceptibility to benznidazole , the standard treatment for Chagas . Fexinidazole and benznidazole were shown to have similar activ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "histology", "infectious", "diseases", "drugs", "and", "devices", "biology" ]	2012	Fexinidazole: A Potential New Drug Candidate for Chagas Disease
Survival of Borrelia burgdorferi in ticks and mammals is facilitated , at least in part , by the selective expression of lipoproteins . Outer surface protein ( Osp ) A participates in spirochete adherence to the tick gut . As ospB is expressed on a bicistronic operon with ospA , we have now investigated the role of Osp...	Lyme disease is the most common vector-borne disease in North America and Europe . The causative agent Borrelia burgdorferi is a bacterium that is maintained in an enzoonotic cycle between Ixodes ticks and a large range of mammals . Accidental encounters of infected Ixodes ticks with humans results in the transmission ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "infectious", "diseases", "arthropods", "microbiology", "mus", "(mouse)", "eubacteria" ]	2007	Outer Surface Protein B Is Critical for Borrelia burgdorferi Adherence and Survival within Ixodes Ticks
Beneficial microbial symbionts serve important functions within their hosts , including dietary supplementation and maintenance of immune system homeostasis . Little is known about the mechanisms that enable these bacteria to induce specific host phenotypes during development and into adulthood . Here we used the tsets...	Beneficial bacterial symbionts , which are ubiquitous in nature , are often characterized by the extent to which they interact with the host . In the case of mutualistic symbioses , both partners benefit so that each one can inhabit diverse ecological niches where neither could survive on its own . Unfortunately , litt...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/innate", "immunity", "microbiology/immunity", "to", "infections" ]	2011	Tsetse Immune System Maturation Requires the Presence of Obligate Symbionts in Larvae
Complex cutaneous and muco-cutaneous leishmaniasis ( CL and MCL ) often requires systemic therapy . Liposomal amphotericin B ( L-AmB ) has a strong potential for a solid clinical benefit in this indication . We conducted a retrospective analysis of data from a French centralized referral treatment program and from the ...	Cutaneous and muco-cutaneous leishmaniasis ( CL/MCL ) are disfiguring diseases caused by a worldwide distributed parasite called Leishmania and its 20 species . Clinical manifestations span a wide continuum from single nodular lesion to disseminated form with mucosal involvement . Though local treatment with cryotherap...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "clinical", "research", "design", "drugs", "tropical", "diseases", "microbiology", "antifungals", "parasitic", "diseases", "parasitic", "protozoans", "physiological", ...	2017	Liposomal amphotericin B in travelers with cutaneous and muco-cutaneous leishmaniasis: Not a panacea
Brain anatomy and physiology support the human ability to navigate a complex space of perceptions and actions . To maneuver across an ever-changing landscape of mental states , the brain invokes cognitive control—a set of dynamic processes that engage and disengage different groups of brain regions to modulate attentio...	Brain networks support the human ability to navigate a complex space of perceptions and actions through cognitive control . Here we ask , “How do brain networks coordinate task-relevant information as individuals adapt to cognitive demands imposed by a task ? ” We study the fMRI BOLD signal of twenty-eight healthy subj...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "reaction", "time", "social", "sciences", "neuroscience", "magnetic", "resonance", "imaging", "perception", "cognitive", "neuroscien...	2018	Subgraphs of functional brain networks identify dynamical constraints of cognitive control
Along the transformation process , cells accumulate DNA aberrations , including mutations , translocations , amplifications , and deletions . Despite numerous studies , the overall effects of amplifications and deletions on the end point of gene expression—the level of proteins—is generally unknown . Here we use large-...	In the course of cancer development , cells lose regulation of the cell cycle and quality control of DNA replication . As a result , many genomic alterations accumulate , among them amplifications and deletions of chromosomal regions of varying sizes . Oncogenes that drive transformation often reside in amplified regio...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "oncology", "oncology/breast", "cancer", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/chromosome", "biology", "biochemistry/bioinformatics", "biochemistry/macromolecular", "assemblies", "and", "machines", ...	2010	Proteomic Changes Resulting from Gene Copy Number Variations in Cancer Cells
Canonical Wnt signaling plays a rate-limiting role in regulating self-renewal and differentiation in mouse embryonic stem cells ( ESCs ) . We have previously shown that mutation in the Apc ( adenomatous polyposis coli ) tumor suppressor gene constitutively activates Wnt signaling in ESCs and inhibits their capacity to ...	The future successes of regenerative medicine largely rely on our knowledge of , and our capacity to manipulate , the cellular and molecular mechanisms governing stem cell differentiation . A growing body of evidence suggests that , in mouse embryonic stem cells , canonical Wnt/β-catenin signaling not only enhances sel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "networks", "rna", "interference", "histone", "modification", "gene", "function", "stem", "cells", "epigenetics", "cell", "potency", "embryonic", "stem", "cells", "gene", "expression", "biology", "dna", "modification", "rna", "signal", "transduction", "rna", ...	2013	Wnt Signaling Regulates the Lineage Differentiation Potential of Mouse Embryonic Stem Cells through Tcf3 Down-Regulation
Defective-Interfering RNAs ( DI-RNAs ) have long been known to play an important role in virus replication and transmission . DI-RNAs emerge during virus passaging in both cell-culture and their hosts as a result of non-homologous RNA recombination . However , the principles of DI-RNA emergence and their subsequent evo...	Defective RNAs are versions of a viral genome that arise naturally during viral infections but have been truncated or rearranged by non-homologous recombination . While not encoding for functional viruses , they can be amplified and co-passaged with the wild-type virus , effectively parasitizing the normal viral machin...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "organismal", "evolution", "microbiology", "invertebrate", "genomics", "viruses", "rna", "viruses", "genome", "analysis", "microbial", "evolution", "molecular", "biology", "techniques", "nucleotide", "mapping", "rna", "sequencing", "microbial", ...	2017	Parallel ClickSeq and Nanopore sequencing elucidates the rapid evolution of defective-interfering RNAs in Flock House virus
Genome-wide association studies ( GWAS ) examine a large number of markers across the genome to identify associations between genetic variants and disease . Most published studies examine only single markers , which may be less informative than considering multiple markers and multiple genes jointly because genes may i...	Statistical methods used in most GWAS are based on the analysis of single markers . Prior biological information about markers , genes , and pathways is not commonly incorporated in the detection of associated disease loci . Recently a number of methods have been developed to incorporate such information , and it has b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mathematics/statistics", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics" ]	2011	Incorporating Biological Pathways via a Markov Random Field Model in Genome-Wide Association Studies
Small mammals serve as most important reservoirs for Leptospira spp . , the causative agents of Leptospirosis , which is one of the most neglected and widespread zoonotic diseases worldwide . The knowledge about Leptospira spp . occurring in small mammals from Germany is scarce . Thus , this study’s objectives were to ...	Leptospirosis is one of the most widespread zoonotic diseases and is caused by Leptospira spp . Small mammals often serve as maintenance hosts . We evaluated host-pathogen relations for Leptospira species and sequence types in different small mammal species captured at three German study sites . Leptospira spp . was de...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "tropical", "diseases", "animals", "mammals", "bacterial", "diseases", "neglected", "tropical", "d...	2016	Prevalence and Genotype Allocation of Pathogenic Leptospira Species in Small Mammals from Various Habitat Types in Germany
Plasmodium and soil transmitted helminth infections ( STH ) are a major public health problem , particularly among children . There are conflicting findings on potential association between these two parasites . This study investigated the Plasmodium and helminth co-infections among children aged 2 months to 9 years li...	Parasitic infectious agents rarely occur in isolation and multiparasitism is a norm specifically in children living in endemic areas of Tanzania . We studied the pattern and predictors of Plasmodium and STH co-infections in rural Bagamoyo district , coastal region of Tanzania . Parents/guardians of healthy children age...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Distribution and Risk Factors for Plasmodium and Helminth Co-infections: A Cross-Sectional Survey among Children in Bagamoyo District, Coastal Region of Tanzania
Type IV pilus ( T4P ) systems are complex molecular machines that polymerize major pilin proteins into thin filaments displayed on bacterial surfaces . Pilus functions require rapid extension and depolymerization of the pilus , powered by the assembly and retraction ATPases , respectively . A set of low abundance minor...	Bacterial pathogens utilize a number of highly complex and sophisticated molecular systems to colonize their hosts and alter them , creating customized niches in which to reproduce . One such system is the Type IV pilus system , made up of dozens of proteins that form a macromolecular machine to polymerize small pilin ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "vibrio", "biological", "cultures", "microbiology", "immunoblotting", "enzymology", "neisseria", "gonorrhoeae", "pili", "and"...	2016	The Vibrio cholerae Minor Pilin TcpB Initiates Assembly and Retraction of the Toxin-Coregulated Pilus
