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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Epilepsy—the condition of recurrent , unprovoked seizures—manifests in brain voltage activity with characteristic spatiotemporal patterns . These patterns include stereotyped semi-rhythmic activity produced by aggregate neuronal populations , and organized spatiotemporal phenomena , including waves . To assess these sp...	Nearly 50 million people worldwide suffer from epilepsy , a chronic neurological condition characterized by recurrent , unprovoked seizures . Although some clinical and biological principles of seizures are known , many aspects of spontaneous human seizures remain poorly understood . Recordings from electrodes placed d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Biologically Constrained, Mathematical Model of Cortical Wave Propagation Preceding Seizure Termination
Chagas disease induced by Trypanosoma cruzi ( T . cruzi ) infection is a major cause of mortality and morbidity affecting the cardiovascular system for which presently available therapies are largely inadequate . Transforming Growth Factor beta ( TGFß ) has been involved in several regulatory steps of T . cruzi invasio...	Cardiac damage and dysfunction are prominent features in patients with chronic Chagas disease , which is caused by infection with the protozoan parasite Trypanosoma cruzi ( T . cruzi ) and affects 10–12 million individuals in South and Central America . Our group previously reported that transforming growth factor beta...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "drugs", "and", "devices", "cardiovascular" ]	2012	Oral Administration of GW788388, an Inhibitor of Transforming Growth Factor Beta Signaling, Prevents Heart Fibrosis in Chagas Disease
The IL-1β and type I interferon-β ( IFN-β ) molecules are important inflammatory cytokines elicited by the eukaryotic host as innate immune responses against invading pathogens and danger signals . Recently , a predominantly nuclear gamma-interferon-inducible protein 16 ( IFI16 ) involved in transcriptional regulation ...	Herpesviruses establish a latent infection in the nucleus of specific cells and reactivation results in the nuclear viral dsDNA replication and infectious virus production . Host innate responses are initiated by the presence of viral genomes and their products , and nucleus associated IFI16 protein has recently emerge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Herpesvirus Genome Recognition Induced Acetylation of Nuclear IFI16 Is Essential for Its Cytoplasmic Translocation, Inflammasome and IFN-β Responses
The p53 tumor suppressor protein plays a critical role in cellular stress and cancer prevention . A number of post-transcriptional regulators , termed microRNAs , are closely connected with the p53-mediated cellular networks . While the molecular interactions among p53 and microRNAs have emerged , a systems-level under...	DNA damage triggered activities of the tumor suppressor protein p53 could be significantly dynamical . The functional role of p53 oscillations in cellular decision making during cancer development has been appreciated . A set of recent studies have revealed extensive crosstalk between the p53 network and microRNAs , bu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	MiR-192-Mediated Positive Feedback Loop Controls the Robustness of Stress-Induced p53 Oscillations in Breast Cancer Cells
In many bacteria , inhibition of cell wall synthesis leads to cell death and lysis . The pathways and enzymes that mediate cell lysis after exposure to cell wall-acting antibiotics ( e . g . beta lactams ) are incompletely understood , but the activities of enzymes that degrade the cell wall ( ‘autolysins’ ) are though...	Inhibition of bacterial cell wall synthesis by antibiotics such as penicillin can lead to unbalanced activity of a poorly defined set of lytic enzymes , termed ‘autolysins , ’ which degrade the cell wall and typically cause cell lysis . Here , we report that in Vibrio cholerae ( the cause of cholera ) , inhibition of c...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Endopeptidase-Mediated Beta Lactam Tolerance
DNA damage recognition by the nucleotide excision repair pathway requires an initial step identifying helical distortions in the DNA and a proofreading step verifying the presence of a lesion . This proofreading step is accomplished in eukaryotes by the TFIIH complex . The critical damage recognition component of TFIIH...	Preserving the structural integrity of DNA , and hence the genetic information stored in this molecule , is essential for cellular survival . It is estimated that the DNA in each human cell acquires about 104 lesions per day . Consequently , efficient DNA repair mechanisms have evolved to protect the genome . One of th...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry" ]	2008	Crystal Structure of the FeS Cluster–Containing Nucleotide Excision Repair Helicase XPD
Cellular microscopy images contain rich insights about biology . To extract this information , researchers use features , or measurements of the patterns of interest in the images . Here , we introduce a convolutional neural network ( CNN ) to automatically design features for fluorescence microscopy . We use a self-su...	To understand the cell biology captured by microscopy images , researchers use features , or measurements of relevant properties of cells , such as the shape or size of cells , or the intensity of fluorescent markers . Features are the starting point of most image analysis pipelines , so their quality in representing c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "learning", "fluorescence", "imaging", "engineering", "and", "technology", "signal", "processing", "social", "sciences", "light", "microscopy", "green", "fluorescent", "protein", "neuroscience", "learning", "and", "memory", "luminescent", "proteins", "cognitive", "psychol...	2019	Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting
The axon plasma membrane consists of the membrane skeleton , which comprises ring-like actin filaments connected to each other by spectrin tetramers , and the lipid bilayer , which is tethered to the skeleton via , at least , ankyrin . Currently it is unknown whether this unique axon plasma membrane skeleton ( APMS ) s...	The axon plasma membrane skeleton consists of repeated periodic actin ring-like structures along its length connected via spectrin tetramers and anchored to the lipid bilayer at least via ankyrin . However , it is currently unclear whether this structure controls diffusion of lipids and proteins in the axon . Here , we...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience", "spectrins", "membrane", "proteins", "nerve", "fibers", "cellular", "structures", "and", "organelles", "contractile", "proteins", "lipids", "actins", "animal", "cells", "proteins", "axons", "chemistry", "cell", "membranes", "physics", "biochemistry", "cy...	2019	Modeling of the axon plasma membrane structure and its effects on protein diffusion
Merkel cell polyomavirus ( MCV or MCPyV ) appears to be a causal factor in the development of Merkel cell carcinoma , a rare but highly lethal form of skin cancer . Although recent reports indicate that MCV virions are commonly shed from apparently healthy human skin , the precise cellular tropism of the virus in healt...	Strong evidence suggests that Merkel cell polyomavirus ( MCV or MCPyV ) is a causative factor in the development of a large proportion of cancers arising from epidermal Merkel cells . While Merkel cell carcinoma is rare , it appears that infection with MCV is common , and many healthy people chronically shed MCV virion...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "viral", "attachment", "coreceptors", "viral", "entry", "viral", "transmission", "and", "infection", "virology", "biology", "microbiology" ]	2011	Glycosaminoglycans and Sialylated Glycans Sequentially Facilitate Merkel Cell Polyomavirus Infectious Entry
Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates . P . vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays , or for studying in ...	In this study we compare the genome sequences of Plasmodium vivax collected directly from patients with those of parasites propagated in laboratory monkeys . We show that the adaptation and continuous propagation of Plasmodium vivax in monkeys does not induce systematic changes in the genome and , therefore , that thes...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Comparative Analysis of Field-Isolate and Monkey-Adapted Plasmodium vivax Genomes
Biliary vessel pathology due to alveolar echicococcosis ( AE ) results in variable combinations of stenosis , necrosis and inflammation . Modern management strategies for patients with cholestasis are desperately needed . The aim is proof of principle of serial ERC ( endoscopic retrograde cholangiography ) balloon dila...	Alveolar echinococcosis ( AE ) is a zoonosis causing infiltrative liver lesions . A subgroup of patients presents with central liver lesions and biliary obstruction . At present there is no clear concept for the treatment of biliary obstruction in AE of the liver , and data from high quality trials to base treatment de...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biliary", "system", "medicine", "and", "health", "sciences", "liver", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "parasitic", "diseases", "surgical", "and", "invasive", "medical", "procedures", "endoscopy", "signs", "and", "symptoms", "negl...	2016	Endoscopic Treatment of Biliary Stenosis in Patients with Alveolar Echinococcosis – Report of 7 Consecutive Patients with Serial ERC Approach
Alpha herpesvirus genomes encode the capacity to establish quiescent infections ( i . e . latency ) in the peripheral nervous system for the life of their hosts . Multiple times during latency , viral genomes can reactivate to start a productive infection , enabling spread of progeny virions to other hosts . Replicatio...	Alpha herpesvirus infections stay life-long in infected human and animal hosts`nervous systems in a silent state ready to reactivate upon various stress signals . Remarkably , infection of epithelial cells with these viruses results in productive infection whereas infection of peripheral nervous system neurons results ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "microbiology", "viral", "structure", "neuroscience", "nerve", "fibers", "microbial", "genomics", "viral", "genomics", "animal", "cells", "axons", "viral", "replication", "virions", "tegument", "proteins", "cellular", "neuroscience", "cell", "biology", "viral", "persist...	2017	Compartmented neuronal cultures reveal two distinct mechanisms for alpha herpesvirus escape from genome silencing
Humans inhale hundreds of Aspergillus conidia without adverse consequences . Powerful protective mechanisms may ensure prompt control of the pathogen and inflammation . Here we reveal a previously unknown mechanism by which the danger molecule S100B integrates pathogen– and danger–sensing pathways to restrain inflammat...	Inflammation results from recognition of invading microorganisms through pathogen–associated molecular patterns ( PAMPs ) and from reaction to tissue damage–associated molecular patterns ( DAMPs ) . Despite the identification of specific signaling pathways negatively regulating responses to PAMPs or DAMPs , the unexpec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "immunology/immunomodulation", "infectious", "diseases/fungal", "infections", "microbiology/innate", "immunity", "immunology/innate", "immunity", "immunology/immunity", "to", "infections" ]	2011	The Danger Signal S100B Integrates Pathogen– and Danger–Sensing Pathways to Restrain Inflammation
