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To replicate , viruses must gain access to the host cell's resources . Interferon ( IFN ) regulates the actions of a large complement of interferon effector genes ( IEGs ) that prevent viral replication . The interferon inducible transmembrane protein family members , IFITM1 , 2 and 3 , are IEGs required for inhibition...	Influenza epidemics exact a great toll on world health . Thus research to identify new anti-influenza virus strategies would be useful . Each of our cells contains antiviral factors that work to inhibit infection . A large component of this antiviral program is regulated by the interferon family of signaling molecules ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	IFITM3 Inhibits Influenza A Virus Infection by Preventing Cytosolic Entry
Cyclic GMP-AMP ( cGAMP ) synthase ( cGAS , a . k . a . MB21D1 ) , a cytosolic DNA sensor , catalyzes formation of the second messenger 2’3’-cGAMP that activates the stimulator of interferon genes ( STING ) signaling . How the cGAS activity is modulated remains largely unknown . Here , we demonstrate that sentrin/SUMO-s...	The Cyclic GMP-AMP ( cGAMP ) synthase ( cGAS , a . k . a . MB21D1 ) is critical for monitoring the pathogen-derived DNA upon microbial infection . Its activity should be dynamically modulated in case the inadvertent recognition of the aberrant self nucleic acids in cytosol leads to severe autoimmune diseases . Protein ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "chemical", "compounds", "gene", "regulation", "immunology", "organic", "compounds", "fluorophotometry", "sumoylation", "immunoprecipitation", "basic", "amino", "acids", "amino...	2017	SENP7 Potentiates cGAS Activation by Relieving SUMO-Mediated Inhibition of Cytosolic DNA Sensing
Our ability to control diseases caused by parasitic nematodes is constrained by a limited portfolio of effective drugs and a paucity of robust tools to investigate parasitic nematode biology . RNA interference ( RNAi ) is a reverse-genetics tool with great potential to identify novel drug targets and interrogate parasi...	Lymphatic filariasis is a debilitating tropical disease caused by parasitic nematodes such as Brugia malayi that are transmitted to humans through the bite of infected mosquitoes . Controlling lymphatic filariasis , and other parasitic nematode diseases , is made difficult by a limited repertoire of sub-optimal drugs a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "genetics", "and", "genomics/gene", "function", "biochemistry/drug", "discovery" ]	2010	Development of an In Vivo RNAi Protocol to Investigate Gene Function in the Filarial Nematode, Brugia malayi
The laboratory diagnosis of Chagas disease is challenging because the usefulness of different diagnostic tests will depend on the stage of the disease . Serology is the preferred method for patients in the chronic phase , whereas PCR can be successfully used to diagnose acute and congenital cases . Here we present data...	Chagas disease is endemic in several Latin American countries and affects approximately 8 to 11 million people . The protozoan parasite , Trypanosoma cruzi , is the agent of Chagas disease , a zoonotic disease that can be transmitted to humans by blood-sucking triatomine bugs . Other routes of infection include congeni...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "clinical", "laboratory", "sciences", "diagnostic", "medicine", "chagas", "disease", "neglected", "tropical", "diseases", "biology", "microbiology", "parasitic", "diseases...	2012	Sensitive and Specific Detection of Trypanosoma cruzi DNA in Clinical Specimens Using a Multi-Target Real-Time PCR Approach
Dengue can cause plasma leakage that may lead to dengue shock syndrome ( DSS ) . In approximately 30% of DSS cases , recurrent episodes of shock occur . These patients have a higher risk of fluid overload , respiratory distress and poor outcomes . We investigated the association of echocardiographically-derived cardiac...	Dengue is a viral illness that can lead to severe and potentially fatal complications . The most common complication is fluid leakage from blood vessels , which can cause low blood pressure or dengue shock syndrome ( DSS ) . The majority of patients recover with simple intravenous fluid replacement , however in approxi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "ultrasound", "imaging", "cardiovascular", "physiology", "tropical", "diseases", "echocardiography", "health", "care", "pediatrics", "cardiovascular", "analysis", "neglected", "tropical", "diseases", "bioas...	2017	Cardio-haemodynamic assessment and venous lactate in severe dengue: Relationship with recurrent shock and respiratory distress
Isoflavones comprise a group of secondary metabolites produced almost exclusively by plants in the legume family , including soybean [Glycine max ( L . ) Merr . ] . They play vital roles in plant defense and have many beneficial effects on human health . Isoflavone content is a complex quantitative trait controlled by ...	Isoflavones are bioactive substances with various benefits , and increasing isoflavone content is one of the major aims of soybean quality improvement . Isoflavone biosynthesis is regulated by multiple genes and complex metabolic networks . The modification of certain structural genes in the isoflavone pathway by genet...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "gene", "regulation", "regulatory", "proteins", "brassica", "dna-binding", "proteins", "genetic", "mapping", "model", "organisms", "genome", "analysis", "transcription", "factors", "crops", "experimental", "organism", "systems", "p...	2017	An R2R3-type MYB transcription factor, GmMYB29, regulates isoflavone biosynthesis in soybean
The source of symmetry breaking in vertebrate oocytes is unknown . Animal—vegetal oocyte polarity is established by the Balbiani body ( Bb ) , a conserved structure found in all animals examined that contains an aggregate of specific mRNAs , proteins , and organelles . The Bb specifies the oocyte vegetal pole , which i...	In most vertebrates , an early event in egg development involves the establishment of the so-called animal—vegetal axis; this sets up the embryonic body axes and contributes to germ-line specification , and therefore , is key to embryonic development . The animal—vegetal axis is established during oogenesis by the Balb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	Oocyte Polarization Is Coupled to the Chromosomal Bouquet, a Conserved Polarized Nuclear Configuration in Meiosis
Eosinophilic meningitis ( angiostrongyliasis ) caused by Angiostrongylus cantonensis is emerging in mainland China . However , the distribution of A . cantonensis and its intermediate host snails , and the role of two invasive snail species in the emergence of angiostrongyliasis , are not well understood . A national s...	Eosinophilic meningitis is caused by the rat lungworm ( Angiostrongylus cantonensis ) . This parasite is endemic in Southeast Asia , Australia , the Caribbean , and on Pacific Islands . Moreover , the disease is emerging in mainland China , which might be related to the spread of two invasive snail species ( Achatina f...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/infectious", "diseases", "of", "the", "nervous", "system", "public", "health", "and", "epidemiology/infectious", "diseases", "ecology" ]	2009	Invasive Snails and an Emerging Infectious Disease: Results from the First National Survey on Angiostrongylus cantonensis in China
Lentiviral Nef proteins have multiple functions and are important for viral pathogenesis . Recently , Nef proteins from many simian immunodefiency viruses were shown to antagonize a cellular antiviral protein , named Tetherin , that blocks release of viral particles from the cell surface . However , the mechanism by wh...	Primate lentiviruses express several small proteins which antagonize cellular proteins that inhibit virus replication . One such viral protein , Nef , has recently been shown to antagonize the cellular protein Tetherin that prevents newly formed viral particles from leaving the surface of infected cells . In this study...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	SIV Nef Proteins Recruit the AP-2 Complex to Antagonize Tetherin and Facilitate Virion Release
The piRNA pathway is a surveillance system that guarantees oogenesis and adult fertility in a range of animal species . The pathway is centered on PIWI clade Argonaute proteins and the associated small non-coding RNAs termed piRNAs . In this study , we set to investigate the evolutionary conservation of the piRNA pathw...	Rhodnius prolixus together with other blood-feeding bugs of the Triatominae family are primary vectors of the protozoan Trypanosoma cruzi , the causative agent of the Chagas disease . It has been estimated that 7–8 million people are affected by this life-threatening illness worldwide , which makes the Chagas disease o...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "animals", "invertebrate", "genomics", "reproductive", "physiology", "animal", "models", "germ", "cells", "oocytes", "drosophila", "melanogaster", "model", "organisms", "experimental", "or...	2018	Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus
Differentiation of secretory cells leads to sharp increases in protein synthesis , challenging endoplasmic reticulum ( ER ) proteostasis . Anticipatory activation of the unfolded protein response ( UPR ) prepares cells for the onset of secretory function by expanding the ER size and folding capacity . How cells ensure ...	During differentiation , cells that specialize in secretion of proteins , such as antibody-secreting B cells , prepare for the onset of secretory function by expanding the size of the major secretory organelle , the endoplasmic reticulum ( ER ) , and by increasing the expression of molecular chaperones and folding enzy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "skin", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "integumentary", "system", "caenorhabditis", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "regulatory", "proteins", "cell", "processes", "endoplasmic", "reticul...	2019	HSP-4/BiP expression in secretory cells is regulated by a developmental program and not by the unfolded protein response
Many unicellular organisms live in multicellular communities that rely on cooperation between cells . However , cooperative traits are vulnerable to exploitation by non-cooperators ( cheaters ) . We expand our understanding of the molecular mechanisms that allow multicellular systems to remain robust in the face of che...	Although bacteria are not multicellular organisms , they commonly live in large communities and engage in many cooperative behaviors . Cooperation can allow bacteria to access additional nutrients , but it requires the secretion of products that will be shared by the community . How bacteria make the molecular decision...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Integration of Metabolic and Quorum Sensing Signals Governing the Decision to Cooperate in a Bacterial Social Trait
