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Store-operated Ca2+ entry ( SOCE ) has been associated with two types of channels: CRAC channels that require Orai1 and STIM1 and SOC channels that involve TRPC1 , Orai1 , and STIM1 . While TRPC1 significantly contributes to SOCE and SOC channel activity , abrogation of Orai1 function eliminates SOCE and activation of ...	Store-operated Ca2+ entry is present in all cell types and determines sustained cytosolic [Ca2+] increases that are critical for regulating a wide variety of physiological functions . This Ca2+ entry mechanism is activated in response to depletion of Ca2+ in the endoplasmic reticulum ( ER ) . When ER [Ca2+] is decrease...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "physiology", "biochemistry", "ion", "channels", "proteins", "physiology", "biology", "anatomy", "and", "physiology" ]	2011	Local Ca2+ Entry Via Orai1 Regulates Plasma Membrane Recruitment of TRPC1 and Controls Cytosolic Ca2+ Signals Required for Specific Cell Functions
Autoimmune thyroid diseases ( AITD ) are common , affecting 2-5% of the general population . Individuals with positive thyroid peroxidase antibodies ( TPOAbs ) have an increased risk of autoimmune hypothyroidism ( Hashimoto's thyroiditis ) , as well as autoimmune hyperthyroidism ( Graves' disease ) . As the possible ca...	Individuals with thyroid peroxidase antibodies ( TPOAbs ) have an increased risk of autoimmune thyroid diseases ( AITD ) , which are common in the general population and associated with increased cardiovascular , metabolic and psychiatric morbidity and mortality . As the causative genes of TPOAbs and AITD remain largel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "hypothyroidism", "endocrinology", "graves'", "disease", "thyroid", "hashimoto", "disease" ]	2014	Identification of Novel Genetic Loci Associated with Thyroid Peroxidase Antibodies and Clinical Thyroid Disease
The mouse cytomegaloviral ( MCMV ) protein pM27 represents an indispensable factor for viral fitness in vivo selectively , antagonizing signal transducer and activator of transcription 2 ( STAT2 ) -mediated interferon signal transduction . We wished to explore by which molecular mechanism pM27 accomplishes this effect ...	Cytomegaloviruses are strictly species-specific . Mouse cytomegalovirus ( MCMV ) is a prototypical β-herpesvirus , infecting Mus musculus as natural host and is closely related to the human pathogenic cytomegalovirus ( HCMV , HHV-5 ) which both establish lifelong infection . Thus , MCMV infection constitutes an importa...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunity", "innate", "immunity", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "viral", "diseases" ]	2011	Identification of DNA-Damage DNA-Binding Protein 1 as a Conditional Essential Factor for Cytomegalovirus Replication in Interferon-γ-Stimulated Cells
The succession of molecular events leading to eukaryotic translation reinitiation—whereby ribosomes terminate translation of a short open reading frame ( ORF ) , resume scanning , and then translate a second ORF on the same mRNA—is not well understood . Density-regulated reinitiation and release factor ( DENR ) and mul...	Usually , eukaryotic ribosomes translate only a single open reading frame ( ORF ) on an mRNA and then dissociate from the mRNA . In some cases , when there is a short upstream open reading frame ( uORF ) that precedes the main ORF , ribosomes can translate the uORF , terminate translation , and then undergo a poorly un...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfer", "rna", "chemical", "characterization", "crystal", "structure", "gel", "shift", "assay", "hela", "cells", "gene", "regulation", "biological", "cultures", "condensed", "matter", "physics", "cell", "cultures", "molecular", "biology", "techniques", "crystallogra...	2018	DENR–MCTS1 heterodimerization and tRNA recruitment are required for translation reinitiation
Bacterial cell-surface proteins play integral roles in host-pathogen interactions . These proteins are often architecturally and functionally sophisticated and yet few studies of such proteins involved in host-pathogen interactions have defined the domains or modules required for specific functions . Streptococcus pneu...	The adherence of bacteria to host cells is a critical step in most bacterial infections; yet , mechanisms are poorly understood for many bacteria , including Streptococcus pneumoniae ( pneumococcus ) , a human pathogen of global relevance . The surface of this bacterium is decorated with a landscape of large and struct...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "interactions", "pneumococcus", "enzymes", "enzymology", "microbiology", "glycoside", "hydrolases", "protein", "structure", "glycosylation", "glycoproteins", "bacterial", "pathogens", "protein", "structure", "determination", "proteins", "medical", "microbiology", "...	2014	Unravelling the Multiple Functions of the Architecturally Intricate Streptococcus pneumoniae β-galactosidase, BgaA