Insecticide-treated nets ( ITNs ) are one of the main interventions used for malaria control . However , these nets may also be effective against other vector borne diseases ( VBDs ) . We conducted a systematic review and meta-analysis to estimate the efficacy of ITNs , insecticide-treated curtains ( ITCs ) and insecti...	Malaria is a deadly disease caused by a parasite which is transmitted by anopheline mosquitoes . Bednets treated with insecticide are one of the key tools used to prevent malaria and they have been distributed on a large scale in many countries , particularly in Africa . It may be possible to control other diseases tra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "vector-borne", "diseases", "microbiology", "sand", "flies", "animals", "viral", "vectors", "mathematics", "statistics", "(mathematics)", "global", "health", "insect", ...	2014	Benefit of Insecticide-Treated Nets, Curtains and Screening on Vector Borne Diseases, Excluding Malaria: A Systematic Review and Meta-analysis
Genetic factors play an important role in the etiology of breast cancer . We carried out a multi-stage genome-wide association ( GWA ) study in over 28 , 000 cases and controls recruited from 12 studies conducted in Asian and European American women to identify genetic susceptibility loci for breast cancer . After anal...	Breast cancer is one of the most common malignancies among women worldwide . Genetic factors play an important role in the etiology of breast cancer . To identify genetic susceptibility loci for breast cancer , we performed a genome-wide association study in 15 , 468 breast cancer cases and 13 , 001 controls . A single...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/epidemiology" ]	2010	Identification of a Functional Genetic Variant at 16q12.1 for Breast Cancer Risk: Results from the Asia Breast Cancer Consortium
Pathogens rely on a complex virulence gene repertoire to successfully attack their hosts . We were therefore surprised to find that a single fimbrial gene reconstitution can return the virulence-attenuated commensal strain Escherichia coli 83972 to virulence , defined by a disease phenotype in human hosts . E . coli 83...	Urinary tract infections affect millions of individuals annually , and many patients suffer from recurring infections several times a year . Antibiotic resistance is increasing rapidly and new strategies are needed to treat even these common bacterial infections . One approach is to use the protective power of asymptom...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "bladder", "microbiology", "pili", "and", "fimbriae", "urine", "bacterial", "diseases", "regulator", "genes", "g...	2019	Fimbriae reprogram host gene expression – Divergent effects of P and type 1 fimbriae
Disruption of the centromere protein J gene , CENPJ ( CPAP , MCPH6 , SCKL4 ) , which is a highly conserved and ubiquitiously expressed centrosomal protein , has been associated with primary microcephaly and the microcephalic primordial dwarfism disorder Seckel syndrome . The mechanism by which disruption of CENPJ cause...	Mutation of the gene CENPJ has been found to cause primary microcephaly , an inherited disorder that is characterised by severely reduced brain size . More recently , mutation of CENPJ has been associated with Seckel syndrome , a disorder that is characterised by a severe reduction in both brain and body size that is a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "model", "organisms", "organism", "development", "mouse", "genetics", "biology", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2012	Disruption of Mouse Cenpj, a Regulator of Centriole Biogenesis, Phenocopies Seckel Syndrome
In pathogenic HIV and SIV infections of humans and rhesus macaques ( RMs ) , preferential depletion of CD4+ Th17 cells correlates with mucosal immune dysfunction and disease progression . Interleukin ( IL ) -21 promotes differentiation of Th17 cells , long-term maintenance of functional CD8+ T cells , and differentiati...	In the gastrointestinal tract , preferential depletion of CD4+ Th17 cells occurs during the early stage of pathogenic HIV/SIV infections and correlates with loss of mucosal integrity , microbial translocation , immune activation and disease progression . As such , therapeutic intervention aimed at preserving intestinal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "inflammation", "immune", "cells", "cytokines", "immunity", "sexually", "transmitted", "diseases", "aids", "immune", "activation", "t", "cells", "immunology", "immune", "deficiency", "biology", "immunoregulation", "immune", "response"...	2013	Maintenance of Intestinal Th17 Cells and Reduced Microbial Translocation in SIV-infected Rhesus Macaques Treated with Interleukin (IL)-21
The release of Ca from intracellular stores is key to cardiac muscle function; however , the molecular control of intracellular Ca release remains unclear . Depletion of the intracellular Ca store ( sarcoplasmic reticulum , SR ) may play an important role , but the ability to measure local SR Ca with fluorescent Ca ind...	Calcium levels inside myocytes regulate the heart's force of contraction . Calcium is released from the primary intracellular store called the sarcoplasmic reticulum . Calcium release was directly observed as ‘calcium sparks’ using fluorescent calcium indicators inside the cell . More recently , calcium levels inside t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "anatomy", "and", "physiology", "neuroscience", "signaling", "pathways", "calcium", "signaling", "biophysics", "simulations", "neuroimaging", "signaling", "in", "cellular", "processes", "biology", "biophysics", "calcium", "signaling", "cascade", "calcium", "imaging", "phy...	2013	Extraction of Sub-microscopic Ca Fluxes from Blurred and Noisy Fluorescent Indicator Images with a Detailed Model Fitting Approach
There are currently a large number of “orphan” G-protein-coupled receptors ( GPCRs ) whose endogenous ligands ( peptide hormones ) are unknown . Identification of these peptide hormones is a difficult and important problem . We describe a computational framework that models spatial structure along the genomic sequence ...	Peptide hormones , or neuropeptides , are made up of a string of amino acids ranging from approximately 3 to 50 residues . These peptides are processed from a larger protein called a prohormone and activate a class of proteins called G-protein-coupled receptors ( GPCRs ) . Neuropeptides signal neurons and other cells l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "computational", "biology/comparative", "sequence", "analysis", "evolutionary", "biology/genomics", "computational", "biology/evolutionary", "modeling", "neuroscience/neuronal", "signaling", "mechanisms", "molecular", "biolo...	2009	Evolutionary Sequence Modeling for Discovery of Peptide Hormones
Long noncoding RNAs ( lncRNAs ) participate in various biological processes such as apoptosis . The function of lncRNAs is closely correlated with their localization within the cell . While regulatory potential of many lncRNAs has been revealed at specific subcellular location , the biological significance of discrete ...	As the reveal of tens of thousands of long noncoding RNAs ( lncRNAs ) from mammalian genomes , there is increasing interest to understand how these transcripts function in physiological and pathological processes . The regulatory potential of many lncRNAs has been revealed at specific subcellular location . Nevertheles...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "rnase", "inhibitors", "cell", "death", "messenger", "rna", "rna", "extraction", "cell", "processes", "enzymology", "long", "non-coding", "rnas", "epigenetics", "dna", "enzyme", "inhibitors", "extraction", "techniques", "chromatin", "dna", "methylation", "research", "...	2019	A long noncoding RNA distributed in both nucleus and cytoplasm operates in the PYCARD-regulated apoptosis by coordinating the epigenetic and translational regulation
Ductal carcinoma in situ ( DCIS ) is a heterogeneous group of non-invasive lesions of the breast that result from abnormal proliferation of mammary epithelial cells . Pathologists characterize DCIS by four tissue morphologies ( micropapillary , cribriform , solid , and comedo ) , but the underlying mechanisms that dist...	Breast cancer is a complex disease that affects women worldwide . One heterogeneous group of lesions , ductal carcinoma in situ ( DCIS ) , often begins as a nonmalignant disease but can readily progress if left untreated . The progression of this disease is not well understood because DCIS is typically removed upon det...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "biotechnology", "bioengineering", "cell", "biology", "engineering", "and", "technology", "biology", "and", "life", "sciences" ]	2014	Lattice-Based Model of Ductal Carcinoma In Situ Suggests Rules for Breast Cancer Progression to an Invasive State
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability . We show that the coding space of a given protein family—the total number of sequences in that family—can be estimated using models of maximum entropy trained on multiple sequence alignments of nat...	Natural protein molecules are only a small subset of the possible strings of amino acids . This naturally calls the question of how many protein sequences theoretically exist that are functional , and how many have already been explored by nature . To help answer this question , we developed a statistical method to cal...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "protein", "interactions", "split-decomposition", "method", "multiple", "alignment", "calculation", "mutation", "phylogenetics", "data", "management", "protein", "structure", "thermodynamics", "research", "and", "analysis", "methods", "sequence", "analysis", "co...	2019	Size and structure of the sequence space of repeat proteins
Identifying when past exposure to an infectious disease will protect against newly emerging strains is central to understanding the spread and the severity of epidemics , but the prediction of viral cross-protection remains an important unsolved problem . For foot-and-mouth disease virus ( FMDV ) research in particular...	New strains of viruses arise continually . Consequently , predicting when past exposure to closely related strains will protect against infection by novel strains is central to understanding the dynamics of a broad range of the world's most important infectious diseases . While previous research has developed valuable ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/immunity", "to", "infections", "virology/vaccines", "computational", "biology/comparative", "sequence", "analysis", "infectious", "diseases/viral", "infections", "mathematics/statistics", "immunology/immunity", "to", "infections" ]	2010	Sequence-Based Prediction for Vaccine Strain Selection and Identification of Antigenic Variability in Foot-and-Mouth Disease Virus