Efforts to engineer synthetic gene networks that spontaneously produce patterning in multicellular ensembles have focused on Turing's original model and the “activator-inhibitor” models of Meinhardt and Gierer . Systems based on this model are notoriously difficult to engineer . We present the first demonstration that ...	The production of patterns in gene expression in an ensemble of cells is a phenomenon central to the development of multi-cellular organisms . Here we provide an exciting new result regarding diffusion-driven instability , a mechanism for spontaneous pattern formation originally proposed by Alan Turing . Efforts along ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "prokaryotic", "models", "model", "organisms", "synthetic", "biology", "molecular", "genetics", "biology", "computational", "biology", "microbiology", "molecular", "biology", "genetics", "and", "genomics" ]	2012	A Feedback Quenched Oscillator Produces Turing Patterning with One Diffuser
Clustered , regularly interspaced , short palindromic repeat ( CRISPR ) –CRISPR-associated 9 ( Cas9 ) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases . While editing of immortalized cell lines has become relatively easy , editing of therapeutically relev...	Clustered , regularly interspaced , short palindromic repeat ( CRISPR ) –CRISPR-associated 9 ( Cas9 ) genome editing is transforming fundamental research , as it allows researchers to make targeted changes to the genome of cells . For efficient editing , the Cas9 protein ( a DNA nuclease ) and a guide RNA ( gRNA ) , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "medicine", "and", "health", "sciences", "nucleic", "acid", "synthesis", "enzymes", "immunology", "rna", "extraction", "enzymology", "phosphatases", "molecular", "biology", "techniques", "rna", "synthesis", "extraction", "techniques", "chemical", "synthesi...	2018	In vitro–transcribed guide RNAs trigger an innate immune response via the RIG-I pathway
Shp2 is a cytoplasmic protein-tyrosine phosphatase that is essential for normal development . Activating and inactivating mutations have been identified in humans to cause the related Noonan and LEOPARD syndromes , respectively . The cell biological cause of these syndromes remains to be determined . We have used the z...	Shp2 is a protein-tyrosine phosphatase and mutations in Shp2 cause the related Noonan and LEOPARD syndromes in humans . We used the zebrafish to investigate the cell biological role of Shp2 in early development . Shp2 knockdown and expression of mutant Shp2 that contained mutations corresponding to those found in human...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "developmental", "biology", "cell", "biology", "danio", "(zebrafish)", "in", "vitro", "homo", "(human)", "genetics", "and", "genomics" ]	2007	Shp2 Knockdown and Noonan/LEOPARD Mutant Shp2–Induced Gastrulation Defects
In animals , circadian rhythms in physiology and behavior result from coherent rhythmic interactions between clocks in the brain and those throughout the body . Despite the many tissue specific clocks , most understanding of the molecular core clock mechanism comes from studies of the suprachiasmatic nuclei ( SCN ) of ...	Various aspects of our daily rhythms in physiology and behavior such as the sleep-wake cycle are regulated by endogenous circadian clocks that are present in nearly every cell . It is generally accepted that these oscillators share a similar biochemical negative feedback mechanism , consisting of transcriptional activa...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "gene", "regulatory", "networks", "genetics", "biology", "and", "life", "sciences", "cellular", "types", "molecular", "genetics", "computational", "biology", "molecular", "cell", "biology", "gene", "function" ]	2014	Cell Type-Specific Functions of Period Genes Revealed by Novel Adipocyte and Hepatocyte Circadian Clock Models
The most common cystic fibrosis ( CF ) causing mutation , deletion of phenylalanine 508 ( ΔF508 or Phe508del ) , results in functional expression defect of the CF transmembrane conductance regulator ( CFTR ) at the apical plasma membrane ( PM ) of secretory epithelia , which is attributed to the degradation of the misf...	Cystic fibrosis ( CF ) is one of the most common autosomal recessive diseases in Caucasians . It is caused by mutations in the CF transmembrane conductance regulator ( CFTR ) , which functions as an anion channel at the apical plasma membrane of secretory epithelia . The most common CF mutation , a deletion of the phen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "transfection", "hela", "cells", "molecular", "probe", "techniques", "gene", "regulation", "biological", "cultures", "immunoblotting", "membrane", "proteins", "fungi", "luminescent", "proteins", "model", "organisms", "yellow", "fluorescent", "protein", "cell", "cultures",...	2016	Ribosomal Stalk Protein Silencing Partially Corrects the ΔF508-CFTR Functional Expression Defect
Hepatitis C virus ( HCV ) infection constitutes a significant health burden worldwide , because it is a major etiologic agent of chronic liver disease , cirrhosis and hepatocellular carcinoma . HCV replication cycle is closely tied to lipid metabolism and infection by this virus causes profound changes in host lipid ho...	Hepatitis C virus ( HCV ) infection is an important biomedical problem worldwide because it causes severe liver disease and cancer . Although immunological events are major players in HCV pathogenesis , interference with host cell metabolism contribute to HCV-associated pathologies . HCV utilizes resources of the cellu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "luciferase", "vesicles", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "enzymes", "microbiology", "enzymology", "viruses", "physiological", "processes", "rna", "viruses", "homeostasis", "infectious", "d...	2018	Host phosphatidic acid phosphatase lipin1 is rate limiting for functional hepatitis C virus replicase complex formation
Alpha-Synuclein ( aSyn ) misfolding and aggregation is common in several neurodegenerative diseases , including Parkinson’s disease and dementia with Lewy bodies , which are known as synucleinopathies . Accumulating evidence suggests that secretion and cell-to-cell trafficking of pathological forms of aSyn may explain ...	Synucleinopathies are neurodegenerative diseases characterized by the abnormal accumulation of a neuronal protein called alpha-Synuclein ( aSyn ) . The normal function of this protein in the cell remains unclear , but plays a role in synaptic function and plasticity , cell differentiation and vesicular trafficking . Du...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunocytochemistry", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "molecular", "probe", "techniques", "immunoblotting", "light", "microscopy", "toxicology", "physiological", "processes", "toxicity", "microscopy", "materials", "sci...	2016	shRNA-Based Screen Identifies Endocytic Recycling Pathway Components That Act as Genetic Modifiers of Alpha-Synuclein Aggregation, Secretion and Toxicity
Aging is an inherently stochastic process , and its hallmark is heterogeneity between organisms , cell types , and clonal populations , even in identical environments . The replicative lifespan of primary human cells is telomere dependent; however , its heterogeneity is not understood . We show that mitochondrial super...	After a limited number of cell divisions , somatic cells lose the capacity for proliferation , called cellular replicative senescence . Senescence , which is triggered by the loss of DNA sequences at the ends of chromosomes ( telomeres ) , is often seen as an example of a regular “biological clock . ” However , cell se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "eukaryotes" ]	2007	Mitochondrial Dysfunction Accounts for the Stochastic Heterogeneity in Telomere-Dependent Senescence
The outer membrane ( OM ) of Gram-negative bacteria is a complex bilayer composed of proteins , phospholipids , lipoproteins , and lipopolysaccharides . Despite recent advances revealing the molecular pathways underlying protein and lipopolysaccharide incorporation into the OM , the spatial distribution and dynamic reg...	All Gram-negative bacteria share common structural features , including an inner membrane , a stiff cell wall , and an outer membrane . Balancing growth in all three of these layers is critical for bacterial proliferation and survival , and malfunctions in growth often lead to cellular deformations and/or cell death . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "physics", "bacterial", "physiology", "molecular", "cell", "biology", "cell", "biology", "cell", "growth", "membranes", "and", "sorting", "biology", "microbiology", "biophysics", "simulations", "biophysics" ]	2012	Analysis of Surface Protein Expression Reveals the Growth Pattern of the Gram-Negative Outer Membrane
Morocco has achieved the goal of leprosy elimination as a public health problem several years ago ( less than 1 case/ 10 000 habitant ) . The aim of this study was to analyze trends of leprosy detection during the last 17 years taking into consideration the implementation of single dose rifampicin chemoprophylaxis ( SD...	After the introduction of effective therapy for leprosy by the world health organization in early eighties , there has been a marked reduction in new case detection all over the world . Despite the decline in case detection of leprosy , incidence reduction to zero and suppression of infection source is still not possib...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "morocco", "medicine", "and", "health", "sciences", "immune", "cells", "disabilities", "statistics", "antigen-presenting", "cells", "immunology", "tropical", "diseases", "geographical", "locations", "regression", "analysis", "bacterial", "diseases", "mathematics", "neglecte...	2018	Trend analysis of leprosy in Morocco between 2000 and 2017: Evidence on the single dose rifampicin chemoprophylaxis
Opisthorchis viverrini is distinct among helminth infections as it drives a chronic inflammatory response in the intrahepatic bile duct that progresses from advanced periductal fibrosis ( APF ) to cholangiocarcinoma ( CCA ) . Extensive research shows that oxidative stress ( OS ) plays a critical role in the transition ...	Opisthorchis viverrini is a food-borne helminth infection that drives a strong inflammatory response in the bile duct that can result in bile duct fibrosis and bile duct cancer ( intrahepatic cholangiocarcinoma ) . Extensive research shows that oxidative stress ( OS ) plays a critical role in chronic O . viverrini infe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusion" ]	[]	2015	Levels of 8-OxodG Predict Hepatobiliary Pathology in Opisthorchis viverrini Endemic Settings in Thailand
DnaK is a molecular chaperone that has important roles in protein folding . The hydrolysis of ATP is essential to this activity , and the effects of nucleotides on the structure and function of DnaK have been extensively studied . However , the key residues that govern the conformational motions that define the apo , A...	DnaK belongs to the highly conserved heat shock protein 70 ( Hsp70 ) family , a group of ATP-dependent molecular chaperones that regulates proteostasis . Studies have suggested that global movements of the subdomains in the nucleotide-binding domain ( NBD ) of DnaK regulate its catalytic activity . However , there is l...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[]	2013	Identification of Key Hinge Residues Important for Nucleotide-Dependent Allostery in E. coli Hsp70/DnaK