Most bacteria contain both eukaryotic-like Ser/Thr kinases ( eSTKs ) and eukaryotic-like Ser/Thr phosphatases ( eSTPs ) . Their role in bacterial physiology is not currently well understood in large part because the conditions where the eSTKs are active are generally not known . However , all sequenced Gram-positive ba...	A central question in bacterial physiology is how bacteria sense and respond to their environment . The archetype of bacterial signaling systems is the two-component signaling system composed of a sensor protein histidine kinase that activates a transcription factor response regulator in response to a specific signal ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Eukaryotic-Like Ser/Thr Kinase PrkC Regulates the Essential WalRK Two-Component System in Bacillus subtilis
Vibrio parahaemolyticus is a foodborne pathogen that has become a public health concern at the global scale . The epidemiological significance of V . parahaemolyticus infections in Latin America received little attention until the winter of 1997 when cases related to the pandemic clone were detected in the region , cha...	Infections caused by Vibrio parahaemolyticus have increased significantly over the last two decades , with cases now regularly reported globally . The emergence of cholera at global scale has brought the attention toward other Vibrio diseases in developing countries . This was the situation in Peru , where the investig...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "molecular", "epidemiology", "infectious", "disease", "epidemiology", "microbial", "evolution", "epidemiology", "microbial", "pathogens", "biology", "microbiology" ]	2013	Molecular Epidemiology and Genetic Variation of Pathogenic Vibrio parahaemolyticus in Peru
Using the genomic sequences of Drosophila melanogaster subgroup , the pattern of gene duplications was investigated with special attention to interlocus gene conversion . Our fine-scale analysis with careful visual inspections enabled accurate identification of a number of duplicated blocks ( genomic regions ) . The or...	Eukaryote genomes have a number of duplicated genes , which could potentially coevolve by exchanging DNA sequences by interlocus gene conversion . However , the extent of gene conversion on a genomic scale is not well understood , except that an extensive role of gene conversion was reported in yeast . Here , we show a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2008	Duplication and Gene Conversion in the Drosophila melanogaster Genome
Lipopolysaccharide ( LPS ) is a major component on the surface of Gram negative bacteria and is composed of lipid A-core and the O antigen polysaccharide . O polysaccharides of the gastric pathogen Helicobacter pylori contain Lewis antigens , mimicking glycan structures produced by human cells . The interaction of Lewi...	Bacterial surfaces are decorated with glycans . The human stomach pathogen Helicobacter pylori exposes lipopolysaccharide ( LPS ) containing Lewis antigens that mimic human glycan structures . H . pylori alters its Lewis antigen display in adaptation to the individual host . Lewis antigens can interact with human dendr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "biochemistry/macromolecular", "assemblies", "and", "machines", "microbiology", "infectious", "diseases/bacterial", "infections", "microbiology/cellular", "microbiology", "and", "pathogenesis", "infectious", "d...	2010	Helicobacter pylori Lipopolysaccharide Is Synthesized via a Novel Pathway with an Evolutionary Connection to Protein N-Glycosylation
Lyme disease in humans is caused by several genospecies of the Borrelia burgdorferi sensu lato ( s . l . ) complex of spirochetal bacteria , including B . burgdorferi , B . afzelii and B . garinii . These bacteria exist in nature as obligate parasites in an enzootic cycle between small vertebrate hosts and Ixodid tick ...	Lyme disease is a tick-borne infection of humans that is caused by a spirochetal bacterium called Borrelia burgdorferi . It is a zoonosis , which means that these bacteria exist in nature outside of people . Many different strains of B . burgdorferi are stably maintained in the same local population of infected wild an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "borrelia", "infection", "rheumatology", "medicine", "and", "health", "sciences", "immune", "physiology", "ixodes", "pathology", "and", "laboratory", "medicine", "body", "fluids", "enzyme-linked", "immunoassays", "pathogens", "immunology", "microbiology", ...	2018	Infection history of the blood-meal host dictates pathogenic potential of the Lyme disease spirochete within the feeding tick vector
Alternative splicing of genes is an efficient means of generating variation in protein function . Several disease states have been associated with rare genetic variants that affect splicing patterns . Conversely , splicing efficiency of some genes is known to vary between individuals without apparent ill effects . What...	Genetic variation , through its effects on gene expression , influences many aspects of the human phenotype . Understanding the impact of genetic variation on human disease risk has become a major goal for biomedical research and has the potential of revealing both novel disease mechanisms and novel functional elements...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "homo", "(human)", "genetics", "and", "genomics" ]	2007	Identification of Common Genetic Variation That Modulates Alternative Splicing
The RNase III enzyme DICER generates both microRNAs ( miRNAs ) and endogenous short interfering RNAs ( endo-siRNAs ) . Both small RNA species silence gene expression post-transcriptionally in association with the ARGONAUTE ( AGO ) family of proteins . In mammals , there are four AGO proteins ( AGO1-4 ) , of which only ...	In animals , the three main classes of small RNAs are microRNAs , short interfering RNAs , and PIWI-interacting RNAs . All three RNA species silence gene expression post-transcriptionally through interaction with the ARGONAUTE family of proteins . In mammals in particular , microRNAs are ubiquitously expressed , are es...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Essential Role for Endogenous siRNAs during Meiosis in Mouse Oocytes
Modulation of host DNA synthesis is essential for many viruses to establish productive infections and contributes to viral diseases . Human cytomegalovirus ( HCMV ) , a large DNA virus , blocks host DNA synthesis and deregulates cell cycle progression . We report that pUL117 , a viral protein that we recently identifie...	Inhibition of host DNA synthesis is pivotal for many viruses to establish productive infection and cause disease . Human cytomegalovirus ( HCMV ) is the top viral cause of birth defects in newborns and leads to life-threatening diseases in individuals with compromised immunity . HCMV blocks host DNA synthesis and creat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "virology/viral", "replication", "and", "gene", "regulation", "virology/effects", "of", "virus", "infection", "on", "host", "gene", "expression", "virology" ]	2010	Human Cytomegalovirus Protein pUL117 Targets the Mini-Chromosome Maintenance Complex and Suppresses Cellular DNA Synthesis
Typical bacterial strain differentiation methods are often challenged by high genetic similarity between strains . To address this problem , we introduce a novel in silico peptide fingerprinting method based on conventional wet-lab protocols that enables the identification of potential strain-specific peptides . These ...	Molecular based differentiation of bacterial species is important in phylogenetic studies , diagnostics and epidemiological surveillance , particularly where unusual phenotype makes the classical phenotypic identification of bacteria difficult . Typical bacterial differentiation methods are often challenged by a high g...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "pathogens", "bacillus", "microbiology", "phylogenetics", "data", "management", "phylogenetic", "analysis", "genome", "analysis", "molecular", "bi...	2016	Improving Phylogeny Reconstruction at the Strain Level Using Peptidome Datasets
Mouse Embryonic Stem ( ES ) cells express a unique set of microRNAs ( miRNAs ) , the miR-290-295 cluster . To elucidate the role of these miRNAs and how they integrate into the ES cell regulatory network requires identification of their direct regulatory targets . The difficulty , however , arises from the limited comp...	Stem cells in plants and animals contain many small RNAs , which help to regulate differentiation into diverse cell types . Mutation in a gene necessary for the maturation of small RNAs in plants causes the stem cells ( called meristem cells ) to remain in an indeterminate , overproliferating state . Similarly in worms...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "developmental", "biology/stem", "cells", "molecular", "biology", "genetics", "and", "genomics", "cell", "biology/gene", "expression" ]	2010	Genome-Wide Identification of Targets and Function of Individual MicroRNAs in Mouse Embryonic Stem Cells
The checkpoint kinases ATM and ATR are redundantly required for maintenance of stable telomeres in diverse organisms , including budding and fission yeasts , Arabidopsis , Drosophila , and mammals . However , the molecular basis for telomere instability in cells lacking ATM and ATR has not yet been elucidated fully in ...	Stable maintenance of telomeres is critical to preserve genomic integrity and to prevent accumulation of undesired mutations that might lead to formation of tumor cells . Fission yeast cells serve as a particularly attractive model system to study telomere maintenance mechanisms , since proteins critical for telomere m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "replication", "molecular", "biology/recombination", "molecular", "biology/chromosome", "structure", "molecular", "biology/dna", "repair" ]	2009	Fission Yeast Tel1ATM and Rad3ATR Promote Telomere Protection and Telomerase Recruitment
Leptospirosis occurs worldwide , but the global incidence of human disease and its mortality are not well understood . Many patients are undiagnosed and untreated due to its non-specific symptoms and a lack of access to diagnostics . This study systematically reviews the literature to clarify the mortality from untreat...	Leptospirosis is a common cause of fever in the developing world but often goes undiagnosed and untreated due to its non-specific clinical features and the limited availability of point-of-care diagnostics . This review systematically evaluated available literature to clarify the mortality from untreated leptospirosis ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	A Systematic Review of the Mortality from Untreated Leptospirosis