The architectonic type principle relates patterns of cortico-cortical connectivity to the relative architectonic differentiation of cortical regions . One mechanism through which the observed close relation between cortical architecture and connectivity may be established is the joint development of cortical areas and ...	The mechanisms that govern the establishment of cortico-cortical connections during the development of the mammalian brain are poorly understood . In computational simulation experiments reported here , we explored the foundations of an architectonic type principle , which attributes adult cortical connectivity to the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neurogenesis", "medicine", "and", "health", "sciences", "nervous", "system", "neuronal", "differentiation", "vertebrates", "neuroscience", "animals", "mammals", "cell", "differentiation", "primates", "developmental", "biology", "mathematics", "brain", "mapping", "nerve", ...	2018	Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle
All materials enter or exit the cell nucleus through nuclear pore complexes ( NPCs ) , efficient transport devices that combine high selectivity and throughput . NPC-associated proteins containing phenylalanine–glycine repeats ( FG nups ) have large , flexible , unstructured proteinaceous regions , and line the NPC . A...	The DNA at the heart of our cells is contained in the nucleus . This nucleus is surrounded by a barrier in which are buried gatekeepers , termed nuclear pore complexes ( NPCs ) , which allow the quick and efficient passage of certain materials while excluding all others . It has long been known that materials must bind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "cell", "biology", "eukaryotes", "computational", "biology" ]	2007	Efficiency, Selectivity, and Robustness of Nucleocytoplasmic Transport
Septins are critical for numerous cellular processes through the formation of heteromeric filaments and rings indicating the importance of structural regulators in septin assembly . Several posttranslational modifications ( PTMs ) mediate the dynamics of septin filaments in yeast . However , little is known about the r...	Septin polymerization into filaments and rings are built for numerous cellular processes , and misregulation of septin filaments is implicated in several human diseases . Therefore , it is important to identify structural regulator of septin assembly . We showed that SEPT12 was phosphorylated on the Ser198 residue , an...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "293t", "cells", "biological", "cultures", "germ", "cells", "animal", "models", "model", "organisms", "animal", "anatomy", "immunoprecipitation", "septins", "experimental", "organism", "systems", "mitochondria", "bioenergetics", "cellular", "structures", ...	2017	SEPT12 phosphorylation results in loss of the septin ring/sperm annulus, defective sperm motility and poor male fertility
Mosquito-borne viruses have been estimated to cause over 100 million cases of human disease annually . Many methodologies have been developed to help identify areas most at risk from transmission of these viruses . However , generally , these methodologies focus predominantly on the effects of climate on either the vec...	Mosquito-borne viruses , such as dengue , are believed to cause over 100 million cases of human disease annually . Current mathematical models that aim to predict risk of virus transmission are generally either highly “mosquito-centric” or “virus-centric” . For virus transmission to occur , conditions need to be suitab...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "togaviruses", "viral", "transmission", "and", "infection", "pathogens", "geographical", "regions", "microbiology", "temperate", "regions", "animals"...	2017	Co-occurrence of viruses and mosquitoes at the vectors’ optimal climate range: An underestimated risk to temperate regions?
The Cut homeobox 1 ( CUX1 ) gene is a target of loss-of-heterozygosity in many cancers , yet elevated CUX1 expression is frequently observed and is associated with shorter disease-free survival . The dual role of CUX1 in cancer is illustrated by the fact that most cell lines with CUX1 LOH display amplification of the r...	In the context of tumor development and progression , mutations are believed to accumulate owing to compromised DNA repair . Such mutations promote oncogenic growth . Yet cancer cells also need to sustain a certain level of DNA repair in order to replicate their DNA and successfully proliferate . Here we show that canc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "medicine", "biochemistry", "cellular", "stress", "responses", "nucleic", "acids", "dna", "dna", "repair", "biology", "molecular", "cell", "biology" ]	2014	RAS Transformation Requires CUX1-Dependent Repair of Oxidative DNA Damage
Viral myocarditis is a serious disease , commonly caused by type B coxsackieviruses ( CVB ) . Here we show that innate immune protection against CVB3 myocarditis requires the IFIT ( IFN-induced with tetratricopeptide ) locus , which acts in a biphasic manner . Using IFIT locus knockout ( IFITKO ) cardiomyocytes we show...	Viruses can infect the heart , causing inflammation–termed myocarditis–which is a serious , and sometimes fatal , disease . One way to combat the infection is by stimulating our immune system , encouraging it to fight the virus . However , the treatment that is currently used “revs up” many different parts of our immun...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "&", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "muscle", "tissue", "cardiovascular", "anatomy", "immunology", "microbiology", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "research", "and", "analysis", ...	2019	Biphasic and cardiomyocyte-specific IFIT activity protects cardiomyocytes from enteroviral infection
One of the paramount goals of synthetic biology is to have the ability to tune transcriptional networks to targeted levels of expression at will . As a step in that direction , we have constructed a set of unique binding sites for E . coli RNA Polymerase ( RNAP ) holoenzyme , designed using a model of sequence-dependen...	One of the most fundamental tuning parameters governing expression of a given gene is the strength of its promoter . But what are the sequence rules that govern promoter strength ? Recent high throughput mutagenesis experiments present an improved method for constructing an energy function that maps sequence to protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "statistical", "mechanics", "gene", "expression", "genetics", "biology", "genetics", "and", "genomics", "dna", "transcription" ]	2012	Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli
Staphylococcus epidermidis remains the predominant pathogen in prosthetic-device infections . Ventricular assist devices , a recently developed form of therapy for end-stage congestive heart failure , have had considerable success . However , infections , most often caused by Staphylococcus epidermidis , have limited t...	This study investigates the manner in which heart pumps become infected . Infections involving the driveline , the cord that connects the pump to its external power source , are a major complication of implantation of these devices . In this study , we examined why Staphylococcus epidermidis , a bacteria that is common...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/bacterial", "infections", "microbiology" ]	2009	SdrF, a Staphylococcus epidermidis Surface Protein, Contributes to the Initiation of Ventricular Assist Device Driveline–Related Infections
To identify new proteins required for faithful meiotic chromosome segregation , we screened a Schizosaccharomyces pombe deletion mutant library and found that deletion of the dbl2 gene led to missegregation of chromosomes during meiosis . Analyses of both live and fixed cells showed that dbl2Δ mutant cells frequently f...	Meiosis produces haploid gametes from diploid precursor cells . This reduction of chromosome number is achieved by two successive divisions after only a single round of DNA replication . To identify novel regulators of meiosis , we screened a library of fission yeast deletion mutants and found that deletion of the dbl2...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "anaphase", "enzymes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "enzymology", "germ", "cells", "zygotes", "fungi", "model", "organisms", "dna", "recombination", "dna", "schizosaccharomyces", "homologous", "recombination", "research", ...	2016	Dbl2 Regulates Rad51 and DNA Joint Molecule Metabolism to Ensure Proper Meiotic Chromosome Segregation
Distributed neural processing likely entails the capability of networks to reconfigure dynamically the directionality and strength of their functional connections . Yet , the neural mechanisms that may allow such dynamic routing of the information flow are not yet fully understood . We investigated the role of gamma ba...	Complex and flexible behavior likely results from the ability of groups of neurons in the brain to reconfigure dynamically the information flow across different brain areas , depending on what the brain is engaged in ( processing a stimulus or carrying out a task ) . Here , we investigate how oscillations of cortical a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Shifts of Gamma Phase across Primary Visual Cortical Sites Reflect Dynamic Stimulus-Modulated Information Transfer
The control of Aedes albopictus , a major vector for viral diseases , such as dengue fever and chikungunya , has been largely reliant on the use of the larvicide temephos for many decades . This insecticide remains a primary control tool for several countries and it is a potential reliable reserve , for emergency epide...	Some of the most immediate challenges that the world faces are caused by insecticide-resistant mosquitoes that seriously threaten human health , via the diseases they transmit . Temephos is a major larvicide that has been used extensively for the control of Ae . albopictus and its often sympatric Ae . aegypti . Here we...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Transcriptome Profiling and Genetic Study Reveal Amplified Carboxylesterase Genes Implicated in Temephos Resistance, in the Asian Tiger Mosquito Aedes albopictus
The well-studied DNA replication origins of the model budding and fission yeasts are A/T-rich elements . However , unlike their yeast counterparts , both plant and metazoan origins are G/C-rich and are associated with transcription start sites . Here we show that an industrially important methylotrophic budding yeast ,...	Genome duplication in eukaryotes initiates at loci called replication origins . Origins in most budding and fission yeasts are A/T-rich DNA sequences , while metazoan origins are G/C-rich and are often associated with promoters . Here we have globally mapped replication origins and nucleosome positions in an industrial...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "model", "organisms", "chromosome", "biology", "genetic", "screens", "genetics", "molecular", "genetics", "comparative", "genomics", "biology", "genomics", "yeast", "and", "fungal", "models" ]	2014	GC-Rich DNA Elements Enable Replication Origin Activity in the Methylotrophic Yeast Pichia pastoris
Computational strain design protocols aim at the system-wide identification of intervention strategies for the enhanced production of biochemicals in microorganisms . Existing approaches relying solely on stoichiometry and rudimentary constraint-based regulation overlook the effects of metabolite concentrations and sub...	Computational strain design procedures aim at assisting metabolic engineering efforts by identifying metabolic interventions leading to the targeted overproduction of a desired chemical using network models of cellular metabolism . The effect of metabolite concentrations and substrate-level enzyme regulation cannot be ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bioengineering", "systems", "biology", "biochemistry", "biological", "systems", "engineering", "operations", "research", "social", "and", "behavioral", "sciences", "metabolic", "pathways", "mathematical", "optimization", "metabolic", "networks", "biology", "computational", ...	2014	k-OptForce: Integrating Kinetics with Flux Balance Analysis for Strain Design