The relationships between heterogeneities in host infection and infectiousness ( transmission to arthropod vectors ) can provide important insights for disease management . Here , we quantify heterogeneities in Leishmania infantum parasite numbers in reservoir and non-reservoir host populations , and relate this to the...	Zoonotic visceral leishmaniasis is a sandfly-borne disease of humans and dogs caused by the intracellular parasite Leishmania infantum . Dogs are the proven reservoir . The disease is usually fatal unless treated , and is of global health significance . Diagnosis of canine infections relies on serum antibody-based test...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2014	Heterogeneities in Leishmania infantum Infection: Using Skin Parasite Burdens to Identify Highly Infectious Dogs
Phosphatidylinositol 3-phosphate ( PtdIns ( 3 ) P ) is a signaling molecule important for many membrane trafficking events , including phagosome maturation . The level of PtdIns ( 3 ) P on phagosomes oscillates in two waves during phagosome maturation . However , the physiological significance of such oscillation remai...	During animal development and in adulthood many cells are programmed to die by an active process called apoptosis . These dead or dying apoptotic cells are swiftly taken up by scavenger cells into membrane-bound compartments—phagosomes—where they are subsequently degraded when other intracellular organelles containing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "developmental", "biology", "cellular", "structures", "model", "organisms", "molecular", "cell", "biology", "cell", "biology", "genetics", "biology", "genetics", "and", "genomics" ]	2012	Two PI 3-Kinases and One PI 3-Phosphatase Together Establish the Cyclic Waves of Phagosomal PtdIns(3)P Critical for the Degradation of Apoptotic Cells
Identifying the major routes of disease transmission and reservoirs of infection are needed to increase our understanding of disease dynamics and improve disease control . Despite this , transmission events are rarely observed directly . Here we had the unique opportunity to study natural transmission of Bordetella bro...	A lack of understanding regarding determinants of infectious disease transmission has hindered improved disease control efforts . Here we had the unique opportunity to study the natural transmission of the respiratory pathogen Bordetella bronchiseptica within a commercial rabbitry . B . bronchiseptica is a directly tra...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "ecology/evolutionary", "ecology", "respiratory", "medicine/respiratory", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/bacterial", "infections", "ecolog...	2010	Identifying the Age Cohort Responsible for Transmission in a Natural Outbreak of Bordetella bronchiseptica
The dengue virus has a single-stranded positive-sense RNA genome of ∼10 . 700 nucleotides with a single open reading frame that encodes three structural ( C , prM , and E ) and seven nonstructural ( NS1 , NS2A , NS2B , NS3 , NS4A , NS4B , and NS5 ) proteins . It possesses four antigenically distinct serotypes ( DENV 1–...	Most of the molecular phylogeny studies of dengue fever , an important public health problem , use convenience samples for their analysis , and they do not evaluate the spatial and temporal features involved in the spread of the different serotypes ( and genotypes ) circulating in urban settings during an outbreak . Ou...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "virology/virus", "evolution", "and", "symbiosis", "virology", "virology/emerging", "viral", "diseases", "genetics", "and", "genomics/population", "genetics" ]	2009	Spatio-Temporal Tracking and Phylodynamics of an Urban Dengue 3 Outbreak in São Paulo, Brazil
Vascular calcification is an advanced feature of atherosclerosis for which no effective therapy is available . To investigate the modulation or reversal of calcification , we identified calcifying progenitor cells and investigated their calcifying/decalcifying potentials . Cells from the aortas of mice were sorted into...	Atherosclerosis involves hardening of the arteries and can lead to heart disease . Calcium accumulation in blood vessels contributes to this process , and this process is regulated by cells that promote calcium accumulation ( osteoblasts ) and cells that reverse the accumulation ( osteoclasts ) . In this study , we sho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cardiovascular", "stem", "cells", "atherosclerosis", "mesenchymal", "stem", "cells", "adult", "stem", "cells", "stem", "cell", "niche", "biology", "hematopoietic", "stem", "cells", "cell", "biology", "vascular", "biology", "cellular", "types", "molecular"...	2013	Vascular Calcifying Progenitor Cells Possess Bidirectional Differentiation Potentials
Several viruses encode factors that promote host mRNA degradation to silence gene expression . It is unclear , however , whether cellular mRNA turnover pathways are engaged to assist in this process . In Kaposi's sarcoma-associated herpesvirus this phenotype is enacted by the host shutoff factor SOX . Here we show that...	Viruses use a number of strategies to commandeer host machinery and create an optimal environment for their replication . One strategy employed by oncogenic gammaherpesviruses such as Kaposi's sarcoma-associated herpesvirus ( KSHV ) is to block cellular gene expression through extensive destruction of mRNAs . A single ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "rna", "molecular", "cell", "biology", "nucleic", "acids", "virology", "viral", "enzymes", "biology", "microbiology", "rna", "stability", "molecular", "biology" ]	2011	Coordinated Destruction of Cellular Messages in Translation Complexes by the Gammaherpesvirus Host Shutoff Factor and the Mammalian Exonuclease Xrn1
The intimate synapsis of homologous chromosome pairs ( homologs ) by synaptonemal complexes ( SCs ) is an essential feature of meiosis . In many organisms , synapsis and homologous recombination are interdependent: recombination promotes SC formation and SCs are required for crossing-over . Moreover , several studies i...	Gamete cells , such as sperm and eggs , form via the specialized cell division called meiosis . Essential and interdependent features of meiosis include the pairing , recombination , and segregation of maternal and paternal chromosomes . Chromosome pairing culminates with formation of synaptonemal complexes ( SCs ) , z...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "animal", "genetics", "chromosome", "structure", "and", "function", "centromeres", "gene", "function", "animal", "models", "telomeres", "model", "organisms", "cell", "division", "dna", "chromosomal", "inheritance", "chromosome", "biology", "biology", "mouse",...	2012	Interplay between Synaptonemal Complex, Homologous Recombination, and Centromeres during Mammalian Meiosis
In October 2010 , cholera importation in Haiti triggered an epidemic that rapidly proved to be the world's largest epidemic of the seventh cholera pandemic . To establish effective control and elimination policies , strategies rely on the analysis of cholera dynamics . In this report , we describe the spatio-temporal d...	Cholera is the prototypical “waterborne” disease that can provoke deadly acute watery diarrhea epidemics in settings deprived of clean water and proper sanitation . In spite chronic deprivation , Haiti had been spared cholera for a century until the vibrio was imported in October 2010 , which triggered the largest nati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "disease", "mapping", "infectious", "diseases", "cholera", "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "spatial", "epidemiology" ]	2013	Spatio-Temporal Dynamics of Cholera during the First Year of the Epidemic in Haiti
Few genetic differences between human populations conform to the classic model of positive selection , in which a newly arisen mutation rapidly approaches fixation in one lineage , suggesting that adaptation more commonly occurs via moderate changes in standing variation at many loci . Detecting and characterizing this...	Identifying regions of the human genome that differ among populations because of natural selection is both essential for understanding evolutionary history and a powerful method for finding functionally important variants that contribute to phenotypic diversity and disease . Adaptive events on timescales corresponding ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "population", "genetics", "parallel", "evolution", "population", "biology", "forms", "of", "evolution", "genetic", "polymorphism", "evolutionary", "modeling", "biology", "evolutionary", "genetics", "adaptation", "natural", "selection", "genetics", "computational", "biology"...	2011	Parallel Adaptive Divergence among Geographically Diverse Human Populations
Lymphatic filariasis ( LF ) , a morbid disease caused by the tissue-invasive nematodes Wuchereria bancrofti , Brugia malayi , and Brugia timori , affects millions of people worldwide . Global eradication efforts have significantly reduced worldwide prevalence , but complete elimination has been hampered by limitations ...	Brugia malayi is a parasitic nematode and one of the causative agents of lymphatic filariasis , a disease that affects 70 million people worldwide . Currently , there are no effective therapeutics that kill adult filarial parasites when given as a short course . This limitation has hampered global eradication efforts ....	[ "Abstract", "Introduction", "Results", "Methods", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "immune", "physiology", "laboratory", "equipment", "engineering", "and", "technology", "gene", "regulation", "immunology", "biological", "cultures", "animals", "vaccines", "culture", "media", "brugia", "infectious"...	2019	Intestinal UDP-glucuronosyltransferase as a potential target for the treatment and prevention of lymphatic filariasis
Decisions involve two fundamental problems , selecting goals and generating actions to pursue those goals . While simple decisions involve choosing a goal and pursuing it , humans evolved to survive in hostile dynamic environments where goal availability and value can change with time and previous actions , entangling ...	Choosing between alternative options requires assigning and integrating values along a multitude of dimensions . For instance , when buying a car , different cars may vary for their price , quality , fuel economy and more . Solving this problem requires finding a common currency to allow integration of disparate value ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Dynamic Integration of Value Information into a Common Probability Currency as a Theory for Flexible Decision Making
A fundamental challenge in neuroscience is to understand what structure in the world is represented in spatially distributed patterns of neural activity from multiple single-trial measurements . This is often accomplished by learning a simple , linear transformations between neural features and features of the sensory ...	It has been demonstrated that deep networks can achieve state of the art results on a number of classic machine learning tasks , but it is not currently clear whether deep networks can enjoy the same success in science , where not only accuracy but scientific understanding is desired . For example , the relationship be...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "syllables", "acoustics", "linguistics", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "social", "sciences", "neuroscience", "consonants", "computer", "and", "information", "sciences", "vowels", "speech", "grammar", "phonetics", "physic...	2019	Deep learning as a tool for neural data analysis: Speech classification and cross-frequency coupling in human sensorimotor cortex