Binocular rivalry and cross-orientation suppression are well-studied forms of competition in visual cortex , but models of these two types of competition are in tension with one another . Binocular rivalry occurs during the presentation of dichoptic grating stimuli , where two orthogonal gratings presented separately t...	Binocular rivalry is a visual illusion that occurs when the two eyes are presented with incompatible images . Instead of perceiving a mixture of the two images , most people tend to experiences alternations in which they only see one image at a time . Binocular rivalry is more than just an interesting illusion: it refl...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "visual", "system", "neural", "networks", "computational", "neuroscience", "biology", "sensory", "systems", "neuroscience" ]	2013	A Model of Binocular Rivalry and Cross-orientation Suppression
Praziquantel at 40 mg/kg in a single dose is the WHO recommended treatment for all forms of schistosomiasis , but 60 mg/kg is also deployed nationally . Four trial sites in the Philippines , Mauritania , Tanzania and Brazil enrolled 856 patients using a common protocol , who were randomised to receive praziquantel 40 m...	Control of urinary and intestinal schistosomiasis is based on mass administration of praziquantel at the World Health Organization ( WHO ) recommended dose of 40 mg/kg , though some countries use 60 mg/kg . This multi-country randomized clinical trial compared the efficacy ( cure and egg reduction rates three weeks pos...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "health", "medicine", "infectious", "diseases", "schistosomiasis", "public", "health", "and", "epidemiology", "clinical", "research", "design", "clinical", "trials", "drug", "policy", "neglected", "tropical", "diseases", "parasitic", "diseases", "meta-analyses" ...	2011	A Multicentre Randomized Controlled Trial of the Efficacy and Safety of Single-Dose Praziquantel at 40 mg/kg vs. 60 mg/kg for Treating Intestinal Schistosomiasis in the Philippines, Mauritania, Tanzania and Brazil
Parkinson's disease ( PD ) -mimicking drugs and pesticides , and more recently PD-associated gene mutations , have been studied in cell cultures and mammalian models to decipher the molecular basis of PD . Thus far , a dozen of genes have been identified that are responsible for inherited PD . However they only account...	In Parkinson's disease ( PD ) , motor neurons that produce dopamine degenerate , leading to a characteristic syndrome including tremor , rigidity , and bradykinesia . The mechanisms leading to PD have been under intense investigation , identifying hereditary mutations responsible for about 8% of the cases . However , m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "neurological", "disorders", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2010	Extracellular Dopamine Potentiates Mn-Induced Oxidative Stress, Lifespan Reduction, and Dopaminergic Neurodegeneration in a BLI-3–Dependent Manner in Caenorhabditis elegans
Lung granulomas are the pathologic hallmark of tuberculosis ( TB ) . T cells are a major cellular component of TB lung granulomas and are known to play an important role in containment of Mycobacterium tuberculosis ( Mtb ) infection . We used cynomolgus macaques , a non-human primate model that recapitulates human TB w...	The characteristic feature of Mycobacterium tuberculosis ( Mtb ) infection is the formation of lesions , which are organized structures of immune cells in the lungs called granulomas , which contain the bacteria . When the granuloma functions effectively , it can kill the bacteria . T cells ( a type of immune cell , al...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Variability in Tuberculosis Granuloma T Cell Responses Exists, but a Balance of Pro- and Anti-inflammatory Cytokines Is Associated with Sterilization
Mollicutes is a class of parasitic bacteria that have evolved from a common Firmicutes ancestor mostly by massive genome reduction . With genomes under 1 Mbp in size , most Mollicutes species retain the capacity to replicate and grow autonomously . The major goal of this work was to identify the minimal set of proteins...	In all cells , proteins are synthesized from the message encoded by mRNA using complex machineries involving many proteins and RNAs . In this process , named translation , the ribosome plays a central role . The elements involved in both ribosome biogenesis and its function are extremely conserved in all organisms from...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "bacillus", "microbiology", "escherichia", "coli", "prokaryotic", "models", "model", "organisms", "molecular", "cell", "biology", "rna", "synthesis", "bacterial", "pathogens", "research", "and", "analysis", "methods", "proteins", "medical", "microbiology", "gene", "expr...	2014	Predicting the Minimal Translation Apparatus: Lessons from the Reductive Evolution of Mollicutes