Amino-terminal acetylation is probably the most common protein modification in eukaryotes with as many as 50%–80% of proteins reportedly altered in this way . Here we report a systematic analysis of the predicted N-terminal processing of cytosolic proteins versus those destined to be sorted to the secretory pathway . W...	The eukaryotic cell comprises several distinct compartments , called organelles , required to perform specific functions . The proteins in these compartments are almost always synthesised in the cytoplasm and so require complex sorting mechanisms to ensure their delivery to the appropriate organelle . Of course , not a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "subcellular", "organelles", "cell", "biology", "membranes", "and", "sorting", "biology", "molecular", "cell", "biology" ]	2011	N-Terminal Acetylation Inhibits Protein Targeting to the Endoplasmic Reticulum
New strategies to eliminate dengue have been proposed that specifically target older Aedes aegypti mosquitoes , the proportion of the vector population that is potentially capable of transmitting dengue viruses . Evaluation of these strategies will require accurate and high-throughput methods of predicting mosquito age...	Once infected with dengue virus , a female Aedes aegypti mosquito must survive longer than twelve days before it can transmit the virus to an uninfected person . New dengue control strategies therefore aim to circumvent dengue transmission using entomopathogenic microorganisms that shorten mosquito lifespan . Accurate ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry/transcription", "and", "translation", "infectious", "diseases/neglected", "tropical", "diseases", "ecology/population", "ecology" ]	2010	Field Validation of a Transcriptional Assay for the Prediction of Age of Uncaged Aedes aegypti Mosquitoes in Northern Australia
Following an epidemiological study carried out in 2006 showing a high prevalence of blinding trachoma in the Far North Region of Cameroon , a trachoma elimination programme using the SAFE strategy was initiated: three yearly trachoma mass treatments were to be performed . The entire district population ( 120 , 000 pers...	Trachoma is the leading cause of infectious blindness worldwide , accounting for 1 . 3 million cases of blindness . Although it has disappeared in many regions of the world , trachoma is still endemic in Africa , Eastern Mediterranean , Latin America , Asia , and Australia . The WHO has currently set a target of 2020 f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "ophthalmology/eye", "infections" ]	2010	Elimination of Active Trachoma after Two Topical Mass Treatments with Azithromycin 1.5% Eye Drops
The fitness effect of mutations can be influenced by their interactions with the environment , other mutations , or both . Previously , we constructed 32 ( = 25 ) genotypes that comprise all possible combinations of the first five beneficial mutations to fix in a laboratory-evolved population of Escherichia coli . We f...	The fitness effect of beneficial mutations can depend on how they interact with their genetic and external environment . The form of these interactions is important because it can alter adaptive outcomes , selecting for or against certain combinations of beneficial mutations . Here , we examine how interactions between...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "processes", "population", "genetics", "biology", "evolutionary", "theory", "evolutionary", "biology", "evolutionary", "genetics" ]	2013	The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape
Zinc ( Zn ) is essential for the optimal growth of plants but is toxic if present in excess , so Zn homeostasis needs to be finely tuned . Understanding Zn homeostasis mechanisms in plants will help in the development of innovative approaches for the phytoremediation of Zn-contaminated sites . In this study , Zn tolera...	Plants are adapted to soils in which the amounts of different nutrients vary widely , like Zn-deficient or Zn-contaminated soils . Exploring the molecular bases of plant adaptation to Zn-contaminated soils is important in determining strategies for phytoremediation . Here , we describe the mapping and characterization ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "plant", "biology", "plant", "genetics", "biology", "plant", "physiology" ]	2012	Natural Variation at the FRD3 MATE Transporter Locus Reveals Cross-Talk between Fe Homeostasis and Zn Tolerance in Arabidopsis thaliana
Parkinson’s disease ( PD ) is a neurodegenerative disorder characterized by the loss of dopamine ( DA ) neurons in the substantia nigra pars compacta ( SNc ) . Rare genetic mutations in genes such as Parkin , Pink1 , DJ-1 , α-synuclein , LRRK2 and GBA are found to be responsible for the disease in about 15% of the case...	Parkinson’s disease motor symptoms have been linked to age-dependent degeneration of a class of neurons in the brain that release the chemical messenger dopamine . The reason for the selective loss of these neurons represents a key unsolved mystery . One hypothesis is that the neurons most at risk in this disease are t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "oxidative", "stress", "neurodegenerative", "diseases", "brain", "vertebrates", "mice", "neuroscience", "animals", "mammals", "animal", "models", "luminescent", "proteins", "model", "organisms", "yellow", "fluorescent", "protein", ...	2019	Increased vulnerability of nigral dopamine neurons after expansion of their axonal arborization size through D2 dopamine receptor conditional knockout
Leptospirosis is a potentially fatal bacterial zoonosis that is endemic throughout the tropics and may be misdiagnosed as dengue . Delayed hospital admission of leptospirosis patients is associated with increased mortality . During a concurrent dengue/leptospirosis epidemic in Puerto Rico in 2010 , suspected dengue pat...	Leptospirosis is a common tropical illness that results from exposure to the urine of animals infected with Leptospira bacteria . Because leptospirosis shares signs and symptoms with other common tropical illnesses such as dengue , identification of patients with leptospirosis can be challenging . Early identification ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "clinical", "laboratory", "sciences", "pathology", "and", "laboratory", "medicine", "drugs", "tropical", "diseases", "geographical", "locations", "microbiology", "biomarkers", "north", "america", "bacterial", "dis...	2016	Early Indicators of Fatal Leptospirosis during the 2010 Epidemic in Puerto Rico
Chemosensory pheromonal information regulates aggression and reproduction in many species , but how pheromonal signals are transduced to reliably produce behavior is not well understood . Here we demonstrate that the pheromonal signals detected by Gr32a-expressing chemosensory neurons to enhance male aggression are fil...	To mate or fight ? When meeting other members of their species , male fruit flies must determine whether a second fly is male or female and proceed with the appropriate behavioral patterns . The taste receptor , Gr32a , has been reported to respond to chemical messages ( pheromones ) that are important for gender recog...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Octopamine Neuromodulation Regulates Gr32a-Linked Aggression and Courtship Pathways in Drosophila Males
In contrast to human cells , very few HSV-1 genes are known to be spliced , although the same pre-mRNA processing machinery is shared . Here , through global analysis of splice junctions in cells infected with HSV-1 and an HSV-1 mutant virus with deletion of infectious cell culture protein 27 ( ICP27 ) , one of two vir...	Little is known regarding to how HSV , a large DNA virus and known to contain very few spliced genes , escapes host pre-mRNA splicing machinery . Here , by establishing a high throughput splice junction identification platform and quantitative analysis method to assess splicing efficiency based on high throughput data ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "vero", "cells", "biological", "cultures", "microbiology", "alternative", "splicing", "dna", "replication", "molecular", "biology", "techniques", "dna", "microbial", "genetics", "research", "and", "analysis", "me...	2019	Hidden regulation of herpes simplex virus 1 pre-mRNA splicing and polyadenylation by virally encoded immediate early gene ICP27
Mutations in the leucine-rich repeat kinase 2 ( LRRK2 ) gene are associated with late-onset , autosomal-dominant , familial Parkinson's disease ( PD ) and also contribute to sporadic disease . The LRRK2 gene encodes a large protein with multiple domains , including functional Roc GTPase and protein kinase domains . Mut...	Parkinson's disease ( PD ) is the second most common neurodegenerative disorder . PD is considered to be caused by a combination of risk factors including environmental exposure , age , and a positive family history for disease . Several genes have been unambiguously implicated in PD . However , our knowledge is still ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/neurobiology", "of", "disease", "and", "regeneration", "neurological", "disorders/movement", "disorders" ]	2010	GTPase Activity Plays a Key Role in the Pathobiology of LRRK2
Drug molecules not only interact with specific targets , but also alter the state and function of the associated biological network . How to design drugs and evaluate their functions at the systems level becomes a key issue in highly efficient and low–side-effect drug design . The arachidonic acid metabolic network is ...	Inflammation is a basic way in which the body reacts to infection , irritation , or other injury . When it is uncontrolled and misdirected , it causes diseases such as rheumatoid arthritis , inflammatory bowel disease , asthma , and others . In the United States , more than 1% of the population uses nonsteroidal anti-i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "homo", "(human)", "computational", "biology" ]	2007	Dynamic Simulations on the Arachidonic Acid Metabolic Network
Here we investigate the correlations between coding sequence substitutions as a function of their separation along the protein sequence . We consider both substitutions between the reference genomes of several Drosophilids as well as polymorphisms in a population sample of Zimbabwean Drosophila melanogaster . We find t...	Genes are templates for proteins , yet evolutionary studies of genes and proteins often bear little resemblance . Analyses of gene evolution typically treat each codon independently , quantifying gene evolution by summing over the constituent codons . In contrast , studies of protein evolution generally incorporate pro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/structural", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "molecular", "biology/molecular", "evolution", "evolutionary", "biology/genomics", "evolutionary", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2011	Correlated Evolution of Nearby Residues in Drosophilid Proteins