Increased susceptibility to influenza virus infection during pregnancy has been attributed to immunological changes occurring before and during gestation in order to “tolerate” the developing fetus . These systemic changes are most often characterized by a suppression of cell-mediated immunity and elevation of humoral ...	Maternal immunology is finely balanced to maintain a tolerant and supportive molecular environment for the developing fetus while continuing surveillance against foreign microbial threats . Influenza viral infection during pregnancy is a significant clinical risk for mothers and their newborns , increasing hospitalizat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "reproductive", "system", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "pathogens", "immunology", "microbiology", "orthomyxoviruses", ...	2017	H1N1 influenza virus infection results in adverse pregnancy outcomes by disrupting tissue-specific hormonal regulation
Tumor Necrosis Factor receptor-associated factor-3 ( TRAF3 ) is a central mediator important for inducing type I interferon ( IFN ) production in response to intracellular double-stranded RNA ( dsRNA ) . Here , we report the identification of Sec16A and p115 , two proteins of the ER-to-Golgi vesicular transport system ...	In response to pathogens , such as viruses and bacteria , infected cells defend themselves by generating a set of cytokines called type I interferon ( IFN ) . Since Type I IFN ( namely IFN alpha and beta ) are potent antiviral agents , understanding the cellular mechanisms by which infected cells produce type I IFN is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "innate", "immunity", "immunity", "to", "infections", "immunology", "biology", "immune", "response" ]	2012	Proteomic Profiling of the TRAF3 Interactome Network Reveals a New Role for the ER-to-Golgi Transport Compartments in Innate Immunity
Cell-cycle progression and cell division in eukaryotes are governed in part by the cyclin family and their regulation of cyclin-dependent kinases ( CDKs ) . Cyclins are very well characterised in model systems such as yeast and human cells , but surprisingly little is known about their number and role in Plasmodium , t...	The malaria parasite is a single-celled organism that multiplies asexually in a non-canonical way in both vertebrate host and mosquito vector . In the mosquito midgut , atypical cell division occurs in oocysts , where repeated nuclear division ( endomitosis ) precedes cell division , which then gives rise to many sporo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Plasmodium P-Type Cyclin CYC3 Modulates Endomitotic Growth during Oocyst Development in Mosquitoes
Many redundancies play functional roles in motor control and motor learning . For example , kinematic and muscle redundancies contribute to stabilizing posture and impedance control , respectively . Another redundancy is the number of neurons themselves; there are overwhelmingly more neurons than muscles , and many com...	There are overwhelmingly more neurons than muscles in the motor system . The functional roles of this neuronal redundancy remains unknown . Our analysis , which uses a redundant neural network model , reveals that learning speed reaches its maximum value if and only if the model includes sufficient neuronal redundancy ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "neuroscience" ]	2012	Maximization of Learning Speed in the Motor Cortex Due to Neuronal Redundancy
Although bone has a unique restorative capacity , i . e . , it has the potential to heal scarlessly , the conditions for spontaneous bone healing are not always present , leading to a delayed union or a non-union . In this work , we use an integrative in vivo - in silico approach to investigate the occurrence of non-un...	In 5–10% of fracture patients , the bone fractures do not heal in the normal healing period ( delayed healing ) or do not heal at all ( non-union ) . In order to investigate the causes of impaired healing and design potential treatment strategies , we have used a combined experimental and computational approach . More ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "theoretical", "biology", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	Size Does Matter: An Integrative In Vivo-In Silico Approach for the Treatment of Critical Size Bone Defects
Q fever is an endemic disease in different parts of Iran . This study aimed to investigate the prevalence of acute Q fever disease among at-risk individuals in northwestern Iran . An etiological study was carried out in 2013 in Tabriz County . A total of 116 individuals who were in contact with livestock and had a nons...	Q fever is a zoonotic contagious disease caused by a bacterium called Coxiella burnetii . It is mostly asymptomatic in livestock and animals . Clinical manifestations of Q fever in humans includes asymptomatic , acute and chronic to fatigue syndrome . The most frequent clinical manifestation of acute Q fever is a flu-l...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "fatigue", "pathogens", "geographical", "locations", "microbiology", "headaches", "bacterial", "diseases", "signs", "and", "symptoms", "imm...	2017	Acute Q fever in febrile patients in northwestern of Iran
In a previous work by Alvarez-Martinez et al . ( 2011 ) , the authors pointed out some fallacies in the mainstream interpretation of the prion amyloid formation . It appeared necessary to propose an original hypothesis able to reconcile the in vitro data with the predictions of a mathematical model describing the probl...	Understanding the mechanism of prions is an important issue . Indeed , it involves a mechanism modifying the structure of the proteins that are of high interest in theoretical biology . Knowing the underlying mechanism that leads to prion disease could help further investigations in the world of amyloid disease and for...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "computer", "and", "information", "sciences", "mathematical", "computing", "mathematics", "protein", "interactions", "molecular", "complexes", "theoretical", "biology", "proteins", "applied", "mathematics", "biology", "and", "life", "sciences", "computing", ...	2014	A Micellar On-Pathway Intermediate Step Explains the Kinetics of Prion Amyloid Formation
Although the Factor V Leiden ( FVL ) gene variant is the most prevalent genetic risk factor for venous thrombosis , only 10% of FVL carriers will experience such an event in their lifetime . To identify potential FVL modifier genes contributing to this incomplete penetrance , we took advantage of a perinatal synthetic ...	Abnormal blood clotting in veins ( venous thrombosis ) or arteries ( arterial thrombosis ) are major health problems , with venous thrombosis affecting approximately 1 in every thousand individuals annually in the United States . Susceptibility to venous thrombosis is governed by both genes and environment , with appro...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "cardiovascular", "medicine", "thrombosis", "mutation", "molecular", "biology", "techniques", "dna", "sequencing", "mammalian", "genomics", "research", "and", "analysis", "methods", "coagulation", "disor...	2018	Whole exome sequencing of ENU-induced thrombosis modifier mutations in the mouse
Regular treatment with praziquantel ( PZQ ) is the strategy for human schistosomiasis control aiming to prevent morbidity in later life . With the recent resolution on schistosomiasis elimination by the 65th World Health Assembly , appropriate diagnostic tools to inform interventions are keys to their success . We pres...	Schistosomiasis remains one of the most prevalent parasitic diseases in developing countries , with Schistosoma mansoni being the most widespread of the human-infecting schistosomes . For the routine surveillance of human S . mansoni infection more “field-applicable , ” sensitive , and cost-effective diagnostics that r...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	A Latent Markov Modelling Approach to the Evaluation of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda
Major histocompatibility complex class I ( MHC-I ) molecules present antigenic peptides to CD8+ T cells , and are also important for natural killer ( NK ) cell immune surveillance against infections and cancers . MHC-I molecules are assembled via a complex assembly pathway in the endoplasmic reticulum ( ER ) of cells ....	Human leukocyte antigen ( HLA ) class I molecules present pathogen-derived components ( peptides ) to cytotoxic T cells , thereby inducing the T cells to kill virus-infected cells . A complex cellular pathway involving the transporter associated with antigen processing ( TAP ) is typically required for the loading of p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "flow", "cytometry", "innate", "immune", "system", "medicine", "and", "health", "sciences", "antigen", "presentation", "immune", "cells", "molecular", "probe", "techniques", "immunology", "immunoblotting", "cytotoxic", "t", "cells", "molecular", "bio...	2018	Selected HLA-B allotypes are resistant to inhibition or deficiency of the transporter associated with antigen processing (TAP)
Goat raising is a growing industry in Lao People’s Democratic Republic , with minimal disease investigation to date , especially zoonoses . This study determined the proportional seropositivity of two zoonotic diseases: Q fever ( causative agent Coxiella burnetii ) and Brucellosis ( Brucella species ) in goats across f...	Goat raising is a growing industry in Lao People’s Democratic Republic however there is very little information whether or not goat raising poses a disease threat to farmers and the general population through diseases that may be transmitted between animals and humans ( i . e . , zoonotic diseases ) . To determine this...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "ruminants", "pathogens", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "brucellosis", "bacterial", "diseases"...	2018	Serosurveillance of Coxiellosis (Q-fever) and Brucellosis in goats in selected provinces of Lao People’s Democratic Republic
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment . To understand and model the evolution of HIV quantitatively , the parameters governing genetic diversification and the strength of selection need to be...	Evolution , in viruses and other organisms , is the result of random genetic diversification by mutation or recombination and selection for survival . In most organisms , evolution is too slow to be observed directly and the evolutionary past has to be reconstructed from static snapshots of the population . This recons...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2010	Recombination Rate and Selection Strength in HIV Intra-patient Evolution