To understand the molecular basis of how hosts evolve resistance to their parasites , we have investigated the genes that cause variation in the susceptibility of Drosophila melanogaster to viral infection . Using a host-specific pathogen of D . melanogaster called the sigma virus ( Rhabdoviridae ) , we mapped a major-...	Though much is known about host–parasite coevolution in plants , relatively little is understood in animals . Most studies using animal systems have focused on either generalist parasites or those that do not naturally occur in the host . The sigma virus is specific to Drosophila melanogaster , which provides the uniqu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "immunity", "to", "infections", "population", "genetics", "immunology", "gene", "function", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "coevolution", "immune", "defense", "molecular", "genetics", "forms", "of", "evoluti...	2011	Successive Increases in the Resistance of Drosophila to Viral Infection through a Transposon Insertion Followed by a Duplication
Flavivirus nonstructural protein 5 ( NS5 ) consists of methyltransferase ( MTase ) and RNA-dependent RNA polymerase ( RdRp ) domains , which catalyze 5’-RNA capping/methylation and RNA synthesis , respectively , during viral genome replication . Although the crystal structure of flavivirus NS5 is known , no data about ...	Many plus-strand RNA viruses encode a viral RNA polymerase and capping enzymes to synthesize a 5’-capped RNA genome . However , how these two activities are coordinated during viral replication is not understood . In flaviviruses , polymerase and capping enzymes are encoded in a single multifunctional protein , where s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "crystal", "structure", "condensed", "matter", "physics", "microbiology", "dna-binding", "proteins", "viral", "structure", "limbs", "(anatomy)", "thumbs", "crystals", "polymerases", "materials", "s...	2016	Dengue Virus Nonstructural Protein 5 (NS5) Assembles into a Dimer with a Unique Methyltransferase and Polymerase Interface
The polymeric mucin component of the intestinal mucus barrier changes during nematode infection to provide not only physical protection but also to directly affect pathogenic nematodes and aid expulsion . Despite this , the direct interaction of the nematodes with the mucins and the mucus barrier has not previously bee...	Gastrointestinal parasitic worm infections cause significant morbidity , affecting up to a third of the world's populationand their domestic pets and livestock . Mucus , the gel-like material that blankets the surface of the intestine , forms a protective barrier that is an important part of our innate immune system . ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "immunity", "immune", "defense", "immunology", "biology", "immunity", "to", "infections" ]	2012	Serine Protease(s) Secreted by the Nematode Trichuris muris Degrade the Mucus Barrier
Despite advances in experimental techniques and accumulation of large datasets concerning the composition and properties of the cortex , quantitative modeling of cortical circuits under in-vivo-like conditions remains challenging . Here we report and publicly release a biophysically detailed circuit model of layer 4 in...	How can we capture the incredible complexity of brain circuits in quantitative models , and what can such models teach us about mechanisms underlying brain activity ? To answer these questions , we set out to build extensive , bio-realistic models of brain circuitry by employing systematic datasets on brain structure a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "optogenetics", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "simulation", "and", "modeling", "brain", "mapping", "bioassays", "and", "physiological", "analysis", "neuro...	2018	Visual physiology of the layer 4 cortical circuit in silico
Influenza A virus ( IAV ) is a seasonal pathogen with the potential to cause devastating pandemics . IAV infects multiple epithelial cell subsets in the respiratory tract , eliciting damage to the lungs . Clearance of IAV is primarily dependent on CD8+ T cells , which must balance control of the infection with immunopa...	Influenza A virus is a seasonal respiratory pathogen that can cause severe lung damage and death . We previously made the discovery that cells infected with influenza virus do not have a death sentence . An infected cell can survive both influenza virus infection and the immune response to eliminate the virus , specifi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "cell", "cycle", "and", "cell", "division", "immunology", "cell", "processes", "microbiology", "cloning", "o...	2019	Long-term surviving influenza infected cells evade CD8+ T cell mediated clearance
The interplay between polycomb and trithorax complexes has been implicated in embryonic stem cell ( ESC ) self-renewal and differentiation . It has been shown recently that WRD5 and Dpy-30 , specific components of the SET1/MLL protein complexes , play important roles during ESC self-renewal and differentiation of neura...	Embryonic stem cells ( ESCs ) are capable of differentiating into any type of cell or tissue of the body . It is important to understand how developmental genes are controlled during differentiation of ESCs into specific cell types . The hSET1/MLL histone modifying protein complexes add methyl groups to lysine 4 on the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "hematopoiesis", "gene", "expression", "genetics", "epigenetics", "biology", "hematology", "gene", "function" ]	2013	USF1 and hSET1A Mediated Epigenetic Modifications Regulate Lineage Differentiation and HoxB4 Transcription
Insertions and deletions ( indels ) cause numerous genetic diseases and lead to pronounced evolutionary differences among genomes . The macaque sequences provide an opportunity to gain insights into the mechanisms generating these mutations on a genome-wide scale by establishing the polarity of indels occurring in the ...	Insertions and deletions ( indels ) represent a significant source of evolutionary change . In this manuscript , the authors investigate the patterns of genome-wide rate variation for indels that occurred in the human lineage since its divergence from chimpanzee . Earlier work suggested that insertion and deletion rate...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "computational", "biology" ]	2007	A Macaque's-Eye View of Human Insertions and Deletions: Differences in Mechanisms
Polyglutamine expansion causes diseases in humans and other mammals . One example is Huntington's disease . Fragments of human huntingtin protein having an expanded polyglutamine stretch form aggregates and cause cytotoxicity in yeast cells bearing endogenous QN-rich proteins in the aggregated ( prion ) form . Attachme...	Polyglutamine diseases , including Huntington disease , are associated with expansions of polyglutamine tracts , resulting in aggregation of respective proteins . The severity of Huntington disease is controlled by both DNA and non–DNA factors . Mechanisms of such a control are poorly understood . Polyglutamine may seq...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Polyglutamine Toxicity Is Controlled by Prion Composition and Gene Dosage in Yeast
Lymphatic filariasis ( LF ) and human immunodeficiency virus ( HIV ) are major public health problems . Individuals may be co-infected , raising the possibility of important interactions between these two pathogens with consequences for LF elimination through annual mass drug administration ( MDA ) . We analysed circul...	Lymphatic filariasis ( LF ) and HIV are both major public health problems worldwide and where they co-exist have the potential to interact . The main strategy for LF elimination is annual mass drug administration ( MDA ) . A particular concern is whether HIV , through its impact on the immune system , will interfere wi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Human Immunodeficiency Virus, Antiretroviral Therapy and Markers of Lymphatic Filariasis Infection: A Cross-sectional Study in Rural Northern Malawi
Strongyloides stercoralis is a worldwide disseminated parasitic disease that can be transmitted from solid organ transplant ( SOT ) donors to recipients . We determined the serological prevalence of S . stercoralis among deceased individuals from endemic areas considered for SOT donation , using our institution’s serum...	Strongyloidiasis is a neglected tropical disease caused by a parasite which is endemic in most parts of the world . It can cause a life-threatening disease among immunosuppressed individuals and can be transmitted from solid organ transplant donors to recipients . We retrospectively investigated the prevalence of stron...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "organ", "transplantation", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "surgical", "and", "invasive", "medical", "procedures", ...	2018	High seroprevalence of Strongyloides stercoralis among individuals from endemic areas considered for solid organ transplant donation: A retrospective serum-bank based study
Dicer ribonucleases of plants and invertebrate animals including Caenorhabditis elegans recognize and process a viral RNA trigger into virus-derived small interfering RNAs ( siRNAs ) to guide specific viral immunity by Argonaute-dependent RNA interference ( RNAi ) . C . elegans also encodes three Dicer-related helicase...	The genome of Caenorhabditis elegans encodes three Dicer-related helicases ( DRHs ) highly homologous to the DExD/H box helicase domain found in two distinct families of virus sensors , Dicer ribonucleases and RIG-I-like helicases ( RLRs ) . Dicer initiates the specific , RNAi-mediated viral immunity in plants , fungi ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/host", "antiviral", "responses", "immunology/innate", "immunity" ]	2009	An RIG-I-Like RNA Helicase Mediates Antiviral RNAi Downstream of Viral siRNA Biogenesis in Caenorhabditis elegans
Recent years have seen progress in the development of statistically rigorous frameworks to infer outbreak transmission trees ( “who infected whom” ) from epidemiological and genetic data . Making use of pathogen genome sequences in such analyses remains a challenge , however , with a variety of heuristic approaches hav...	Understanding how infectious diseases are transmitted from one individual to another is essential for designing containment strategies and epidemic prevention . Recently , the reconstruction of transmission trees ( “who infected whom” ) has been revolutionized by the availability of pathogen genome sequences . Exploiti...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "mathematics", "epidemiology", "statistics", "statistical", "methods", "biostatistics", "biology", "computational", "biology" ]	2014	Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