A cluster of eleven patients , including eight family members and three healthcare workers with fever and thrombocytopenia occurred in Yixing County , Jiangsu Province , China , from October to November 1996 . However , the initial investigation failed to identify its etiology . Severe fever with thrombocytopenia syndr...	SFTSV was first discovered in 2009 . It can be transmitted through tick bites , direct contact with SFTS patients’ blood or bloody secretion , and probable aerosol transmission . SFTS was listed as one of the nine infectious diseases on the WHO priority list in 2017 because of its trend of wider distribution and rising...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "body", "fluids", "china", "immunology", "geographical", "locations", "signs", "and", "symptoms", "antibodies", "immunologic", ...	2018	A cluster of cases of severe fever with thrombocytopenia syndrome bunyavirus infection in China, 1996: A retrospective serological study
We assess the variability of protein function in protein sequence and structure space . Various regions in this space exhibit considerable difference in the local conservation of molecular function . We analyze and capture local function conservation by means of logistic curves . Based on this analysis , we propose a m...	Proteins are an essential class of molecules playing a variety of roles within a cell . They can be described in various ways: amongst others , by sequence , structure , and function . Determining protein function by wet lab procedures is challenging and tedious . Simultaneously , sequencing and structural genomics pro...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/macromolecular", "structure", "analysis", "computational", "biology/systems", "biology", "computational", "biology/protein", "homology", "detection" ]	2008	Local Function Conservation in Sequence and Structure Space
Human Cytomegalovirus ( HCMV ) infection induces several metabolic activities that have been found to be important for viral replication . The cellular AMP-activated protein kinase ( AMPK ) is a metabolic stress response kinase that regulates both energy-producing catabolic processes and energy-consuming anabolic proce...	Human Cytomegalovirus ( HCMV ) is a ubiquitous human pathogen that is a major cause of birth defects . HCMV can also cause severe disease in immunocompromised individuals including transplant recipients , leukemia patients and those infected with HIV . It is clear that upon infection , HCMV takes control of numerous ce...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "biology", "microbiology", "molecular", "cell", "biology" ]	2012	HCMV Targets the Metabolic Stress Response through Activation of AMPK Whose Activity Is Important for Viral Replication
EMBRYONIC FLOWER1 ( EMF1 ) is a plant-specific gene crucial to Arabidopsis vegetative development . Loss of function mutants in the EMF1 gene mimic the phenotype caused by mutations in Polycomb Group protein ( PcG ) genes , which encode epigenetic repressors that regulate many aspects of eukaryotic development . In Ara...	Polycomb group ( PcG ) proteins are epigenetic repressors maintaining developmental states in eukaryotic organisms . Plant PcG proteins are expected to be general epigenetic repressors; however , their overall impact on growth and differentiation and their mechanism of repression are still unclear . Here we identified ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	EMF1 and PRC2 Cooperate to Repress Key Regulators of Arabidopsis Development
Loss-of-function mutations in PINK1 , which encodes a mitochondrially targeted serine/threonine kinase , result in an early-onset heritable form of Parkinson's disease . Previous work has shown that PINK1 is constitutively degraded in healthy cells , but selectively accumulates on the surface of depolarized mitochondri...	Mitochondria are essential organelles that provide most of the cell's energy and perform many other critical functions . The gradual accumulation of defective mitochondria is thought to play a role in aging and in diseases of the nervous system , including Parkinson's disease . The selective elimination of defective mi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "molecular", "neuroscience", "neurobiology", "of", "disease", "and", "regeneration", "cellular", "neuroscience", "medicine", "and", "health", "sciences", "model", "organisms", "cell", "biology", "neurology", "genetics", "biology", "and", "life", "science...	2014	PINK1-Parkin Pathway Activity Is Regulated by Degradation of PINK1 in the Mitochondrial Matrix
Susceptibility to HIV has been linked to systemic CD4+ T cell activation in cohorts of seronegative individuals with high HIV-exposure risk . We recently described an increased risk of HIV transmission in individuals infected with Wuchereria bancrofti , the causative agent for lymphatic filariasis , in a prospective co...	The importance of CD4 T cell activation for HIV susceptibility has been emphasized in several studies focusing on HIV transmission and prevention . Particularly , activated HLA-DR+ CD4 T cells may play a major role in HIV susceptibility . In this analysis we describe systemic activation of CD4 T cells in individuals in...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "t", "helper", "cells", "invertebrates", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "helminths", "pathogens", "immunology", "microbiology", "parasitic", "diseases", "animals", "retroviruses...	2019	Wuchereria bancrofti infection is linked to systemic activation of CD4 and CD8 T cells
The aim of this study was to evaluate the potential use of nasal , oral , and ear swabs for molecular diagnosis of canine visceral leishmaniasis ( CVL ) in an endemic urban area in Brazil . Sixty-two naturally infected and ten healthy dogs were enrolled in this study . Bone marrow aspirates , peripheral blood , skin bi...	Visceral leishmaniasis ( VL ) is an important public health problem in different regions of the world . It presents high lethality in human cases without suitable treatment and is considered one of the most important disorders in dogs , the main domestic reservoir of the etiological agent of VL ( Leishmania infantum ) ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "veterinary", "diseases", "veterinary", "parasitology", "nucleic", "acids", "parasitology", "dna", "biology", "dna", "amplification", "microbiology", "veterinary", "science", "quantitative", "parasitology" ]	2013	Nasal, Oral and Ear Swabs for Canine Visceral Leishmaniasis Diagnosis: New Practical Approaches for Detection of Leishmania infantum DNA
Host shifts–where a pathogen jumps between different host species–are an important source of emerging infectious disease . With on-going climate change there is an increasing need to understand the effect changes in temperature may have on emerging infectious disease . We investigated whether species’ susceptibilities ...	Emerging infectious diseases are often the result of a host shift , where a pathogen jumps from one host species into another . Understanding the factors underlying host shifts is a major goal for infectious disease research . This effort has been further complicated by the fact that host-parasite interactions are now ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "atmospheric", "science", "microbiology...	2018	Changes in temperature alter the potential outcomes of virus host shifts
Evolution by natural selection is fundamentally shaped by the fitness landscapes in which it occurs . Yet fitness landscapes are vast and complex , and thus we know relatively little about the long-range constraints they impose on evolutionary dynamics . Here , we exhaustively survey the structural landscapes of RNA mo...	Evolutionary biology tells us much about the immediate fate of a mutation once it appears , but relatively little about its long-term evolutionary implications . Major evolutionary transitions from one trait to another may depend on a long sequence of interacting mutations , each arising by chance and surviving natural...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/evolutionary", "modeling", "evolutionary", "biology", "evolutionary", "biology/bioinformatics" ]	2008	The Ascent of the Abundant: How Mutational Networks Constrain Evolution
Plant pathogens secrete an arsenal of effector proteins to impair host immunity . Some effectors possess enzymatic activities that can modify their host targets . Previously , we demonstrated that a Phytophthora sojae RXLR effector Avr3b acts as a Nudix hydrolase when expressed in planta; and this enzymatic activity is...	Phytophthora sojae , an oomycete pathogen that causes the Phytophthora root and stem rot disease of soybean , delivers variety of effectors into host cell to reprogram host immunity . Genome sequencing uncovers that P . sojae genome encode several hundreds of effector genes . However , the mode of action of most of the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Activation of Phytophthora Effector Avr3b by Plant Cyclophilin is Required for the Nudix Hydrolase Activity of Avr3b
Rift Valley fever virus ( RVFV ) , a member of the genus Phlebovirus within the family Bunyaviridae , causes periodic outbreaks in livestocks and humans in countries of the African continent and Middle East . RVFV NSs protein , a nonstructural protein , is a major virulence factor that exhibits several important biolog...	Rift Valley fever virus ( RVFV ) has a significant impact on the livestock industry because of its high mortality rate in young ruminants and causation of a high abortion rate in pregnant animals . Human RVFV infections generally manifest as self-limiting and non-fatal illnesses . However , a small percentage of patien...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "microbial", "mutation", "rift", "valley", "fever", "virus", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "messenger", "rna", "microbiology", "dna", "transcription", "viruses", ...	2016	Mechanistic Insight into the Host Transcription Inhibition Function of Rift Valley Fever Virus NSs and Its Importance in Virulence
The key molecular event that marks entry into the cell cycle is transcription of G1 cyclins , which bind and activate cyclin-dependent kinases . In yeast cells , initiation of G1 cyclin transcription is linked to achievement of a critical cell size , which contributes to cell-size homeostasis . The critical cell size i...	A critical point in the cell cycle occurs in G1 phase , when cells must decide whether to enter a new round of cell division . At this time , cells assess nutrient availability to ensure that they have sufficient resources to complete cell growth and division . Vertebrate cells also assess growth factors that control c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/gene", "function", "cell", "biology/gene", "expression", "cell", "biology/cell", "signaling" ]	2009	The Rts1 Regulatory Subunit of Protein Phosphatase 2A Is Required for Control of G1 Cyclin Transcription and Nutrient Modulation of Cell Size
The protozoan parasite Plasmodium is transmitted by female Anopheles mosquitoes and undergoes obligatory development within a parasitophorous vacuole in hepatocytes before it is released into the bloodstream . The transition to the blood stage was previously shown to involve the packaging of exoerythrocytic merozoites ...	Malaria is one of the most important infectious diseases in the developing world . It is caused by Plasmodium parasites , which are transmitted by female Anopheles mosquitoes during blood feeding . In the mammalian host , Plasmodium first develops within liver cells , growing from one parasite into many thousands . Aft...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biology", "microbiology", "host-pathogen", "interaction", "parasitology", "parasite", "physiology" ]	2011	Hostile Takeover by Plasmodium: Reorganization of Parasite and Host Cell Membranes during Liver Stage Egress