The small G-protein Ras is a conserved regulator of cell and tissue growth . These effects of Ras are mediated largely through activation of a canonical RAF-MEK-ERK kinase cascade . An important challenge is to identify how this Ras/ERK pathway alters cellular metabolism to drive growth . Here we report on stimulation ...	The Ras oncogene is one of the primary drivers of cell and tissue growth in both normal development and in diseases such as cancer . In this report , we identify the stimulation of tRNA synthesis as an important mechanism by which Ras functions . Using fruit fly genetics , we show that Ras promotes tRNA synthesis by in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "transfer", "rna", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "rn...	2018	Ras/ERK-signalling promotes tRNA synthesis and growth via the RNA polymerase III repressor Maf1 in Drosophila
Phenotypic states and evolutionary trajectories available to cell populations are ultimately dictated by complex interactions among DNA , RNA , proteins , and other molecular species . Here we study how evolution of gene regulation in a single-cell eukaryote S . cerevisiae is affected by interactions between transcript...	Specialized proteins called transcription factors turn genes on and off by binding to short stretches of DNA in their regulatory regions . Precise gene regulation is essential for cellular survival and proliferation , and its evolution and maintenance under mutational pressure are central issues in biology . Here we di...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "modeling", "biophysics", "theory", "biology", "and", "life", "sciences", "computational", "biology", "biophysics" ]	2014	Biophysical Fitness Landscapes for Transcription Factor Binding Sites
Members of the COE family of transcription factors are required for central nervous system ( CNS ) development . However , the function of COE in the post-embryonic CNS remains largely unknown . An excellent model for investigating gene function in the adult CNS is the freshwater planarian . This animal is capable of r...	COE transcription factors are conserved across widely divergent animals and are crucial for organismal development . COE genes also play roles in adult animals and have been implicated in central nervous system ( CNS ) diseases; however , the function of COE in the post-embryonic CNS remains poorly understood . Planari...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "neurobiology", "of", "disease", "and", "regeneration", "medicine", "and", "health", "sciences", "stem", "cells", "animal", "cells", "cell", "biology", "regeneration", "neurology", "biology", "and", "life", "sciences", "cellular", "types", ...	2014	COE Loss-of-Function Analysis Reveals a Genetic Program Underlying Maintenance and Regeneration of the Nervous System in Planarians
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers , hybridizations or gene flow . Not all species follow the paradigm of vertical inheritance of their genetic material . While a great deal of research has flourished into the inferen...	Phylogenetic networks display the evolutionary history of groups of individuals ( species or populations ) including reticulation events such as hybridization , horizontal gene transfer or migration . Here , we present a likelihood method to learn networks from molecular sequences at multiple genes . Our model accounts...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "taxonomy", "genetic", "networks", "population", "genetics", "vertebrates", "animals", "animal", "phylogenetics", "animal", "models", "osteichthyes", "phylogenetics", "data", "management", "model", "organisms", "phylogenetic", "analysis", "network", "analysis", "genome", ...	2016	Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting
Human mitochondrial DNA ( mtDNA ) replication is first initiated at the origin of H-strand replication . The initiation depends on RNA primers generated by transcription from an upstream promoter ( LSP ) . Here we reconstitute this process in vitro using purified transcription and replication factors . The majority of ...	Human mitochondria contain a double-stranded DNA genome that codes for key components of the oxidative phosphorylation system . The mitochondrial DNA ( mtDNA ) is replicated by a replication machinery distinct from that operating in the nucleus and mutations affecting individual replication factors have been associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "nucleic", "acid", "synthesis", "nucleases", "mitochondrial", "dna", "enzymes", "dna-binding", "proteins", "enzymology", "dna", "replication", "forms", "of", "dna", "mitochondria", "dna", "rna", "synthesis", "bioenergetics", "molecular", "bio...	2019	RNase H1 directs origin-specific initiation of DNA replication in human mitochondria
DNA lesions are sensed by a network of proteins that trigger the DNA damage response ( DDR ) , a signaling cascade that acts to delay cell cycle progression and initiate DNA repair . The Mediator of DNA damage Checkpoint protein 1 ( MDC1 ) is essential for spreading of the DDR signaling on chromatin surrounding Double ...	MDC1 recruit Tankyrases to DNA lesions to regulate homologous recombination and to control check-point activation .	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunofluorescence", "staining", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "light", "microscopy", "dna", "damage", "immunoprecipitation", "microscopy", "confocal", "microscopy", "dna", "epigenetics", "chromatin", "research", ...	2016	Tankyrases Promote Homologous Recombination and Check Point Activation in Response to DSBs
Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders . Nephronophthisis 1 ( NPHP1 , MIM# 256100 ) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 reg...	Genomic instability due to the intrinsic sequence architecture of the genome , such as low copy repeats ( LCRs ) , is a major contributor to de novo mutations that can occur in the process of human genome evolution . LCRs can mediate genomic rearrangements associated with genomic disorders by acting as substrates for n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates
The morphogenesis of sex combs ( SCs ) , a male trait in many species of fruit flies , is an excellent system in which to study the cell biology , genetics and evolution of a trait . In Drosophila melanogaster , where the incipient SC rotates from horizontal to a vertical position , three signal comb properties have be...	The sex comb ( SC ) is a series of modified bristles on the male forelegs of many species of fruit flies . The size , position and shape of these sex combs vary drastically across different fly species . Therefore , SCs are a model system which illustrates the interaction between evolution and organism development infl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "statistics", "animals", "epithelial", "cells", "simulation", "and", "modeling", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "mathematics", "experimental", "o...	2018	Rotation of sex combs in Drosophila melanogaster requires precise and coordinated spatio-temporal dynamics from forces generated by epithelial cells
The strength and breadth of an individual’s antibody repertoire is an important predictor of their response to influenza infection or vaccination . Although progress has been made in understanding qualitatively how repeated exposures shape the antibody mediated immune response , quantitative understanding remains limit...	Despite most individuals having some preexisting immunity from past influenza infections and vaccinations , a significant proportion of the human population is infected with influenza each year . Predicting how an individual’s antibody profile will change following exposure is therefore useful for evaluating which popu...	[ "Abstract", "Introduction", "Materials", "&", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "influenza", "immunology", "vertebrates", "animals", "mammals", "vaccines", "preventive", "medicine", "immunologic", "adjuvants", "infectious", "disease", "control", "antibodies", "vaccination", "and", "immu...	2019	Characterising antibody kinetics from multiple influenza infection and vaccination events in ferrets
The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability . Here we identified and analyzed the direct targets of CsrA in the human pathogen Legionella pneumophila . Genome wide transcriptome , proteome ...	The RNA binding protein CsrA is the master regulator of the bi-phasic life cycle of Legionella pneumophila governing virulence expression in this intracellular pathogen . Here , we have used deep sequencing of RNA enriched by co-immunoprecipitation with epitope-tagged CsrA to identify CsrA-associated transcripts at the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "electrophoretic", "mobility", "shift", "assay", "gene", "regulation", "pathogens", "messenger", "rna", "microbiology", "operons", "dna", "transcription", "regulator", "genes", "gene"...	2017	The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system
The use of conventional chemical insecticides and bacterial toxins to control lepidopteran pests of global agriculture has imposed significant selection pressure leading to the rapid evolution of insecticide resistance . Transgenic crops ( e . g . , cotton ) expressing the Bt Cry toxins are now used world wide to contr...	Transgenic crops expressing the insecticidal protein Cry2Ab from Bacillus thuringiensis ( Bt ) are used worldwide to suppress damage by lepidopteran pests , often used in combination with Cry1Ac toxin to delay resistance evolution . Until now , the Cry2Ab mode of action and the mechanism of resistance were unknown , wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Insect Resistance to Bacillus thuringiensis Toxin Cry2Ab Is Conferred by Mutations in an ABC Transporter Subfamily A Protein
Coastal marine ecosystems can be managed by actions undertaken both on the land and in the ocean . Quantifying and comparing the costs and benefits of actions in both realms is therefore necessary for efficient management . Here , we quantify the link between terrestrial sediment runoff and a downstream coastal marine ...	Many coastal marine ecosystems are threatened by anthropogenic activities , but often , the best way to restore and protect these important ecosystems is unclear . Conventional wisdom suggests that the 2 most effective conservation actions to benefit coastal marine ecosystems are implementation of marine protected area...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "ecology", "and", "environmental", "sciences", "marine", "ecosystems", "oceans", "marine", "biology", "aquatic", "environments", "geology", "habitats", "bodies", "of", "water", "marine", "environments", "petrology", "ecosystems", "marine", "and", "aquatic", "sciences", ...	2017	Simple rules can guide whether land- or ocean-based conservation will best benefit marine ecosystems
In order to record the stream of autobiographical information that defines our unique personal history , our brains must form durable memories from single brief exposures to the patterned stimuli that impinge on them continuously throughout life . However , little is known about the computational strategies or neural m...	Humans can effortlessly recognize a pattern as familiar even after a single presentation and a long delay , and our capacity to do so even with complex stimuli such as images has been called "almost limitless" . How is the information needed to support familiarity judgements stored so rapidly and held so reliably for s...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "learning", "medicine", "and", "health", "sciences", "action", "potentials", "neural", "networks", "engineering", "and", "technology", "nervous", "system", "signal", "processing", "membrane", "potential", "social", "sciences", "electrophysiology", "neuroscience", "learnin...	2019	How Dendrites Affect Online Recognition Memory