In mammalian meiotic prophase , the initial steps in repair of SPO11-induced DNA double-strand breaks ( DSBs ) are required to obtain stable homologous chromosome pairing and synapsis . The X and Y chromosomes pair and synapse only in the short pseudo-autosomal regions . The rest of the chromatin of the sex chromosomes...	Meiosis is a special cell division that generates genetically divergent haploid germ cells . At the very beginning of this process , during meiotic prophase , the enzyme SPO11 generates hundreds of DNA double-strand breaks ( DSBs ) . Meiotic DSBs are repaired via a mechanism that requires the presence of an intact homo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "chromosome", "biology", "nucleic", "acids", "gene", "expression", "dna", "dna", "repair", "biology", "genomics", "molecular", "cell", "biology", "dna", "transcription" ]	2013	SPO11-Independent DNA Repair Foci and Their Role in Meiotic Silencing
The vertebrate adaptive immune system provides a flexible and diverse set of molecules to neutralize pathogens . Yet , viruses such as HIV can cause chronic infections by evolving as quickly as the adaptive immune system , forming an evolutionary arms race . Here we introduce a mathematical framework to study the coevo...	We normally think of evolution occurring in a population of organisms , in response to their external environment . Rapid evolution of cellular populations also occurs within our bodies when the adaptive immune system works to eliminate infections . Some viruses , such as HIV , are able to evolve as quickly as our immu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "organismal", "evolution", "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "population", "genetics", "microbiolog...	2016	Host-Pathogen Coevolution and the Emergence of Broadly Neutralizing Antibodies in Chronic Infections
Different biomolecules have been identified in bacterial pathogens that sense changes in temperature and trigger expression of virulence programs upon host entry . However , the dynamics and quantitative outcome of this response in individual cells of a population , and how this influences pathogenicity are unknown . H...	The ability of pathogens to sense temperature changes when they enter their mammalian hosts from the environment is crucial to optimize their fitness and adjust expression of their virulence programs . Until now it has been assumed that all cells within a population participate in the thermo-triggered adaptive response...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "flow", "cytometry", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "light", "microscopy", "plasmid", "construction", "microscopy", "yersinia", "lymphatic", "system", "dna", "cons...	2016	A Precise Temperature-Responsive Bistable Switch Controlling Yersinia Virulence
In addition to the previously characterized viruses BK and JC , three new human polyomaviruses ( Pys ) have been recently identified: KIV , WUV , and Merkel Cell Py ( MCV ) . Using an ELISA employing recombinant VP1 capsid proteins , we have determined the seroprevalence of KIV , WUV , and MCV , along with BKV and JCV ...	Polyomaviruses occupy a replicative niche in animals from birds to humans . Two human polyomaviruses , BKV and JCV , were discovered in 1971 and within the last two years , three new polyomaviruses have been found in humans: KI ( KIV ) , WU ( WUV ) , and Merkel Cell ( MCV ) polyomavirus . MCV was identified in Merkel C...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/viruses", "and", "cancer", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases", "virology" ]	2009	Seroepidemiology of Human Polyomaviruses
Existing theory of host-parasite interactions has identified the genetic specificity of interaction as a key variable affecting the outcome of coevolution . The Matching Alleles ( MA ) and Gene For Gene ( GFG ) models have been extensively studied as the canonical examples of specific and non-specific interaction . The...	Coevolution between hosts and parasites is believed to be central to a number of biological phenomena , most notably the observed patterns of biodiversity and the origins of sexual reproduction . However , classical mathematical models of host-parasite coevolution account neither for the hosts' use of bacterial symbion...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "community", "ecology", "evolutionary", "ecology", "coevolution", "ecology", "evolutionary", "biology", "theoretical", "biology", "evolutionary", "modeling", "evolutionary", "immunology", "biology", "computational", "biology", "species", "interactions", "evolutionary", "proce...	2012	On Genetic Specificity in Symbiont-Mediated Host-Parasite Coevolution
The Ty1 retrotransposons present in the genome of Saccharomyces cerevisiae belong to the large class of mobile genetic elements that replicate via an RNA intermediary and constitute a significant portion of most eukaryotic genomes . The retromobility of Ty1 is regulated by numerous host factors , including several subu...	Retrotransposons are mobile genetic elements that copy their RNA genomes into DNA and insert the DNA copies into the host genome . These elements contribute to genome instability , control of host gene expression and adaptation to changing environments . Retrotransposons depend on numerous host factors for their own pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "deletion", "mutation", "nucleic", "acid", "synthesis", "retrotransposons", "chemical", "compounds", "carbohydrates", "organic", "compounds", "glucose", "dna", "transcription", "mutation", "fungi", "model", "organisms", "experimental", "organism", "systems", "genetic", "e...	2018	The Mediator co-activator complex regulates Ty1 retromobility by controlling the balance between Ty1i and Ty1 promoters
Respiratory Syncytial Virus ( RSV ) is a highly pathogenic member of the Paramyxoviridae that causes severe respiratory tract infections . Reports in the literature have indicated that to infect cells the incoming viruses either fuse their envelope directly with the plasma membrane or exploit clathrin-mediated endocyto...	Respiratory Syncytial Virus ( RSV ) is a highly pathogenic paramyxovirus . We developed assays for RSV endocytosis , intracellular trafficking , membrane fusion , and infection . The results showed that RSV was rapidly and efficiently internalized , and that acid-independent membrane fusion occurred intracellularly aft...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Host Cell Entry of Respiratory Syncytial Virus Involves Macropinocytosis Followed by Proteolytic Activation of the F Protein
CD8 T cells protect the host from disease caused by intracellular pathogens , such as the Toxoplasma gondii ( T . gondii ) protozoan parasite . Despite the complexity of the T . gondii proteome , CD8 T cell responses are restricted to only a small number of peptide epitopes derived from a limited set of antigenic precu...	Toxoplasma gondii is a widespread intracellular parasite that can cause severe disease in immunocompromised individuals and lead to fetal abnormalities if contracted during pregnancy . Establishment of protective immunity relies on CD8 T cells , which recognize antigenic peptides presented by MHC class I molecules on t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immune", "cells", "major", "histocompatibility", "complex", "antigen", "processing", "and", "recognition", "clinical", "immunology", "immunity", "antigen-presenting", "cells", "t", "cells", "immunology", "immunity", "to", "infections...	2013	Location of the CD8 T Cell Epitope within the Antigenic Precursor Determines Immunogenicity and Protection against the Toxoplasma gondii Parasite
Natural killer cells provide an important early defense against viral pathogens and are regulated in part by interactions between highly polymorphic killer-cell immunoglobulin-like receptors ( KIRs ) on NK cells and their MHC class I ligands on target cells . We previously identified MHC class I ligands for two rhesus ...	Natural killer ( NK ) cells are an important cellular defense against viral pathogens , and are regulated in part by interactions between killer-cell immunoglobulin-like receptors ( KIRs ) on NK cells and MHC class I ligands on target cells . Using multi-parameter flow cytometry , we report the first longitudinal study...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "vertebrates", "cloning", "animals", "mammals", "retroviruses", "primates", "immunodeficiency", "viruses"...	2017	KIR3DL01 upregulation on gut natural killer cells in response to SIV infection of KIR- and MHC class I-defined rhesus macaques
Resistance-Nodulation-Division ( RND ) efflux pumps are responsible for multidrug resistance in Pseudomonas aeruginosa . In this study , we demonstrate that CpxR , previously identified as a regulator of the cell envelope stress response in Escherichia coli , is directly involved in activation of expression of RND effl...	Pseudomonas aeruginosa is one of the major pathogens associated with cystic fibrosis and multidrug resistant P . aeruginosa has been listed as the Top 10 antibiotic resistance threats in the US CDC report ( http://www . cdc . gov/drugresistance/biggest_threats . html ) . Drug efflux systems play a major role in multidr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "drugs", "microbiology", "operons", "pseudomonas", "aeruginosa", "antibiotic", "resistance", "regulator", ...	2016	CpxR Activates MexAB-OprM Efflux Pump Expression and Enhances Antibiotic Resistance in Both Laboratory and Clinical nalB-Type Isolates of Pseudomonas aeruginosa
Olfactory ensheathing cell ( OEC ) transplantation is a candidate cellular treatment approach for human spinal cord injury ( SCI ) due to their unique regenerative potential and autologous origin . The objective of this study was , through a meta-epidemiologic approach , ( i ) to assess the efficacy of OEC transplantat...	Spinal cord injury converts into a debilitating disease affecting millions of chronic patients worldwide . Despite increased molecular knowledge over the last decades , no causal pharmacological or cellular therapy has proven effective so far . Due to their unique regenerative capabilities and their autologous origin ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusion", "Materials", "and", "Methods" ]	[ "traumatic", "injury", "medicine", "and", "health", "sciences", "nervous", "system", "brain", "neuroscience", "biological", "locomotion", "biomechanics", "surgical", "and", "invasive", "medical", "procedures", "macroglial", "cells", "mathematics", "statistics", "(mathemat...	2016	Olfactory Ensheathing Cell Transplantation in Experimental Spinal Cord Injury: Effect size and Reporting Bias of 62 Experimental Treatments: A Systematic Review and Meta-Analysis