Detecting regular patterns in the environment , a process known as statistical learning , is essential for survival . Neuronal adaptation is a key mechanism in the detection of patterns that are continuously repeated across short ( seconds to minutes ) temporal windows . Here , we found in mice that a subcortical struc...	Some things are learned simply because they are there and not because they are relevant at that moment in time . This is particularly true of surrounding sounds , which we process automatically and continuously , detecting their repetitive patterns or singularities . Learning about rewards and punishment is typically a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "action", "potentials", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "brain", "social", "sciences", "electrophysiology", "vertebrates", "neuroscience", "learning", "and", "memory"...	2018	Auditory midbrain coding of statistical learning that results from discontinuous sensory stimulation
Although the vitamin A metabolite retinoic acid ( RA ) plays a critical role in immune function , RA synthesis during infection is poorly understood . Here , we show that retinal dehydrogenases ( Raldh ) , required for the synthesis of RA , are induced during a retinoid-dependent type-2 immune response elicited by Schi...	Vitamin A deficiency , a major global health concern , increases morbidity and death due to infectious diseases . For vitamin A to be utilized by the immune system , it must be metabolized into retinoic acid ( RA ) , its active form . RA is a key determinant of T cell activity . However , its contribution to protective...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "biology", "microbiology" ]	2012	Upregulation of Retinal Dehydrogenase 2 in Alternatively Activated Macrophages during Retinoid-dependent Type-2 Immunity to Helminth Infection in Mice
Neuritis is a frequent complication of Myocobacteria leprae infection and treatment due to the variety of mechanisms through which it can occur . Not only can mycobacterial invasion into peripheral nerves directly cause damage and inflammation , but immune-mediated inflammatory episodes ( termed leprosy reactions ) can...	Leprosy infection is frequently complicated by peripheral neuritis , but is often difficult to distinguish if it is due to persistent infection , an immune-mediated reaction , or adverse drug reaction . In this case , we present a patient with ulnar neuritis occurring four years after multidrug therapy , with improveme...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "nervous", "system", "immunology", "tropical", "diseases", "corticosteroid", "therapy", "macroglial", "cells", "bacterial", "diseases", "signs", "and", "sym...	2019	Late-onset ulnar neuritis following treatment of lepromatous leprosy infection
Anaplasma phagocytophilum is an emerging pathogen that causes human granulocytic anaplasmosis . Infection with this zoonotic pathogen affects cell function in both vertebrate host and the tick vector , Ixodes scapularis . Global tissue-specific response and apoptosis signaling pathways were characterized in I . scapula...	The continuous human exploitation of environmental resources and the increase in human outdoor activities , which have allowed for the contact with arthropod vectors normally present in the field , has promoted the emergence and resurgence of vector-borne pathogens . Among these , Anaplasma phagocytophilum is an emergi...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Systems Biology of Tissue-Specific Response to Anaplasma phagocytophilum Reveals Differentiated Apoptosis in the Tick Vector Ixodes scapularis
During cell division the genetic material on chromosomes is distributed to daughter cells by a dynamic microtubule structure called the mitotic spindle . Here we establish a reconstitution system to assess the contribution of individual chromosome proteins to mitotic spindle formation around single 10 µm diameter porou...	The mitotic spindle is a bipolar structure that is responsible for separating the two sets of duplicated chromosomes in a dividing cell , thereby delivering one set to each of the two daughter cells . It is built from dynamic filaments called microtubules , as well as hundreds of other components that contribute to the...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "engineering", "biology" ]	2011	Mitotic Spindle Assembly around RCC1-Coated Beads in Xenopus Egg Extracts
Trials to reintroduce chloroquine into regions of Africa where P . falciparum has regained susceptibility to chloroquine are underway . However , there are long-standing concerns about whether chloroquine increases lytic-replication of Epstein-Barr virus ( EBV ) , thereby contributing to the development of endemic Burk...	Viruses that persist for the life of the host , like the herpesvirus Epstein-Barr virus ( EBV ) , tightly regulate lytic replication to reduce killing of host cells and ensure virus survival . We show that repression of EBV replication is disrupted by the antimalarial drug chloroquine which modifies an otherwise normal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "pathogens", "drugs", "microbiology", "immunoblotting", "antimalarials", "viruses", "dna", "damage", "dna", "replication", "immuno...	2017	Chloroquine triggers Epstein-Barr virus replication through phosphorylation of KAP1/TRIM28 in Burkitt lymphoma cells
Following pathogen infection the hosts' nervous and immune systems react with coordinated responses to the danger . A key question is how the neuronal and immune responses to pathogens are coordinated , are there common signaling pathways used by both responses ? Using C . elegans we show that infection by pathogenic s...	Once infected by a pathogen the nervous and immune systems of many animals react with coordinated responses to the danger . A key question is what are the pathways by which responses to infection occur and to what extent are the same pathways involved in differing responses ? Here we demonstrate that a Gαq-RhoA pathway...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "molecular", "neuroscience", "model", "organisms", "molecular", "cell", "biology", "genetics", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	Behavioral and Immune Responses to Infection Require Gαq- RhoA Signaling in C. elegans
Current work in elucidating relationships between diseases has largely been based on pre-existing knowledge of disease genes . Consequently , these studies are limited in their discovery of new and unknown disease relationships . We present the first quantitative framework to compare and contrast diseases by an integra...	Many human diseases are related to each other through shared causes or even shared pathology . Knowledge of these relationships has long been exploited to treat similar diseases with the same therapies . However , most of the traditional approaches to discover these relationships have depended on subjective measures , ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "pharmacology/drug", "development", "pathology/molecular", "pathology" ]	2010	Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets
Parasites of the Leishmania genus infect and survive within macrophages by inhibiting several microbicidal molecules , such as nitric oxide and pro-inflammatory cytokines . In this context , various species of Leishmania have been reported to inhibit or reduce the production of IL-1β both in vitro and in vivo . However...	Leishmania parasites are the causative agent of leishmaniasis , a wide spread disease in tropical and subtropical areas . The microorganisms have been shown to be well-adapted to their hosts and are able to enter their target cells where they replicate themselves . To ensure these processes , Leishmania disrupts a mult...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	PKC/ROS-Mediated NLRP3 Inflammasome Activation Is Attenuated by Leishmania Zinc-Metalloprotease during Infection
Network-based infectious disease models have been highly effective in elucidating the role of contact structure in the spread of infection . As such , pair- and neighbourhood-based approximation models have played a key role in linking findings from network simulations to standard ( random-mixing ) results . Recently ,...	Networks are now widely used to model infectious diseases , but have posed significant mathematical challenges . Recently analytic results have been obtained for ‘one-off’ network epidemics that follow the SIR paradigm , but these results do not carry over to other scenarios—most significantly to many sexually transmit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "approximation", "methods", "infectious", "diseases", "computer", "and", "information", "sciences", "medicine", "and", "health", "sciences", "mathematics", "network", "motifs", "simulation", "and", "modeling", "sexually", "transmitted", "diseases", "network", "analysis", ...	2016	Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks
Glial cells play structural and functional roles central to the formation , activity and integrity of neurons throughout the nervous system . In the retina of vertebrates , the high energetic demand of photoreceptors is sustained in part by Müller glia , an intrinsic , atypical radial glia with features common to many ...	Glia are the caretakers of the nervous system . Like their neighboring neurons , different glial subtypes exist that share many overlapping functions . Despite our recognition of glia as a key component of the brain , the genetic networks that mediate their neuroprotective functions remain relatively poorly understood ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ocular", "anatomy", "vertebrates", "social", "sciences", "neuroscience", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "genome", "analysi...	2017	Multifunctional glial support by Semper cells in the Drosophila retina
A common metaphor for describing development is a rugged “epigenetic landscape” where cell fates are represented as attracting valleys resulting from a complex regulatory network . Here , we introduce a framework for explicitly constructing epigenetic landscapes that combines genomic data with techniques from spin-glas...	Traditionally , standard development has been viewed as a one-way process; an organism starts as a single cell ( embryonic stem cell , ESC ) that divides into a multitude of mature cell types ( skin cells , heart , liver , etc ) . But , in 2006 Takahashi and Yamanaka revolutionized this view by stochastically convertin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "systems", "biology", "theoretical", "biology", "biophysics", "theory", "biology", "and", "life", "sciences", "physical", "sciences", "computational", "biology", "biophysics" ]	2014	Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes
Considering the short lifetime of IgA antibodies in serum and the key advantages of antibody detection ELISAs in terms of sensitivity and specificity , Bio-Rad has just developed a new ELISA test based on the detection of specific anti-dengue IgA . This study has been carried out to assess the performance of this Plate...	Dengue disease has become a major global public health concern , but an ideal diagnostic test that permits early and rapid diagnosis is not yet available . Improving diagnostic performance in this area is a major challenge and necessitates the development and evaluation of new efficient , accurate methods . According t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Evaluation of the Diagnostic Accuracy of a New Dengue IgA Capture Assay (Platelia Dengue IgA Capture, Bio-Rad) for Dengue Infection Detection
Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease , American trypanosomiasis , in Southern Ecuador and Northern Peru . Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vect...	Understanding Chagas disease vector ( triatomine ) population dispersal is key for the design of control measures tailored for the epidemiological situation of a particular region . In Ecuador , Rhodnius ecuadoriensis is a cause of concern for Chagas disease transmission , since it is widely distributed from the centra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "ecuador", "population", "genetics", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "animals", "animal", "models", "genome", "analysis", "experimental", "organism", "systems", "neglec...	2017	2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador
During 2011 a large outbreak of typhoid fever affected an estimated 1430 people in Kikwit , Democratic Republic of Congo . The outbreak started in military camps in the city but then spread to the general population . This paper reports the results of an ecological analysis and a case-control study undertaken to examin...	There was a large outbreak of typhoid fever in Kikwit , DRC , in late 2011 . The outbreak started in military camps in the city but then spread to the general population . Multiple investigations were undertaken to understand how the disease spread . The worst affected areas of the city were mapped and compared to the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "water", "resources", "surface", "water", "pathology", "and", "laboratory", "medicine", "health", "care", "bacterial", "diseases", "research", "design", "signs", "and", "symptoms",...	2018	Typhoid fever outbreak in the Democratic Republic of Congo: Case control and ecological study
The genome sequencing of several Leishmania species has provided immense amounts of data and allowed the prediction of the metabolic pathways potentially operating . Subsequent genetic and proteomic studies have identified stage-specific proteins and putative virulence factors but many aspects of the metabolic adaptati...	Leishmania infections are considered neglected tropical diseases as the parasites affect millions of people worldwide but there are limited research efforts aimed at obtaining vaccines and new drugs . Leishmania has a digenetic life cycle alternating between promastigote forms , which develop in the sand-fly , the vect...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "biochemistry", "infectious", "diseases", "biology", "microbiology", "zoology" ]	2011	Metabolic Variation during Development in Culture of Leishmania donovani Promastigotes
The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks . In Namibia , anthrax outbreaks occur annually in the Etosha National Park ( ENP ) and on private game and livestock farms . We genotyped 38...	Anthrax , the disease caused by Bacillus anthracis , is a neglected zoonotic diseases in the context of its impact on poor rural and periurban communities in Africa and other less developed areas of the world . Several regions of Namibia , the Etosha National Park in particular , are well known as being endemic areas f...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "bacteriology", "veterinary", "diseases", "veterinary", "epidemiology", "veterinary", "microbiology", "biology", "microbiology", "veterinary", "science", "veterinary", "medicine" ]	2012	Distribution and Molecular Evolution of Bacillus anthracis Genotypes in Namibia
Anthropogenic environmental changes may lead to ecosystem destabilization and the unintentional colonization of new habitats by parasite populations . A remarkable example is the outbreak of intestinal schistosomiasis in Northwest Senegal following the construction of two dams in the ‘80s . While many studies have inve...	Schistosoma parasites successfully colonize new regions following the construction of water schemes for power production or agricultural purposes . Here we investigated the colonization history of the human parasite Schistosoma mansoni in Northwest Senegal following the construction of two dams in the ‘80s . Parasites ...	[ "Abstract", "Introduction", "Material", "&", "Methods", "Results", "Discussion" ]	[]	2015	Reconstructing Colonization Dynamics of the Human Parasite Schistosoma mansoni following Anthropogenic Environmental Changes in Northwest Senegal
The epigenetic activity of transposable elements ( TEs ) can influence the regulation of genes; though , this regulation is confined to the genes , promoters , and enhancers that neighbor the TE . This local cis regulation of genes therefore limits the influence of the TE's epigenetic regulation on the genome . TE acti...	The portion of the genome that does not encode for genes is often overlooked as a source of cellular regulatory information . Here , we demonstrate that regulatory information controlling expression and protein production from a gene called UBP1b is coming from a distant non-gene transposable element ( TE ) . TEs are f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transposons", "model", "organisms", "plant", "and", "algal", "models", "molecular", "cell", "biology", "plant", "science", "plant", "biology", "gene", "expression", "genetics", "epigenetics", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2012	Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA
The Mitochondrial Carrier Family ( MCF ) is a signature group of integral membrane proteins that transport metabolites across the mitochondrial inner membrane in eukaryotes . MCF proteins are characterized by six transmembrane segments that assemble to form a highly-selective channel for metabolite transport . We disco...	Mitochondrial carrier proteins evolved during endosymbiosis to transport substrates across the mitochondrial inner membrane . As such the proteins are associated exclusively with eukaryotic organisms . Despite this , we identified putative mitochondrial carrier proteins in the genomes of different intracellular bacteri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "molecular", "cell", "biology", "biology", "genomics", "microbiology", "genetics", "and", "genomics" ]	2012	Legionella pneumophila Secretes a Mitochondrial Carrier Protein during Infection
Self-motion , steering , and obstacle avoidance during navigation in the real world require humans to travel along curved paths . Many perceptual models have been proposed that focus on heading , which specifies the direction of travel along straight paths , but not on path curvature , which humans accurately perceive ...	Much human and primate psychological and electrophysiological research on visually-guided navigation has focused on heading perception , defined as the instantaneous direction of travel . However , the perception of path of travel , or trajectory , is arguably more important , because it informs in a more general sense...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "visual", "system", "psychology", "social", "and", "behavioral", "sciences", "central", "nervous", "system", "neural", "networks", "computational", "neuroscience", "sensory", "systems", "biology", "sensory", "perception", "neuroscience", "neurophysiology", "coding", "mech...	2014	A Unified Model of Heading and Path Perception in Primate MSTd
Apicomplexan parasites can change fundamental features of cell division during their life cycles , suspending cytokinesis when needed and changing proliferative scale in different hosts and tissues . The structural and molecular basis for this remarkable cell cycle flexibility is not fully understood , although the cen...	Apicomplexan parasites infect many different hosts and tissues , causing numerous human diseases , including malaria . These important pathogens have a peculiar cell cycle in which chromosomes sometimes amplify to remarkable levels , followed by concerted cell division—providing an unusual proliferative capacity . This...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Novel Bipartite Centrosome Coordinates the Apicomplexan Cell Cycle
Burkholderia pseudomallei ( B . pseudomallei ) , the causative agent of melioidosis , is a deadly pathogen endemic across parts of tropical South East Asia and Northern Australia . B . pseudomallei can remain latent within the intracellular compartment of the host cell over prolonged periods of time , and cause persist...	Melioidosis is an endemic tropical disease in South East Asia and Northern Australia , which is caused by Burkholderia pseudomallei , an environmental bacterium found in the soils of paddy fields and muddy waters across these regions . The bacterium is known to reside within the host cell for prolonged periods of time ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "spleen", "melioidosis", "animal", "models", "of", "disease", "immunology", "microbiology", "animal", "models", "bacterial"...	2016	Experimental Persistent Infection of BALB/c Mice with Small-Colony Variants of Burkholderia pseudomallei Leads to Concurrent Upregulation of PD-1 on T Cells and Skewed Th1 and Th17 Responses
Regulatory changes have long been hypothesized to play an important role in primate evolution . To identify adaptive regulatory changes in humans , we performed a genome-wide survey for genes in which regulation has likely evolved under natural selection . To do so , we used a multi-species microarray to measure gene e...	It has long been hypothesized that in addition to structural changes to proteins , changes in gene regulation might underlie many of the anatomic and behavioral differences between humans and other primates . However , to date , there are only a handful of examples of regulatory adaptations in humans . In this work , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "evolutionary", "biology/genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures
Screens for epistatic interactions have long been used to characterize functional relationships corresponding to protein complexes , metabolic pathways , and other functional modules . Although epistasis between adaptive mutations is also common in laboratory evolution experiments , the functional basis for these inter...	The effects of mutations often depend on the presence or absence of other mutations . This phenomenon , known as epistasis , has been used extensively to infer functional associations between genes . For example , genes that participate in the same functional module will often show a characteristic pattern of positive ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "deletion", "mutation", "cloning", "epistasis", "mutation", "fungi", "fungal", "evolution", "evolutionary", "adaptation", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "mycology", "fitness", "epistasis", "molecular", "biology", "evolution...	2019	Modular epistasis and the compensatory evolution of gene deletion mutants