Four SIV-infected monkeys with high plasma virus and CNS injury were treated with an anti-α4 blocking antibody ( natalizumab ) once a week for three weeks beginning on 28 days post-infection ( late ) . Infection in the brain and gut were quantified , and neuronal injury in the CNS was assessed by MR spectroscopy , and ...	To determine whether ongoing cell traffic is required for SIV-associated tissue damage , we blocked monocyte and T lymphocyte traffic to the brain and gut during a ) ongoing infection or , b ) at the time of infection . When animals were treated at four weeks post infection ( late ) , once significant neuronal injury a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "immune", "cells", "cytokines", "immunology", "neuroscience", "histology", "developmental", "biology", "molecular", "development", "immunologic", "techniques", "immunohistochemical", "analysis", "neuroimaging", "research", "and", "analysis", "methods", "wh...	2014	Anti-α4 Antibody Treatment Blocks Virus Traffic to the Brain and Gut Early, and Stabilizes CNS Injury Late in Infection
The analysis of microbiome compositions in the human gut has gained increasing interest due to the broader availability of data and functional databases and substantial progress in data analysis methods , but also due to the high relevance of the microbiome in human health and disease . While most analyses infer intera...	Over the last years the composition of microbial communities in the human gut , the gut microbiome , has gained prominence in clinical research . Providing an estimate of the microbial interaction network from compositional data is an important prerequisite for clinical interpretation and for a better theoretical under...	[ "Abstract", "Introduction", "Methods", "Results" ]	[ "ecology", "and", "environmental", "sciences", "microbiome", "metabolic", "networks", "microbiology", "species", "delimitation", "simulation", "and", "modeling", "network", "analysis", "speciation", "thermodynamics", "microbial", "genomics", "research", "and", "analysis", ...	2017	Boolean analysis reveals systematic interactions among low-abundance species in the human gut microbiome
Trypanosoma brucei is the etiological agent of Human African Trypanosomiasis , an endemic parasitic disease of sub-Saharan Africa . TbCatB and rhodesain are the sole Clan CA papain-like cysteine proteases produced by the parasite during infection of the mammalian host and are implicated in the progression of disease . ...	Proteases are ubiquitous in all forms of life and catalyze the enzymatic degradation of proteins . These enzymes regulate and coordinate a vast number of cellular processes and are therefore essential to many organisms . While serine proteases dominate in mammals , parasitic organisms commonly rely on cysteine protease...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/protein", "chemistry", "computational", "biology/macromolecular", "structure", "analysis" ]	2010	Crystal Structures of TbCatB and Rhodesain, Potential Chemotherapeutic Targets and Major Cysteine Proteases of Trypanosoma brucei
Aberrant O-glycosylation of serum immunoglobulin A1 ( IgA1 ) represents a heritable pathogenic defect in IgA nephropathy , the most common form of glomerulonephritis worldwide , but specific genetic factors involved in its determination are not known . We performed a quantitative GWAS for serum levels of galactose-defi...	O-glycosylation is a common type of post-translational modification of proteins; specific abnormalities in the mechanism of O-glycosylation have been implicated in cancer , inflammatory and blood diseases . However , the molecular basis of abnormal O-glycosylation in these complex disorders is not known . We studied th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "gene", "regulation", "mathematics", "statistics", "(mathematics)", "genome", "analysis", "molecular", "biology", "techniques", "genotyping", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "genomic", "sig...	2017	GWAS for serum galactose-deficient IgA1 implicates critical genes of the O-glycosylation pathway
Sri Lanka’s Anti Filariasis Campaign distributed 5 rounds of mass drug administration ( MDA with DEC plus albendazole ) to all endemic regions in the country from 2002–2006 . Post-MDA surveillance results have generally been encouraging . However , recent studies have documented low level persistence of Wuchereria banc...	Lymphatic filariasis ( LF ) is a disabling neglected tropical disease that affects millions of people in 73 countries . The Global Program to Eliminate Lymphatic Filariasis ( GPELF ) is using mass drug administration ( MDA ) to reduce infections in humans below levels required for sustained transmission by mosquitoes ....	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "geographical", "locations", "parasitic", "diseases", "animals", "filariasis", "molecular", "biology", "techniques", "insect", "vectors", "research", "and", "analysis", "methods", "public", "and...	2016	Programmatic Use of Molecular Xenomonitoring at the Level of Evaluation Units to Assess Persistence of Lymphatic Filariasis in Sri Lanka
Almost immediately after a human being is born , so too is a new microbial ecosystem , one that resides in that person's gastrointestinal tract . Although it is a universal and integral part of human biology , the temporal progression of this process , the sources of the microbes that make up the ecosystem , how and wh...	It has been recognized for nearly a century that human beings are inhabited by a remarkably dense and diverse microbial ecosystem , yet we are only just beginning to understand and appreciate the many roles that these microbes play in human health and development . Knowing the composition of this ecosystem is a crucial...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "ecology", "obstetrics", "pediatrics", "and", "child", "health", "immunology", "microbiology", "homo", "(human)", "eubacteria" ]	2007	Development of the Human Infant Intestinal Microbiota
To determine whether variation in the preservative , pore size of the sieve , solvent , centrifugal force and centrifugation time used in the Ridley-Allen Concentration method for examining faecal specimens for parasite stages had any effect on their recovery in faecal specimens . A questionnaire was sent to all partic...	UKNEQAS Parasitology and participants themselves noted poor performance in examining faecal specimens that contained low numbers of parasites . Our survey of methods used showed that 96% of respondents used a concentration method based on the Modified Ridley-Allen technique , but there were differences regarding whethe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "chemical", "compounds", "laboratory", "equipment", "engineering", "and", "technology", "organic", "compounds", "animals", "parasitology", "preservatives", "developmental", "biology", "ascaris", "ascaris", "lumbricoides", "centrifugation", "research", "and", ...	2016	Faecal Parasitology: Concentration Methodology Needs to be Better Standardised
Electroencephalography ( EEG ) provides a non-invasive measure of brain electrical activity . Neural population models , where large numbers of interacting neurons are considered collectively as a macroscopic system , have long been used to understand features in EEG signals . By tuning dozens of input parameters descr...	Electroencephalography ( EEG ) , where electrodes are used to measure electric potential on the outside of the scalp , provides a simple , non-invasive way to study brain activity . Physiological interpretation of features in EEG signals has often involved use of collective models of neural populations . These neural p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "markov", "models", "membrane", "potential", "brain", "electrophysiology", "electrophysiology", "neuroscience", "clinical", "medicine", "systems", "science", "mathematics", "physiological", "parameters", "algebra", "brain", "mapping"...	2019	Parameter estimation and identifiability in a neural population model for electro-cortical activity
DNA double-strand breaks ( DSBs ) are formed during meiosis by the action of the topoisomerase-like Spo11/Rec12 protein , which remains covalently bound to the 5′ ends of the broken DNA . Spo11/Rec12 removal is required for resection and initiation of strand invasion for DSB repair . It was previously shown that buddin...	A diploid zygote arises by fusion of two haploid gametes . The specific cell division leading to haploid gametes with haploid chromosome number , accompanied by recombination of genetic material , is called meiosis . It is essential for sexually reproducing eukaryotes . During meiotic prophase , shortly after DNA repli...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair", "molecular", "biology/recombination", "cell", "biology/developmental", "molecular", "mechanisms", "genetics", "and", "genomics/chromosome", "biology" ]	2009	Ctp1 and the MRN-Complex Are Required for Endonucleolytic Rec12 Removal with Release of a Single Class of Oligonucleotides in Fission Yeast
Leptospirosis has become an urban health problem as slum settlements have expanded worldwide . Efforts to identify interventions for urban leptospirosis have been hampered by the lack of population-based information on Leptospira transmission determinants . The aim of the study was to estimate the prevalence of Leptosp...	Leptospirosis , a life-threatening zoonotic disease , has become an important urban slum health problem . Epidemics of leptospirosis now occur in cities throughout the developing world , as the growth of slum settlements has produced conditions for rat-borne transmission of this disease . In this prevalence survey of m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2008	Impact of Environment and Social Gradient on Leptospira Infection in Urban Slums
Increasing emphasis on integrated control of neglected tropical diseases ( NTDs ) requires identification of co-endemic areas . Integrated surveys for lymphatic filariasis ( LF ) , schistosomiasis and soil-transmitted helminth ( STH ) infection have been recommended for this purpose . Integrated survey designs inevitab...	Control of neglected tropical diseases ( NTDs ) is suggested to be more cost-effective when drugs are co-administered through a single integrated delivery system rather than separate systems . An essential prerequisite for such efficiency gains is sufficient geographical overlap of the targeted diseases – lymphatic fil...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/helminth", "infections", "evidence-based", "healthcare/health", "services", "research", "and", "economics", "public", "health", "and", "epidemiology/health", "services", "research", "and", "economics", "infectious", "diseases/neglected", "tropical", "d...	2010	Integrated Surveys of Neglected Tropical Diseases in Southern Sudan: How Much Do They Cost and Can They Be Refined?