Mammalian Nrf2-Keap1 and the homologous Drosophila CncC-dKeap1 protein complexes regulate both transcriptional responses to xenobiotic compounds as well as native cellular and developmental processes . The relationships between the functions of these proteins in xenobiotic responses and in development were unknown . We...	Human Nrf2-Keap1 and the fruit fly CncC-dKeap1 protein complexes function both in response to foreign chemicals and in development . We found that CncC and dKeap1 control fruit fly development by regulating the production and actions of the principal hormone that controls the transformation of larvae into pupae . In ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "networks", "genetic", "mutation", "protein", "interactions", "mechanisms", "of", "signal", "transduction", "gene", "regulation", "immunology", "dna-binding", "proteins", "anatomy", "and", "physiology", "signaling", "in", "selected", "disciplines", "cytogenetic", ...	2013	Regulation of Drosophila Metamorphosis by Xenobiotic Response Regulators
Long-term potentiation ( LTP ) and long-term depression ( LTD ) are widely accepted to be synaptic mechanisms involved in learning and memory . It remains uncertain , however , which particular activity rules are utilized by hippocampal neurons to induce LTP and LTD in behaving animals . Recent experiments in the denta...	The vast majority of computational studies that model synaptic plasticity neglect the fact that in vivo neurons exhibit an ongoing spontaneous spiking which affects the dynamics of synaptic changes . Here we study how key components of learning mechanisms in the brain , namely spike timing-dependent plasticity and meta...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent “Heterosynaptic” LTD in the Dentate Gyrus In Vivo
The eukaryotic genome is packaged as chromatin with nucleosomes comprising its basic structural unit , but the detailed structure of chromatin and its dynamic remodeling in terms of individual nucleosome positions has not been completely defined experimentally for any genome . We used ultra-high–throughput sequencing t...	The eukaryotic genome is packed in a systematic hierarchy to accommodate it within the confines of the cell's nucleus . This packing , however , presents an impediment to the transcription machinery when it must access genomic DNA to regulate gene expression . A fundamental aspect of genome packing is the spooling of D...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "genetics", "and", "genomics" ]	2008	Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation
The promise of personalized cancer medicine cannot be fulfilled until we gain better understanding of the connections between the genomic makeup of a patient's tumor and its response to anticancer drugs . Several datasets that include both pharmacologic profiles of cancer cell lines as well as their genomic alterations...	There is increasing evidence that altering different functional regions within the same protein can lead to dramatically distinct phenotypes . Here we show how , by focusing on individual regions instead of whole proteins , we are able to identify novel correlations that predict the activity of anticancer drugs . We ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biology", "and", "life", "sciences", "pharmacogenomics", "computational", "biology" ]	2015	Analysis of Individual Protein Regions Provides Novel Insights on Cancer Pharmacogenomics
Wolbachia inherited intracellular bacteria can manipulate the reproduction of their insect hosts through cytoplasmic incompatibility ( CI ) , and certain strains have also been shown to inhibit the replication or dissemination of viruses . Wolbachia strains also vary in their relative fitness effects on their hosts and...	The tiger mosquito Aedes albopictus is an invasive disease vector whose range has expanded throughout the tropics , and some temperate regions , in recent decades from its native South East Asia . It is an important vector of human viruses including dengue and chikungunya; in recent years a mutation has been detected i...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "global", "health", "neglected", "tropical", "diseases", "vectors", "and", "hosts" ]	2013	A Wolbachia wMel Transinfection in Aedes albopictus Is Not Detrimental to Host Fitness and Inhibits Chikungunya Virus
The repeat region of the Plasmodium falciparum circumsporozoite protein ( CSP ) is a major vaccine antigen because it can be targeted by parasite neutralizing antibodies; however , little is known about this interaction . We used isothermal titration calorimetry , X-ray crystallography and mutagenesis-validated modelin...	Vaccines aim to protect by inducing the immune system to make molecules called antibodies that can recognize molecules on the surface of invading pathogens . In the case of malaria , our most advanced vaccine candidates aim to promote the production of antibodies that recognize the circumsporozoite protein ( CSP ) mole...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "physiology", "immune", "cells", "enzyme-linked", "immunoassays", "plasmodium", "immunology", "cloning", "parasitology", "apicomplexa", "molecular", "biology", "techniques", "antibo...	2017	T-dependent B cell responses to Plasmodium induce antibodies that form a high-avidity multivalent complex with the circumsporozoite protein
Genetical genomics is a strategy for mapping gene expression variation to expression quantitative trait loci ( eQTLs ) . We performed a genetical genomics experiment in four functionally distinct but developmentally closely related hematopoietic cell populations isolated from the BXD panel of recombinant inbred mouse s...	Blood cell development from multipotent hematopoietic stem cells to specialized blood cells is accompanied by drastic changes in gene expression for which the triggers remain mostly unknown . Genetical genomics is an approach linking natural genetic variation to gene expression variation , thereby allowing the identifi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "computational", "biology", "molecular", "biology", "genetics", "and", "genomics", "hematology" ]	2009	Expression Quantitative Trait Loci Are Highly Sensitive to Cellular Differentiation State
The Asian tiger mosquito , Aedes albopictus , is an important vector of dengue , chikungunya and Zika viruses and is a highly invasive and aggressive biter . Established populations of this species were first recognised in Australia in 2005 when they were discovered on islands in the Torres Strait , between mainland Au...	Aedes albopictus is a disease vector and biting nuisance of major public health concern . Established populations of Ae . albopictus were first recognised in Australia in 2005 after they were discovered on islands in the Torres Strait . Consequently , a control program was established in the same year to eliminate Ae ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "viral", "transmission", "and", "infection", "pathogens", "geographical", "locations", "microbiology", "australia", "animals", "alphaviruses", "viral", "...	2017	Holding back the tiger: Successful control program protects Australia from Aedes albopictus expansion
Radiation-attenuated Plasmodium sporozoites ( RAS ) are the only vaccine shown to induce sterilizing protection against malaria in both humans and rodents . Importantly , these “whole-parasite” vaccines are currently under evaluation in human clinical trials . Studies with inbred mice reveal that RAS-induced CD8 T cell...	Plasmodium infections are a global health crisis resulting in ∼300 million cases of malaria each year and ∼1 million deaths . Radiation-attenuated Plasmodium sporozoites ( RAS ) are the only vaccines that induce sterilizing anti-malarial immunity in humans . Importantly , “whole parasite” anti-malarial RAS vaccines are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections" ]	2010	Extreme CD8 T Cell Requirements for Anti-Malarial Liver-Stage Immunity following Immunization with Radiation Attenuated Sporozoites
Isogenic bacterial populations can consist of cells displaying heterogeneous physiological traits . Small regulatory RNAs ( sRNAs ) could affect this heterogeneity since they act by fine-tuning mRNA or protein levels to coordinate the appropriate cellular behavior . Here we show that the sRNA RnaC/S1022 from the Gram-p...	Bacterial cells that share the same genetic information can display very different phenotypes , even if they grow under identical conditions . Despite the relevance of this population heterogeneity for processes like drug resistance and development , the molecular players that induce heterogenic phenotypes are often no...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Small Regulatory RNA-Induced Growth Rate Heterogeneity of Bacillus subtilis
Breast cancer is the second largest cause of cancer death among U . S . women and the leading cause of cancer death among women worldwide . Genome-wide association studies ( GWAS ) have identified several genetic variants associated with susceptibility to breast cancer , but these still explain less than half of the es...	Susceptibility to breast cancer is partially encoded in our genomes , but despite the development of new genomic technologies over the past decade , we are still not able to accurately predict disease susceptibility from genome sequences . One reason for this gap is that we lack methods for finding combinations of geno...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "breast", "tumors", "cancers", "and", "neoplasms", "hormones", "oncology", "mathematics", "genome", "analysis", "genetic", "interactions", "discrete", "mathematics", "steroid", "hormones", ...	2017	Pathway-based discovery of genetic interactions in breast cancer