As a major diarrheagenic human pathogen , enterohemorrhagic Escherichia coli ( EHEC ) produce attaching and effacing ( A/E ) lesions , characterized by the formation of actin pedestals , on mammalian cells . A bacterial T3SS effector NleL from EHEC O157:H7 was recently shown to be a HECT-like E3 ligase in vitro , but i...	Enterohemorrhagic Escherichia coli ( EHEC ) can cause attaching and effacing ( A/E ) lesions to form in the colons of animals and humans , contributing to severe bacterial infection . NleL , an E3 ubiquitin ligase from EHEC O157:H7 is one of the bacterial type III secretion effectors that may be involved in the regulat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "transfection", "medicine", "and", "health", "sciences", "nuclear", "staining", "viral", "transmission", "and", "infection", "hela", "cells", "biological", "cultures", "microbiology", "bacterial", "diseases", "immunoprecipitation", "cell", "cultures", "...	2017	Bacterial effector NleL promotes enterohemorrhagic E. coli-induced attaching and effacing lesions by ubiquitylating and inactivating JNK
Campylobacter jejuni is currently the leading cause of bacterial gastroenteritis in humans . Comparison of multiple Campylobacter strains revealed a high genetic and phenotypic diversity . However , little is known about differences in transcriptome organization , gene expression , and small RNA ( sRNA ) repertoires . ...	Many species have evolved into diverse strains with phenotypic and genotypic variations that facilitate adaptation to different ecological niches and , in the case of pathogens , to different hosts . Whereas comparison of genome sequences reveals differences and similarities among strains , the consequences of genomic ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "functional", "genomics", "biological", "data", "management", "gene", "regulation", "microbiology", "gene", "function", "genome", "analysis", "tools", "molecular", "cell", "biology", "emerging", "infectious", "diseases", "molecular", "genetics", "bacterial...	2013	High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates
Interferon ( IFN ) responses are critical for controlling herpes simplex virus 1 ( HSV-1 ) . The importance of neuronal IFN signaling in controlling acute and latent HSV-1 infection remains unclear . Compartmentalized neuron cultures revealed that mature sensory neurons respond to IFNβ at both the axon and cell body th...	Herpes simplex virus type 1 ( HSV-1 ) is a ubiquitous virus that can cause cold sores , blindness , and even death from encephalitis . There is no vaccine against HSV , and although antiviral drugs can control HSV-1 , it persists because it establishes lifelong latent infections in neurons . Humans with deficiencies in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Neuronal Interferon Signaling Is Required for Protection against Herpes Simplex Virus Replication and Pathogenesis
Invasive non-typhoidal Salmonella ( iNTS ) serovars S . Typhimurium and S . Enteritidis are major etiologic agents of invasive bacterial disease among infants and young children in sub-Saharan Africa , including in Mali . Early studies of iNTS serovars in several countries indicated that S . Typhimurium was more preval...	Much remains unknown about the mode of transmission of iNTS or the reservoirs of infection . As such , insight into potential selective pressures on underlying serovars bears importance to public health . Longitudinal studies over the years 2002–2012 identified a shift in the proportion of invasive non-typhoidal Salmon...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "bacterial", "diseases", "phylogenetics", "data", "management", "tetracyclines", "antibiotics", "enterobacteriaceae", "...	2019	Genetic changes associated with the temporal shift in invasive non-typhoidal Salmonella serovars in Bamako Mali
In animal development , secreted signaling molecules evoke all-or-none threshold responses of target gene transcription to specify cell fates . In the chordate Ciona intestinalis , the neural markers Otx and Nodal are induced at early embryonic stages by Fgf9/16/20 signaling . Here we show that three additional signali...	Graded signals often provide positional information to organize gene expression in animal embryos . In the simplest cases , graded signals are translated into all-or-none threshold responses . However , recent studies have shown that signal transduction processes and binding of transcription factors to target sequences...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Multiple Signaling Pathways Coordinate to Induce a Threshold Response in a Chordate Embryo
Recent studies demonstrate that rabies post-exposure prophylaxis ( RPEP ) in international travelers is suboptimal , with only 5–20% of travelers receiving rabies immune globulin ( RIG ) in the country of exposure when indicated . We hypothesized that travelers may not be receiving RIG appropriately , and practices may...	International travelers may be exposed to rabid animals while traveling abroad . Current guidelines recommended that any traveler who was not been vaccinated against rabies before travel and sustained an animal exposure putting him at risk for rabies required rabies post-exposure prophylaxis including rabies immunoglob...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "post-exposure", "prophylaxis", "immunology", "tropical", "diseases", "geographical", "locations", "indonesia", "vaccines", "preventive", "medicine", "rabies", "neglected", "tropical", "diseases", "infectious"...	2018	Rabies post-exposure prophylaxis started during or after travel: A GeoSentinel analysis
CCDC39 and CCDC40 were first identified as causative mutations in primary ciliary dyskinesia patients; cilia from patients show disorganized microtubules , and they are missing both N-DRC and inner dynein arms proteins . In Chlamydomonas , we used immunoblots and microtubule sliding assays to show that mutants in CCDC4...	Cilia are specialized projections found on the surface of eukaryotic cells . They play crucial sensory functions , as well as motile functions needed for clearing airways or propelling cells . Ciliary motility is perturbed in the inherited disease , Primary Ciliary Dyskinesia ( PCD ) . Two coiled coil domain-containing...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A NIMA-Related Kinase Suppresses the Flagellar Instability Associated with the Loss of Multiple Axonemal Structures
Mycobacterium ulcerans causes Buruli ulcer ( BU ) , a debilitating infection of subcutaneous tissue . There is a WHO-recommended antibiotic treatment requiring an 8-week course of streptomycin and rifampicin . This regime has revolutionized the treatment of BU but there are problems that include reliance on daily strep...	Neglected tropical diseases such as Buruli ulcer predominantly afflict the poorest populations in the world and reduce quality of life . Buruli ulcer is a necrotising infection that destroys the skin and soft tissue , frequently presenting as nodules or open ulcers . Buruli ulcer is treated with antibiotics and sometim...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	In-vitro Activity of Avermectins against Mycobacterium ulcerans
Paramount to the success of persistent viral infection is the ability of viruses to navigate hostile environments en route to future targets . In response to such obstacles , many viruses have developed the ability of establishing actin rich-membrane bridges to aid in future infections . Herein through dynamic imaging ...	Dendritic cells represent a unique cell type with respect to HIV , as they are the first point of contact for the virus in the genital mucosa and have the ability to spread virus efficiently in very low numbers to the primary HIV target , CD4 T cells . During the primary immune response , dendritic cells work in small ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "hiv", "retrovirology", "and", "hiv", "immunopathogenesis", "viral", "diseases" ]	2012	Mobilization of HIV Spread by Diaphanous 2 Dependent Filopodia in Infected Dendritic Cells
Fungi contain a remarkable range of metabolic pathways , sometimes encoded by gene clusters , enabling them to digest most organic matter and synthesize an array of potent small molecules . Although metabolism is fundamental to the fungal lifestyle , we still know little about how major evolutionary processes , such as...	Fungi are important primary decomposers of organic material as well as amazing chemical engineers , synthesizing a wide variety of natural products , some with potent toxic activities , including antibiotics and mycotoxins . In fungal genomes , the genes involved in these metabolic pathways can be physically linked on ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "secondary", "metabolism", "fungi", "biology", "and", "life", "sciences", "molecular", "evolution", "evolutionary", "biology", "metabolism", "organisms" ]	2014	The Evolution of Fungal Metabolic Pathways
Female reproductive cessation is one of the earliest age-related declines humans experience , occurring in mid-adulthood . Similarly , Caenorhabditis elegans' reproductive span is short relative to its total life span , with reproduction ceasing about a third into its 15–20 day adulthood . All of the known mutations an...	Female reproductive cessation is the earliest aging phenotype humans experience , and its importance as a clinical issue is growing as more women opt to have children later in life . While much work has been done to understand the general aging process , little is currently known about the regulation of reproductive ag...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics" ]	2009	TGF-ß Sma/Mab Signaling Mutations Uncouple Reproductive Aging from Somatic Aging
Schistosoma haematobium is the etiologic agent for urogenital schistosomiasis , a major source of morbidity and mortality for more than 112 million people worldwide . Infection with S . haematobium results in a variety of immunopathologic sequelae caused by parasite oviposition within the urinary tract , which drives i...	Urogenital schistosomiasis ( infection with parasitic Schistosoma haematobium worms , the most common human-specific Schistosoma species globally ) affects over 112 million people worldwide . S . haematobium worms primarily lay eggs in the bladder , upper urinary and genital tracts , and the host immune response to the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "medicine", "urology", "infectious", "diseases", "model", "organisms", "immune", "cells", "immunity", "global", "health", "neglected", "tropical", "diseases", "immunology", "biology", "microbiology", "zoology", "parasitic", "diseases" ]	2012	A Novel Mouse Model of Schistosoma haematobium Egg-Induced Immunopathology
Various common genetic susceptibility loci have been identified for breast cancer; however , it is unclear how they combine with lifestyle/environmental risk factors to influence risk . We undertook an international collaborative study to assess gene-environment interaction for risk of breast cancer . Data from 24 stud...	Breast cancer involves combined effects of numerous genetic , environmental , and behavioral risk factors that are unique to each individual . High risk genes , such as BRCA1 and BRCA2 , account for only a small proportion of disease occurrence . Recent genome-wide research has identified more than 20 common genetic va...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "public", "health", "and", "epidemiology", "epidemiology", "cancer", "epidemiology", "genetic", "epidemiology" ]	2013	Evidence of Gene–Environment Interactions between Common Breast Cancer Susceptibility Loci and Established Environmental Risk Factors

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