Regulation of transforming growth factor-β ( TGF-β ) signaling is critical in vertebrate development , as several members of the TGF-β family have been shown to act as morphogens , controlling a variety of cell fate decisions depending on concentration . Little is known about the role of intracellular regulation of the...	In development , cells respond to secreted signals ( called morphogens ) by turning on or off sets of target genes . How does gene activity adjust quickly in response to rapidly changing extracellular signals ? This should require efficient removal of old/used signaling effectors ( signal-activated transcription factor...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "developmental", "biology", "mus", "(mouse)", "mammals" ]	2007	Arkadia Enhances Nodal/TGF-β Signaling by Coupling Phospho-Smad2/3 Activity and Turnover
Plasmodium vivax is highly endemic in the lowlands of Papua New Guinea and accounts for a large proportion of the malaria cases in children less than 5 years of age . We collected 2117 blood samples at 2-monthly intervals from a cohort of 268 children aged 1 to 4 . 5 years and estimated the diversity and multiplicity o...	The parasite Plasmodium vivax is the second most frequent cause of malaria in humans . In the Maprik area in lowland Papua New Guinea , P . vivax and P . falciparum are sympatric each with a prevalence of around 50% . Longitudinal samples from 268 children aged 1 to 4 . 5 years over 16 months were collected . The 1162 ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology", "epidemiology", "infectious", "disease", "epidemiology", "biology", "microbiology", "population", "biology", "parasitology" ]	2011	Multiplicity and Diversity of Plasmodium vivax Infections in a Highly Endemic Region in Papua New Guinea
Theoretical models of infection spread on networks predict that targeting vaccination at individuals with a very large number of contacts ( superspreaders ) can reduce infection incidence by a significant margin . These models generally assume that superspreaders will always agree to be vaccinated . Hence , they cannot...	Superspreaders are the small number of individuals responsible for the majority of infections . Theoretical models have shown how vaccinating superspreaders can be a highly efficient way to control disease . However , these models neglect behavior by assuming that superspreaders will always agree to be vaccinated . Thi...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "population", "dynamics", "applied", "mathematics", "spatial", "epidemiology", "mathematics", "population", "modeling", "population", "biology", "infectious", "disease", "control...	2013	Policy Resistance Undermines Superspreader Vaccination Strategies for Influenza
Duplications play a significant role in both extremes of the phenotypic spectrum of newly arising mutations: they can have severe deleterious effects ( e . g . duplications underlie a variety of diseases ) but can also be highly advantageous . The phenotypic potential of newly arisen duplications has stimulated wide in...	DNA duplications are important contributors to the phenotypic differences observed between individuals . These mutations can disrupt the normal functioning of genes and so are often associated with disease . But because they can add genetic information they can also lead to evolutionary change . Understanding how selec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "population", "genetics", "mutational", "hypotheses", "animal", "models", "mutation", "drosophila", "melanogaster", "model", "organisms", "mutation", "types", "effective", "population", "size", "genomics", "genetic", "polymorphism", "comparative", "...	2011	Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome
Leprosy is an infectious disease affecting skin and peripheral nerves resulting in increased morbidity and physical deformities . Early diagnosis provides opportune treatment and reduces its complications , relying fundamentally on the demonstration of impaired sensation in suggestive cutaneous lesions . The loss of ta...	Our study has addressed objectively the rarefaction of cutaneous thin nerve fibers density and its correlation with quantitative thermal sensory test in leprosy patients . Thermal sensitivity evaluation is crucial to the early diagnosis of leprosy , since it is the first type of cutaneous sensitivity lost in the lesion...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "dermatology", "infectious", "diseases", "bacterial", "diseases", "public", "health", "and", "epidemiology", "skin", "infections", "leprosy", "public", "health" ]	2012	Degree of Skin Denervation and Its Correlation to Objective Thermal Sensory Test in Leprosy Patients
The major histocompatibility complex ( MHC ) contains the most polymorphic genetic system in humans , the human leukocyte antigen ( HLA ) genes of the adaptive immune system . High allelic diversity in HLA is argued to be maintained by balancing selection , such as negative frequency-dependent selection or heterozygote...	The adaptive immune system presents antigens derived from pathogenic and normal self proteins on the cell surface using human leukocyte antigen ( HLA ) molecules . The HLA loci coding for these molecules are found in major histocompatibility complex ( MHC ) region , the most polymorphic region in the human genome , wit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "population", "genetics", "immunology", "alleles", "genetic", "mapping", "linkage", "disequilibrium", "clinical", "medicine", "population", "biology", "major", "histocompatibility", "complex", "homozygosity", "genetic", "loci", "ha...	2017	HLA class I haplotype diversity is consistent with selection for frequent existing haplotypes
Pseudomonas entomophila is an entomopathogenic bacterium that infects and kills Drosophila . P . entomophila pathogenicity is linked to its ability to cause irreversible damages to the Drosophila gut , preventing epithelium renewal and repair . Here we report the identification of a novel pore-forming toxin ( PFT ) , M...	Insects are potential reservoirs for microbes and ideal vectors for their transmission due to their motility and capacity to live in bacteria-rich environments . This is exemplified by fruit flies that live in rotting fruits and are capable of transmitting phytopathogenic bacteria . Insects are notably resistant to mic...	[ "Abstract", "Introduction", "Results", "Materials", "and", "Methods" ]	[ "toxicology", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "immune", "response" ]	2011	Monalysin, a Novel ß-Pore-Forming Toxin from the Drosophila Pathogen Pseudomonas entomophila, Contributes to Host Intestinal Damage and Lethality
Toll-like receptor ( TLR ) ligands have been explored as vaccine adjuvants for tumor and virus immunotherapy , but few TLR ligands affecting schistosoma vaccines have been characterized . Previously , we developed a partially protective DNA vaccine encoding the 26-kDa glutathione S-transferase of Schistosoma japonicum ...	There is evidence that TLR activation can block Treg cell responses and thereby break tolerance to self-antigens . It is expected that the use of TLR ligands as vaccine adjuvants will induce potent anti-pathogen immune responses and simultaneously overcome immune inhibition mediated by Tregs . However , the impact of T...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "vaccines", "medicine", "vaccination", "infectious", "diseases", "schistosomiasis", "clinical", "immunology", "immunity", "immunology", "parasitic", "diseases", "immunomodulation" ]	2013	Combined TLR7/8 and TLR9 Ligands Potentiate the Activity of a Schistosoma japonicum DNA Vaccine
Modified vaccinia virus Ankara ( MVA ) is the leading poxvirus vector for development of vaccines against diverse infectious diseases . This distinction is based on high expression of proteins and good immunogenicity despite an inability to assemble infectious progeny in human cells , which together promote efficacy an...	Poxvirus vectors have outstanding properties for development of vaccines against a myriad of infectious agents due to their ability to retain long segments of foreign DNA and high-level gene expression . Safety concerns led to a preference for attenuated poxviruses that lost the ability to produce infectious progeny in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "poxviruses", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "viruses", "virus", "effects", "on", "host", "gene", "expression", "dna", "replication", "dna", "viruses", "genome", "analysis", "dna", ...	2019	SPI-1 is a missing host-range factor required for replication of the attenuated modified vaccinia Ankara (MVA) vaccine vector in human cells
Understanding the computations performed by neuronal circuits requires characterizing the strength and dynamics of the connections between individual neurons . This characterization is typically achieved by measuring the correlation in the activity of two neurons . We have developed a new measure for studying connectiv...	The root of our brain's computational power lies in its trillions of connections . With our increasing ability to study these connections experimentally comes the need for analytical tools that can be used to develop meaningful quantitative characterizations . In this manuscript , we present a new such tool , increment...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2010	Incremental Mutual Information: A New Method for Characterizing the Strength and Dynamics of Connections in Neuronal Circuits
During meiosis , chromosomes undergo a homology search in order to locate their homolog to form stable pairs and exchange genetic material . Early in prophase , chromosomes associate in mostly non-homologous pairs , tethered only at their centromeres . This phenomenon , conserved through higher eukaryotes , is termed c...	Meiosis enables sexual reproduction in eukaryotes by producing gametes . In the process , it increases genetic diversity through recombination of homologous chromosomes from the parents . Genetic diversity constitutes an evolutionary advantage . Prior to finding their unique pairing partner ( homolog ) , chromosomes as...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "homologous", "chromosomes", "chromosome", "structure", "and", "function", "centromeres", "cell", "cycle", "and", "cell", "division", "cell", "processes", "telomeres", "fungi", "model", "organisms", "dna", "homologous", "recombination", "research", "and", "...	2016	Multiple Pairwise Analysis of Non-homologous Centromere Coupling Reveals Preferential Chromosome Size-Dependent Interactions and a Role for Bouquet Formation in Establishing the Interaction Pattern
Genome-wide association studies ( GWASs ) have identified many disease associated loci , the majority of which have unknown biological functions . Understanding the mechanism underlying trait associations requires identifying trait-relevant tissues and investigating associations in a trait-specific fashion . Here , we ...	Identifying trait-relevant tissues is an important step towards understanding disease etiology . Computational methods have been recently developed to integrate SNP functional annotations generated from omics studies to genome-wide association studies ( GWASs ) to infer trait-relevant tissues . However , two important ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "sociology", "dna-binding", "proteins", "social", "sciences", "simulation", "and", "modeling", "probability", "distribution", "mathematics", "statistics", "(mathematics)", "test", "statistics", "genome", "analysis", "molecular", "gen...	2018	Identifying and exploiting trait-relevant tissues with multiple functional annotations in genome-wide association studies
Genetic risk prediction is an important goal in human genetics research and precision medicine . Accurate prediction models will have great impacts on both disease prevention and early treatment strategies . Despite the identification of thousands of disease-associated genetic variants through genome wide association s...	Genetic risk prediction plays a significant role in precision medicine . Accurate prediction models could have great impact on disease prevention and early treatment strategies . For example , mutations in BRCA1 and BRCA2 have been used to evaluate women’s breast cancer risk and as a guideline for early screening . How...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Ethics", "statement", "Data", "access" ]	[ "genome-wide", "association", "studies", "rheumatology", "medicine", "and", "health", "sciences", "breast", "tumors", "functional", "genomics", "immunology", "cancers", "and", "neoplasms", "oncology", "diabetes", "mellitus", "rheumatoid", "arthritis", "clinical", "medicin...	2017	Leveraging functional annotations in genetic risk prediction for human complex diseases
An extraordinarily precise regulation of chlorophyll biosynthesis is essential for plant growth and development . However , our knowledge on the complex regulatory mechanisms of chlorophyll biosynthesis is very limited . Previous studies have demonstrated that miR171-targeted scarecrow-like proteins ( SCL6/22/27 ) nega...	Chlorophyll biosynthesis is essential for plant growth and development . To date , the regulatory mechanisms of chlorophyll biosynthesis have been well understood only in dark conditions . Previous reports showed that miR171-targeted SCL6/22/27 proteins were involved in chlorophyll biosynthesis . However , the molecula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "plant", "science", "plant", "physiology", "leaves", "cell", "biology", "plant", "cell", "biology", "biology", "and", "life", "sciences", "chloroplasts", "cellular", "structures", "and", "organelles" ]	2014	Arabidopsis miR171-Targeted Scarecrow-Like Proteins Bind to GT cis-Elements and Mediate Gibberellin-Regulated Chlorophyll Biosynthesis under Light Conditions