Rice is a facultative short-day plant ( SDP ) , and the regulatory pathways for flowering time are conserved , but functionally modified , in Arabidopsis and rice . Heading date 1 ( Hd1 ) , an ortholog of Arabidopsis CONSTANS ( CO ) , is a key regulator that suppresses flowering under long-day conditions ( LDs ) , but ...	In rice , flowering time affects the potential yield , the growing season and regional adaptability . Change in day length is a key seasonal cue for regulating flowering time in rice , a facultative short-day ( SD ) plant . The photoperiodic pathway of rice contains the evolutionarily conserved Hd1-Hd3a module , which ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "phosphorylation", "plant", "anatomy", "cereal", "crops", "regulator", "genes", "plant", "science", "rice", "model", "organisms", "genetically", "modified", "plants", "crops", "gene", "types", "plant", "genomics", "molecular", "biology", "techniques", ...	2016	The Oryza sativa Regulator HDR1 Associates with the Kinase OsK4 to Control Photoperiodic Flowering
Ubiquitylation is fundamental for the regulation of the stability and function of p53 and c-Myc . The E3 ligase Pirh2 has been reported to polyubiquitylate p53 and to mediate its proteasomal degradation . Here , using Pirh2 deficient mice , we report that Pirh2 is important for the in vivo regulation of p53 stability i...	Tumor suppressors and oncogenes play critical roles in cancer development . The tumor suppressor p53 and the oncogene c-MYC are among the most frequently deregulated genes in human cancer , and their ubiquitylation mediated by several E3 ligases is critical for their turnover and their functions . P53 has been shown to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	Role of Pirh2 in Mediating the Regulation of p53 and c-Myc
The protozoan parasite Theileria inhabits the host cell cytoplasm and possesses the unique capacity to transform the cells it infects , inducing continuous proliferation and protection against apoptosis . The transforming schizont is a multinucleated syncytium that resides free in the host cell cytoplasm and is strictl...	As part of their survival tactics , intracellular parasites often resort to cunning mechanisms to manipulate the cells they inhabit . Theileria , an important and particularly artful parasite of cattle in the tropics , transforms parasitized cells ( that is , it induces continuous proliferation and protection from apop...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "cell", "biology", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "cell", "biology/cytoskeleton" ]	2010	The Transforming Parasite Theileria Co-opts Host Cell Mitotic and Central Spindles to Persist in Continuously Dividing Cells
Human T-cell leukemia virus type 1 ( HTLV-1 ) is an etiological agent of several inflammatory diseases and a T-cell malignancy , adult T-cell leukemia ( ATL ) . HTLV-1 bZIP factor ( HBZ ) is the only viral gene that is constitutively expressed in HTLV-1-infected cells , and it has multiple functions on T-cell signaling...	HTLV-1 is a retrovirus which causes a cancer , ATL , and inflammatory diseases of several tissues , such as the spinal cord , eye , skin , and lung . Although these HTLV-1-mediated malignant and inflammatory diseases are recognized as distinct pathological entities , an increased number of HTLV-1 infected cells and enh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Interferon-γ Promotes Inflammation and Development of T-Cell Lymphoma in HTLV-1 bZIP Factor Transgenic Mice
A complex system of multiple signaling molecules often produce differential gene expression patterns in animal embryos . In the ascidian embryo , four signaling ligands , Ephrin-A . d ( Efna . d ) , Fgf9/16/20 , Admp , and Gdf1/3-r , coordinately induce Otx expression in the neural lineage at the 32-cell stage . Howeve...	It is often difficult to understand a complex system of multiple signaling molecules in animal embryos only with experimental procedures . Although theoretical analysis might solve this problem , it is often difficult to precisely determine parameters for signaling gradients and kinetics of signaling molecules . In the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Boolean Function for Neural Induction Reveals a Critical Role of Direct Intercellular Interactions in Patterning the Ectoderm of the Ascidian Embryo
Protozoan parasites of the genus Leishmania cause a large spectrum of clinical manifestations known as Leishmaniases . These diseases are increasingly important public health problems in many countries both within and outside endemic regions . Thus , an accurate differential diagnosis is extremely relevant for understa...	The different clinical forms of the Leishmaniases range from cutaneous to visceral infections and are caused by organisms belonging to the genus Leishmania . Controversy over the validity of different molecular methods to correctly identify a species hinders the association of a given species with different clinical fo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "condensed", "matter", "physics", "parasitic", "protozoans", "organisms", "protozoans", "leishmania", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "artificial", "gene", "amplification", ...	2016	High Resolution Melting Analysis Targeting hsp70 as a Fast and Efficient Method for the Discrimination of Leishmania Species
Depression is a serious mental disorder that affects a person’s mood , thoughts , behavior , physical health , and life in general . Despite our continuous efforts to understand the disease , the etiology of depressive behavior remains perplexing . Recently , aberrant early life or postnatal neurogenesis has been linke...	Although the majority of the neurons in the brain are generated during embryonic stage , new neurons are continuously being produced postnatally , and at a much lower rate in adulthood . As postnatal neurogenesis is a key component of the brain maturation process that creates dynamic ‘wirings’ in the brain necessary fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Postnatal Loss of Hap1 Reduces Hippocampal Neurogenesis and Causes Adult Depressive-Like Behavior in Mice
Inflammasomes are cytosolic multi-protein complexes that initiate immune responses to infection by recruiting and activating the Caspase-1 protease . Human NLRP1 was the first protein shown to form an inflammasome , but its physiological mechanism of activation remains unknown . Recently , specific variants of mouse an...	Hosts and their pathogens often engage in evolutionary ‘arms races’ , iterative cycles of adaptation , in which each opponent evolves strategies to overcome the other . For example , the anthrax bacterium overcomes the host immune response by producing lethal factor , a proteolytic enzyme that specifically cleaves and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "enzymes", "metabolic", "processes", "293t", "cells", "immunology", "biological", "cultures", "enzymology", "vertebrates", "animals", "mammals", "plasmid", "construction", "primates", "inflammasomes", "amniotes", "dna", "constructi...	2016	Functional and Evolutionary Analyses Identify Proteolysis as a General Mechanism for NLRP1 Inflammasome Activation
A number of machine learning-based predictors have been developed for identifying immunogenic T-cell epitopes based on major histocompatibility complex ( MHC ) class I and II binding affinities . Rationally selecting the most appropriate tool has been complicated by the evolving training data and machine learning metho...	Computationally predicting antigen peptide sequences that elicit T-cell immune response has broad and significant impact on vaccine design . The most widely accepted approach is to rely on machine learning classifier , trained on large-scale major-histocompatibility complex ( MHC ) -binding peptide dataset . Because of...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "mhc", "class", "i", "genes", "innate", "immune", "system", "medicine", "and", "health", "sciences", "antigen", "presentation", "immune", "cells", "immune", "physiology", "statistics", "immunology", "neuroscience", "artificial", "neural", "networks",...	2018	Systematically benchmarking peptide-MHC binding predictors: From synthetic to naturally processed epitopes
The brain uses its intrinsic dynamics to actively predict observed sensory inputs , especially under perceptual ambiguity . However , it remains unclear how this inference process is neurally implemented in biasing perception of ambiguous inputs towards the predicted percepts . The process of perceptual inference can b...	Our subjective perception of the external world is constantly shaped not only by sensory inputs but also by the real-time internal status of our own brain . Upon facing an ambiguous sensory input , our brain employs its intrinsic dynamics to bias perception towards the predicted percept , resolving in this manner perce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "functional", "magnetic", "resonance", "imaging", "neural", "networks", "brain", "electrophysiology", "social", "sciences", "electrophysiology", "neuroscience", "magnetic", "resonance", "imaging", "percepti...	2019	Perceptual inference employs intrinsic alpha frequency to resolve perceptual ambiguity
A small percentage of women with cervical HPV infection progress to cervical neoplasia , and the risk factors determining progression are incompletely understood . We sought to define the genetic loci involved in cervical neoplasia and to assess its heritability using unbiased unrelated case/control statistical approac...	Around 1% of women with cervical human papillomavirus ( HPV ) infection progress to cervical cancer . Previous studies had indicated that a person’s genetic makeup could predispose to HPV-associated cervical cancer , and that some of the genes likely to be involved include the immune-related human leukocyte antigen ( H...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "urology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cervical", "cancer", "pathogens", "immunology", "cancers", "and", "neoplasms", "microbiology", "genetic", "mapping", "oncology", "...	2017	Defining the genetic susceptibility to cervical neoplasia—A genome-wide association study
The single-celled cotton ( Gossypium hirsutum ) fiber provides an excellent model to investigate how human selection affects phenotypic evolution . To gain insight into the evolutionary genomics of cotton domestication , we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq . Analys...	Ever since Darwin biologists have recognized that comparative study of crop plants and their wild relatives offers a powerful framework for generating insights into the mechanisms that underlie evolutionary change . Here , we study the domestication process in cotton , Gossypium hirsutum , an allopolyploid species ( co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "organismal", "evolution", "botany", "crop", "genetics", "plant", "science", "crops", "plant", "genomics", "fibers", "gene", "expression", "plant", "genetics", "ethnobotany", "comparative", "genomics", "biology", "evolutionary", "gene...	2014	Comparative Evolutionary and Developmental Dynamics of the Cotton (Gossypium hirsutum) Fiber Transcriptome