Ciliopathies are a group of human disorders caused by dysfunction of primary cilia , ubiquitous microtubule-based organelles involved in transduction of extra-cellular signals to the cell . This function requires the concentration of receptors and channels in the ciliary membrane , which is achieved by complex traffick...	Ciliopathies are a group of disorders caused by dysfunction of primary cilia , ubiquitous organelles involved in signal transduction . Mutations in CC2D2A cause two ciliopathies , Joubert and Meckel syndromes , and result in loss of ciliary protein localization . The mechanism by which CC2D2A , located at the ciliary t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking
Skin invasion is the initial step in infection of the human host by schistosome blood flukes . Schistosome larvae have the remarkable ability to overcome the physical and biochemical barriers present in skin in the absence of any mechanical trauma . While a serine peptidase with activity against insoluble elastin appea...	Schistosome parasites are a major cause of disease in the developing world , but the mechanism by which these parasites first infect their host has been studied at the molecular level only for S . mansoni . In this paper , we have mined recent genome annotations of S . mansoni and S . japonicum , a zoonotic schistosome...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biochemistry", "biology", "proteomics", "zoology", "parasitology" ]	2011	Proteomic Analysis of Human Skin Treated with Larval Schistosome Peptidases Reveals Distinct Invasion Strategies among Species of Blood Flukes
Adenomatous polyposis coli ( APC ) inactivating mutations are present in most human colorectal cancers and some other cancers . The APC protein regulates the β-catenin protein pool that functions as a co-activator of T cell factor ( TCF ) -regulated transcription in Wnt pathway signaling . We studied effects of reduced...	Enhanced Wnt signaling contributes to colorectal and other cancers . β-catenin functions in Wnt signaling as a T cell factor ( TCF ) transcriptional co-activator . Previous studies showed specific β-catenin dosage favors Wnt signaling-dependent tumorigenesis for some tumor types . However , earlier studies emphasized t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Tissue-Specific Effects of Reduced β-catenin Expression on Adenomatous Polyposis Coli Mutation-Instigated Tumorigenesis in Mouse Colon and Ovarian Epithelium
The intricate molecular details of protein-protein interactions ( PPIs ) are crucial for function . Therefore , measuring the same interacting protein pair again , we expect the same result . This work measured the similarity in the molecular details of interaction for the same and for homologous protein pairs between ...	The number of known protein-protein interactions ( PPIs ) grows rapidly , yet their molecular details remain largely unknown . Over the last years , structural biologists have addressed this issue with an increased output of structurally resolved hetero complexes . This wealth now enables statistically significant quan...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "macromolecular", "complex", "analysis", "biochemistry", "protein", "interactions", "proteome", "genetic", "polymorphism", "proteins", "protein", "structure", "macromolecular", "assemblies", "population", "genetics", "biology", "computational", "biology", "proteomics", "macro...	2012	Alternative Protein-Protein Interfaces Are Frequent Exceptions
Most phenotypic variation present in natural populations is under polygenic control , largely determined by genetic variation at quantitative trait loci ( QTLs ) . These genetic loci frequently interact with the environment , development , and each other , yet the importance of these interactions on the underlying gene...	A principal interest in biology is to understand how natural genetic variation translates into phenotypic variation . A key component of this connection is how the genetic variation interacts with other sources of variation , such as environment ( G×E ) , development ( G×D ) , or other genetic loci ( G×G or epistasis )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "ecology/plant-environment", "interactions", "biochemistry", "plant", "biology/plant", "genomes", "and", "evolution", "evolutionary", "biology/plant", "genomes", "and", "evolution", "developmental", "biology/plant", "growth", "an...	2008	Genetic Networks Controlling Structural Outcome of Glucosinolate Activation across Development
Natural protein sequences contain a record of their history . A common constraint in a given protein family is the ability to fold to specific structures , and it has been shown possible to infer the main native ensemble by analyzing covariations in extant sequences . Still , many natural proteins that fold into the sa...	Unlike most natural proteins that are made with apparently random strings of amino acids , repeat-proteins are formed with tandem stretches of similar elements . The statistical description for these occurrences can be captured with a simple energetic model that accounts for evolutionary mechanism that gave rise to the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "split-decomposition", "method", "globular", "proteins", "multiple", "alignment", "calculation", "mutation", "protein", "structure", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "sequence...	2017	Inferring repeat-protein energetics from evolutionary information
Yersinia pestis , the etiologic agent of the disease plague , has been implicated in three historical pandemics . These include the third pandemic of the 19th and 20th centuries , during which plague was spread around the world , and the second pandemic of the 14th–17th centuries , which included the infamous epidemic ...	Plague is a notorious and fatal human disease caused by the bacterium Yersinia pestis that is endemic in many countries around the world . Three of the most devastating pandemics in human history have been associated with plague . The second pandemic originated in central Asia and peaked in Europe between 1348 and 1350...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "social", "and", "behavioral", "sciences", "biological", "anthropology", "genetics", "biology", "microbiology", "anthropology" ]	2013	Yersinia pestis DNA from Skeletal Remains from the 6th Century AD Reveals Insights into Justinianic Plague
Mutations in human Gli-similar ( GLIS ) 3 protein cause neonatal diabetes . The GLIS3 gene region has also been identified as a susceptibility risk locus for both type 1 and type 2 diabetes . GLIS3 plays a role in the generation of pancreatic beta cells and in insulin gene expression , but there is no information on th...	Pancreatic beta cell dysfunction and death is a central event in the pathogenesis of diabetes . Genome-wide association studies have identified a large number of associations between specific loci and the two main forms of diabetes , namely type 1 and type 2 diabetes , but the mechanisms by which these candidate genes ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "insulin", "gene", "regulation", "endocrine", "system", "genetics", "molecular", "genetics", "gene", "expression", "biology", "anatomy", "and", "physiology", "gene", "splicing", "endocrine", "physiology" ]	2013	GLIS3, a Susceptibility Gene for Type 1 and Type 2 Diabetes, Modulates Pancreatic Beta Cell Apoptosis via Regulation of a Splice Variant of the BH3-Only Protein Bim
Long non-coding RNAs ( lncRNAs ) ( > 200 bp ) play crucial roles in transcriptional regulation during numerous biological processes . However , it is challenging to comprehensively identify lncRNAs , because they are often expressed at low levels and with more cell-type specificity than are protein-coding genes . In th...	Between 70 and 90% of the mammalian genome is transcribed at some point during development; however , only < 2% of the genome is associated with protein-coding genes . Emerging evidence suggests that long non-coding RNAs ( lncRNAs; > 200 bp ) play important roles in cell fate determination . In the present study , we b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination
Chagas disease also known as American trypanosomiasis is caused by the protozoan Trypanosoma cruzi . Over the last 30 years , Chagas disease has expanded from a neglected parasitic infection of the rural population to an urbanized chronic disease , becoming a potentially emergent global health problem . T . cruzi strai...	Chagas disease is one of the most important neglected diseases with an estimated number of 6–7 million infected individuals , the majority living in Central and South America . The Trypanosoma cruzi ( T . cruzi ) protozoan parasite is the etiological agent of Chagas disease . T . cruzi is highly genetically diverse and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "libraries", "tropical", "diseases", "microbiology", "database", "searching", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "developmental", "biology", "protein", "expression", "protozoans", "ne...	2018	Development of a Trypanosoma cruzi strain typing assay using MS2 peptide spectral libraries (Tc-STAMS2)
Rotavirus is the leading agent causing acute gastroenteritis in young children , with the P[8] genotype accounting for more than 80% of infections in humans . The molecular bases for binding of the VP8* domain from P[8] VP4 spike protein to its cellular receptor , the secretory H type-1 antigen ( Fuc-α1 , 2-Gal-β1 , 3-...	The interaction of viruses with host glycans has become an important topic in the study of enteric virus infectivity . This interaction modulates several aspects of the viral cycle , including viral attachment , which in most cases depends on the host glycobiology dictated by the secretor and Lewis genotypes . The capa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "immune", "physiology", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "condensed", "matter", "physics", "microbiology", "reoviruses", "viruses", "rn...	2019	Unraveling the role of the secretor antigen in human rotavirus attachment to histo-blood group antigens
Interactions between HLA class I molecules and killer-cell immunoglobulin-like receptors ( KIR ) control natural killer cell ( NK ) functions in immunity and reproduction . Encoded by genes on different chromosomes , these polymorphic ligands and receptors correlate highly with disease resistance and susceptibility . A...	Natural killer cells are white blood cells with critical roles in human health that deliver front-line immunity against pathogens and nurture placentation in early pregnancy . Controlling these functions are cell-surface receptors called KIR that interact with HLA class I ligands expressed on most cells of the body . K...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Co-evolution of Human Leukocyte Antigen (HLA) Class I Ligands with Killer-Cell Immunoglobulin-Like Receptors (KIR) in a Genetically Diverse Population of Sub-Saharan Africans
Genetically encoded biosensors based on fluorescence resonance energy transfer ( FRET ) have been widely applied to visualize the molecular activity in live cells with high spatiotemporal resolution . However , the rapid diffusion of biosensor proteins hinders a precise reconstruction of the actual molecular activation...	Fluorescence biosensors have been widely used to report the spatial and temporal activity of target molecules in live cells . However , biosensors can move independently of the target molecule and carry its signal to other subcellular locations . Therefore , the observed images appear to be the combination of the targe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "signaling", "biochemistry/bioinformatics", "biotechnology/bioengineering", "biophysics/cell", "signaling", "and", "trafficking", "structures", "computational", "biology/systems", "biology" ]	2008	The Spatiotemporal Pattern of Src Activation at Lipid Rafts Revealed by Diffusion-Corrected FRET Imaging
The CST ( Cdc13/CTC1-STN1-TEN1 ) complex was proposed to have evolved kingdom specific roles in telomere capping and replication . To shed light on its evolutionary conserved function , we examined the effect of STN1 dysfunction on telomere structure in plants . STN1 inactivation in Arabidopsis leads to a progressive l...	Telomeres form an elaborate nucleoprotein structure that may represent an obstacle for replication machinery and renders this region prone to fork stalling . CST is an evolutionary conserved complex that was originally discovered to specifically act at telomeres . Interestingly , the function of CST seems to have diver...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "biotechnology", "chromosome", "structure", "and", "function", "telomeres", "plant", "science", "dna", "replication", "forms", "of", "dna", "plant", "genomics", "dna", "chromosome", "biology", "plant", "genetics", "biochemistry", "cell", "biology", "nucleic", "acids",...	2014	Role of STN1 and DNA Polymerase α in Telomere Stability and Genome-Wide Replication in Arabidopsis

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