Few studies have evaluated the association between quality of life ( QoL ) and functional activity limitations ( FAL ) of leprosy patients as determined by the Screening of Activity Limitation and Safety Awareness scale ( SALSA ) . To identify the association between FALs and the QoL of patients during and post leprosy...	Leprosy is still a neglected public health problem . Leprosy causes disability and functional limitations ( FALs ) if not treated early . We describe the functional activity and quality of life ( QoL ) of adults with leprosy attending two reference centres in Sergipe , Brazil . Patients with leprosy had low QoL , which...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Functional Activity Limitation and Quality of Life of Leprosy Cases in an Endemic Area in Northeastern Brazil
Innate immune recognition is classically mediated by the interaction of host pattern-recognition receptors and pathogen-associated molecular patterns; this triggers a series of downstream signaling events that facilitate killing and elimination of invading pathogens . In this report , we provide the first evidence that...	Multicellular organisms have evolved diversified host defense mechanisms for survival against invading pathogens . Of the mechanisms , the recognition of pathogens is classically mediated by the interaction of host and pathogen , which triggers a series of downstream responses to eliminate pathogens . Proteins that bot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "peroxidases", "body", "fluids", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "enzymes", "pathogens", "microbiology", "enzymology", "immunoblotting", "pseudomonas", "aeruginosa", "animal", "mode...	2018	Peroxidasin contributes to lung host defense by direct binding and killing of gram-negative bacteria
Gene duplication facilitates functional diversification and provides greater phenotypic flexibility to an organism . Expanded gene families arise through repeated gene duplication but the extent of functional divergence that accompanies each paralogous gene is generally unexplored because of the difficulty in isolating...	Gene duplication is a rapid mechanism to generate additional sequences for natural selection to act upon and confer greater organismal fitness . If additional copies of the gene are beneficial , this process may be repeated to produce an expanded gene family containing many copies of related sequences . Following dupli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biofilms", "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "immunology", "microbiology", "fungi", "experimental", "organism", "systems", "fungal", "pathogens"...	2018	Functional diversification accompanies gene family expansion of MED2 homologs in Candida albicans
Defects in the genes encoding the Paf1 complex can cause increased genome instability . Loss of Paf1 , Cdc73 , and Ctr9 , but not Rtf1 or Leo1 , caused increased accumulation of gross chromosomal rearrangements ( GCRs ) . Combining the cdc73Δ mutation with individual deletions of 43 other genes , including TEL1 and YKU...	Maintaining a stable genome is crucial for all organisms , and loss of genome stability has been linked to multiple human diseases , including many cancers . Previously we found that defects in Cdc73 , a component of the Paf1 transcriptional elongation complex , give rise to increased genome instability . Here , we exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "deletion", "mutation", "genetic", "networks", "chromosome", "structure", "and", "function", "telomeres", "mutation", "fungi", "model", "organisms", "network", "analysis", "experimental", "organism", "systems", "research", "and", "analysis", "methods", "saccharomyces", ...	2018	Cdc73 suppresses genome instability by mediating telomere homeostasis
Memory phenotype ( CD44bright , CD25negative ) CD4 spleen and lymph node T cells ( MP cells ) proliferate rapidly in normal or germ-free donors , with BrdU uptake rates of 6% to 10% per day and Ki-67 positivity of 18% to 35% . The rapid proliferation of MP cells stands in contrast to the much slower proliferation of ly...	The class of immune cells called CD4 T lymphocytes consists of two major cell types: naïve cells that have not yet participated in an immune response and memory cells , which are cells that have responded to antigen , expanded in number , and acquired new characteristics . These two cell types can be distinguished from...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology" ]	2011	Memory Phenotype CD4 T Cells Undergoing Rapid, Nonburst-Like, Cytokine-Driven Proliferation Can Be Distinguished from Antigen-Experienced Memory Cells
We provide a novel computational framework on how biological and artificial agents can learn to flexibly couple and decouple neural task modules for cognitive processing . In this way , they can address the stability-plasticity dilemma . For this purpose , we combine two prominent computational neuroscience principles ...	Artificial and biological agents alike face a critical trade-off between being sufficiently adaptive to acquiring novel information ( plasticity ) and retaining older information ( stability ) ; this is known as the stability-plasticity dilemma . Previous work on this dilemma has focused either on computationally effic...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "social", "sciences", "vertebrates", "neuroscience", "learning", "and", "memory", "animals", "mammals", "simulation", "and", "modeling", "primates", "cognitive", "psychology", ...	2019	Learning to synchronize: How biological agents can couple neural task modules for dealing with the stability-plasticity dilemma
The High Pathogenicity Island of Yersinia pseudotuberculosis IP32637 was previously shown to be horizontally transferable as part of a large chromosomal segment . We demonstrate here that at low temperature other chromosomal loci , as well as a non-mobilizable plasmid ( pUC4K ) , are also transferable . This transfer ,...	All living species have the capacity to evolve in order to adapt to new and often hostile conditions . Horizontal gene transfer is a major route for rapid bacterial evolution . Some clearly identified mobile genetic elements ( plasmids , phages , etc . ) are by essence exchanged between bacteria . However , the mechani...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology" ]	2012	A Natural System of Chromosome Transfer in Yersinia pseudotuberculosis
GspB is a serine-rich repeat ( SRR ) adhesin of Streptococcus gordonii that mediates binding of this organism to human platelets via its interaction with sialyl-T antigen on the receptor GPIbα . This interaction appears to be a major virulence determinant in the pathogenesis of infective endocarditis . To address the m...	The binding of bacteria to human platelets is thought to be important for development of infective endocarditis , a life-threatening infection of the cardiovascular system . Streptococcus gordonii is a leading cause of endocarditis . This pathogen uses a protein called GspB to attach to carbohydrates on human platelets...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "medicine", "streptococci", "microbiology", "bacterial", "diseases", "protein", "structure", "bacterial", "pathogens", "animal", "models", "of", "infection", "infectious", "diseases", "virulence", "factors", "and", "mechanisms", "p...	2011	A Structural Model for Binding of the Serine-Rich Repeat Adhesin GspB to Host Carbohydrate Receptors
Listeria monocytogenes ( Lm ) uses InlA to invade the tips of the intestinal villi , a location at which cell extrusion generates a transient defect in epithelial polarity that exposes the receptor for InlA , E-cadherin , on the cell surface . As the dying cell is removed from the epithelium , the surrounding cells reo...	The anatomical context in which attachment and invasion factors find host receptors determines when and where microbes can colonize and invade . For example , Listeria monocytogenes ( Lm ) , a cause of human and animal food-borne disease , invades the villous epithelium only at the intestinal villus tips where dying ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology/cell", "signaling", "cell", "biology", "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/bacterial", "infections", "cell", "biology/cell", "adhesion", "infectious", "diseases/gastrointestinal", "infections" ]	2010	Listeria monocytogenes Internalin B Activates Junctional Endocytosis to Accelerate Intestinal Invasion
Hybrid trials that include both clinical and implementation science outcomes are increasingly relevant for public health researchers that aim to rapidly translate study findings into evidence-based practice . The DeWorm3 Project is a series of hybrid trials testing the feasibility of interrupting the transmission of so...	The DeWorm3 Project is a series of randomized clinical trials testing the feasibility of interrupting the transmission of soil-transmitted helminths . We have integrated implementation science research questions into the trials in order to optimize delivery of trial interventions as well as to speed the translation of ...	[ "Abstract", "Introduction", "Methods" ]	[ "medicine", "and", "health", "sciences", "cost-effectiveness", "analysis", "economic", "analysis", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "health", "care", "research", "design", "global", "health", "neglected", "tropical", "diseases", "re...	2018	Evaluating the sustainability, scalability, and replicability of an STH transmission interruption intervention: The DeWorm3 implementation science protocol
Aneuploidy represents the most prevalent form of genetic instability found in human embryos and is the leading genetic cause of miscarriage and developmental delay in newborns . Telomere DNA deficiency is associated with genomic instability in somatic cells and may play a role in development of aneuploidy commonly foun...	Human eggs ( oocytes ) are exceptionally prone to the erroneous acquisition of too few ( monosomy ) or too many ( trisomy ) chromosomes during development ( meiosis ) . In fact , this type of instability , termed aneuploidy , represents the most common genetic cause of miscarriage in pregnant women ( i . e . trisomy 16...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "developmental", "biology", "embryology", "aneuploidy", "genomics", "telomeres", "chromosomal", "disorders", "chromosome", "biology", "genetics", "biology", "human", "genetics", "genetics", "and", "genomics" ]	2011	Telomere DNA Deficiency Is Associated with Development of Human Embryonic Aneuploidy
Filamentous fungus Penicillium oxalicum produces diverse lignocellulolytic enzymes , which are regulated by the combinations of many transcription factors . Here , a single-gene disruptant library for 470 transcription factors was constructed and systematically screened for cellulase production . Twenty transcription f...	Cellulolytic fungi have evolved into sophisticated lignocellulolytic systems to adapt to their natural habitat . This trait is important for filamentous fungi , which are the main source of cellulases utilized to degrade lignocellulose to fermentable sugars . Penicillium oxalicum , which produces lignocellulolytic enzy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Synergistic and Dose-Controlled Regulation of Cellulase Gene Expression in Penicillium oxalicum
The IAPE ( Intracisternal A-type Particles elements with an Envelope ) family of murine endogenous retroelements is present at more than 200 copies in the mouse genome . We had previously identified a single copy that proved to be fully functional , i . e . which can generate viral particles budding out of the cell and...	In mammals , nearly half the genome is composed of reiterated scattered sequences . Some of them , called endogenous retroviruses , have a structure similar to that observed for the integrated form of infectious retroviruses . The current theory to account for their presence is that an infectious retrovirus once infect...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "viral", "entry", "transposons", "molecular", "cell", "biology", "retrotransposons", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology", "host-pathogen", "interaction", "molecular", "biology" ]	2011	The Mouse IAPE Endogenous Retrovirus Can Infect Cells through Any of the Five GPI-Anchored EphrinA Proteins
In the heart , electrical stimulation of cardiac myocytes increases the open probability of sarcolemmal voltage-sensitive Ca2+ channels and flux of Ca2+ into the cells . This increases Ca2+ binding to ligand-gated channels known as ryanodine receptors ( RyR2 ) . Their openings cause cell-wide release of Ca2+ , which in...	Many transmembrane receptors have been shown to aggregate into supramolecular clusters that enhance sensitivity to external stimuli in a variety of cell types . Advances in super-resolution microscopy have enabled researchers to study these structures with sufficient detail to distinguish the precise locations of indiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "Models" ]	[]	2015	On the Adjacency Matrix of RyR2 Cluster Structures
In the last decade , the number of emerging Flaviviruses described worldwide has increased considerably . Among them Zika virus ( ZIKV ) and Usutu virus ( USUV ) are African mosquito-borne viruses that recently emerged . Recently , ZIKV has been intensely studied due to major outbreaks associated with neonatal death an...	Usutu virus ( USUV ) is an African mosquito-borne virus closely related to West Nile virus and belongs to the Japanese encephalitis virus serogroup in the Flavivirus genus . Recently several neurological disorders such as encephalitis , meningitis and meningoencephalitis were associated with USUV-infection in immunocom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "nervous", "system", "astrocytes", "pathogens", "cell", "processes", "immunology", "microbiology", "neuroscience", "macroglial", "cells", "vir...	2017	Deleterious effect of Usutu virus on human neural cells
A mismatch between optical power and ocular axial length results in refractive errors . Uncorrected refractive errors constitute the most common cause of vision loss and second leading cause of blindness worldwide . Although the retina is known to play a critical role in regulating ocular growth and refractive developm...	Refractive errors mainly occur when changes in ocular size ( ocular axial length ) prevent light from focusing directly on the retina . Myopia ( nearsightedness ) is the most common form of refractive errors in which the focused image falls in front of the retina . The recent unprecedented rise in the incidence of myop...	[ "Abstract", "Introduction", "Methods" ]	[ "medicine", "and", "health", "sciences", "ocular", "anatomy", "alleles", "cell", "differentiation", "animal", "models", "developmental", "biology", "model", "organisms", "experimental", "organism", "systems", "biometrics", "eyes", "research", "and", "analysis", "methods...	2018	Müller glia-derived PRSS56 is required to sustain ocular axial growth and prevent refractive error
Variation among individuals is a prerequisite of evolution by natural selection . As such , identifying the origins of variation is a fundamental goal of biology . We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system...	The variation generating mechanisms of development interact with the variation sorting mechanism of natural selection to produce organismal diversity . While the impacts of natural selection on existing variation have received much study , those of development on the generation of this variation remain less understood ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Relationship between Gene Network Structure and Expression Variation among Individuals and Species
MDA5 belongs to the RIG-I-like receptor family and plays a non-redundant role in recognizing cytoplasmic viral RNA to induce the production of type I IFNs . Upon RNA ligand stimulation , we observed the redistribution of MDA5 from the cytosol to mitochondrial membrane fractions . However , the molecular mechanisms of M...	In this study , we utilized biochemistry and molecular biology approaches to defines the molecular mechanisms by which melanoma differentiation-associated protein 5 ( MDA5 ) , a cytoplasmic RNA helicase and pattern recognition receptor molecule , is regulated by 14-3-3η to govern its innate immune signaling activity . ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "antiviral", "immune", "response", "protein", "interactions", "molecular", "probe", "techniques", "immunology", "immunoblotting", "microbiology", "chaperone", "proteins", "mitochondria", "molecular", "biology", "techniques", "bioener...	2019	The 14-3-3η chaperone protein promotes antiviral innate immunity via facilitating MDA5 oligomerization and intracellular redistribution
IgA nephropathy ( IgAN ) , major cause of kidney failure worldwide , is common in Asians , moderately prevalent in Europeans , and rare in Africans . It is not known if these differences represent variation in genes , environment , or ascertainment . In a recent GWAS , we localized five IgAN susceptibility loci on Chr ...	IgA nephropathy ( IgAN ) is the most common cause of kidney failure in Asia , has lower prevalence in Europe , and is very infrequent among populations of African ancestry . A long-standing question in the field is whether these differences represent variation in genes , environment , or ascertainment . In a recent gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "genetics", "of", "the", "immune", "system", "clinical", "immunology", "chronic", "kidney", "disease", "autoimmune", "diseases", "immunology", "nephrology" ]	2012	Geographic Differences in Genetic Susceptibility to IgA Nephropathy: GWAS Replication Study and Geospatial Risk Analysis
B cells develop high affinity receptors during the course of affinity maturation , a cyclic process of mutation and selection . At the end of affinity maturation , a number of cells sharing the same ancestor ( i . e . in the same “clonal family” ) are released from the germinal center; their amino acid frequency profil...	Antibody engineering can be greatly informed by knowledge about the underlying affinity maturation process . As such this can be probed by sequencing , but unfortunately , in practice often only one member of the clonal family is sequenced , making it difficult to determine a set of possible amino acid mutations that w...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "sequencing", "techniques", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "chemical", "compounds", "statistics", "immunology", "organic", "compounds", "mutation", "substitution", "mutation", "mathematics", "forecasti...	2018	Predicting B cell receptor substitution profiles using public repertoire data
Immunological checkpoints , such as the inhibitory CD200 receptor ( CD200R ) , play a dual role in balancing the immune system during microbial infection . On the one hand these inhibitory signals prevent excessive immune mediated pathology but on the other hand they may impair clearance of the pathogen . We studied th...	Immune responses need to be carefully orchestrated to prevent disease due to an overactive immune system . Immunological checkpoints are provided by immune inhibitory receptors , which set a threshold for activation and dampen the immune system . In the case of a viral infection , this prevents pathology induced by the...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "influenza", "immunity", "to", "infections", "immunology", "immunoregulation", "immunomodulation", "infectious", "diseases", "inflammation", "biology", "immune", "response", "clinical", "immunology", "immunity", "sars", "viral", "diseases" ]	2012	CD200 Receptor Controls Sex-Specific TLR7 Responses to Viral Infection
The dentate gyrus has an important role in learning and memory , and adult neurogenesis in the subgranular zone of the dentate gyrus may play a role in the acquisition of new memories . The homeobox gene Prox1 is expressed in the dentate gyrus during embryonic development and adult neurogenesis . Here we show that Prox...	In the brain , the hippocampus has a crucial role in learning and memory . In mammals , neurogenesis ( the birth of new neurons ) occurs in the dentate gyrus region of the hippocampus throughout adulthood , and this activity is thought to be the basis for the acquisition of new memories . In this study we describe for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/stem", "cells", "developmental", "biology/developmental", "evolution", "developmental", "biology/pattern", "formation", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "developmental", "biology/molecular", "development", "developm...	2010	Prox1 Is Required for Granule Cell Maturation and Intermediate Progenitor Maintenance During Brain Neurogenesis

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