Klebsiella pneumoniae is a significant human pathogen , in part due to high rates of multidrug resistance . RamA is an intrinsic regulator in K . pneumoniae established to be important for the bacterial response to antimicrobial challenge; however , little is known about its possible wider regulatory role in this organ...	Bacteria can rapidly evolve under antibiotic pressure to develop resistance , which occurs when target genes mutate , or when resistance-encoding genes are transferred . Alternatively , microbes can simply alter the levels of intrinsic proteins that allow the organism to “buy” time to resist antibiotic pressure . Klebs...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Elucidation of the RamA Regulon in Klebsiella pneumoniae Reveals a Role in LPS Regulation
The regulatory architecture of gene expression remains an area of active research . Here , we studied how the interplay of genetic and environmental variation affects gene expression by exposing Drosophila melanogaster strains to four different developmental temperatures . At 18°C we observed almost complete canalizati...	Gene expression is the most direct link between the genetically encoded information and the phenotype . We analyzed the patterns of gene expression in two different D . melanogaster genotypes and their offspring at four different temperatures to determine if gene expression regulation is modulated by temperature . Inte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Temperature Stress Mediates Decanalization and Dominance of Gene Expression in Drosophila melanogaster
Overexpression of the inducible heat shock protein 70 , Hsp72 , has broadly cytoprotective effects and improves outcome following stroke . A full understanding of how Hsp72 protects cells against injury is elusive , though several distinct mechanisms are implicated . One mechanism is its anti-inflammatory effects . We ...	Inducing heat shock or overexpressing certain heat shock proteins ( HSPs ) is known to protect against brain injury , such as that resulting from stroke . Understanding the mechanisms underlying protection at the cellular and molecular level is a subject of intense research , as such knowledge may prove beneficial in d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "signal", "transduction", "signaling", "in", "cellular", "processes", "transcriptional", "signaling", "cellular", "stress", "responses", "regulatory", "networks", "signaling", "networks", "biology", "molecular", "cell", "biology", "computational", "b...	2014	Overexpression of Heat Shock Protein 72 Attenuates NF-κB Activation Using a Combination of Regulatory Mechanisms in Microglia
The innate immune system of Anopheles gambiae mosquitoes limits Plasmodium infection through multiple molecular mechanisms . For example , midgut invasion by the parasite triggers an epithelial nitration response that promotes activation of the complement-like system . We found that suppression of the JNK pathway , by ...	The mosquito Anopheles gambiae is a major vector of human malaria , a disease caused by Plasmodium falciparum parasites that results in more than half a million deaths each year . Several signaling pathways in the mosquito have been shown to mediate the mosquito immune responses to Plasmodium infection . In this manusc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "mosquitoes", "vector", "biology", "biology", "microbiology", "vectors", "and", "hosts" ]	2013	The JNK Pathway Is a Key Mediator of Anopheles gambiae Antiplasmodial Immunity
Transcriptional repression of ribosomal components and tRNAs is coordinately regulated in response to a wide variety of environmental stresses . Part of this response involves the convergence of different nutritional and stress signaling pathways on Maf1 , a protein that is essential for repressing transcription by RNA...	The Maf1 protein is an essential negative regulator of transcription by RNA polymerase III in S . cerevisiae and functions to integrate responses from diverse nutritional and stress signaling pathways that coordinately regulate ribosome and tRNA synthesis . These signaling pathways are not well-defined , and efforts to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression" ]	2008	Genetic Interactions of MAF1 Identify a Role for Med20 in Transcriptional Repression of Ribosomal Protein Genes
Cohesin acetyltransferases ESCO1 and ESCO2 play a vital role in establishing sister chromatid cohesion . How ESCO1 and ESCO2 are controlled in a DNA replication-coupled manner remains unclear in higher eukaryotes . Here we show a critical role of CUL4-RING ligases ( CRL4s ) in cohesion establishment via regulating ESCO...	During the cycle of cell division and proliferation , each chromosome is copied into twin sister chromatids . To make sure a complete set of chromosomes are correctly passed on from generation to generation , the twins must be tethered together by a multi-protein ring called cohesin . ESCO1 and ESCO2 have been known to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "293t", "cells", "enzymes", "gene", "regulation", "biological", "cultures", "enzymology", "chromatids", "fungi", "dna", "replication", "dna", "epigenetics", "ligases", "chromatin", "research", "and", "analysis", "methods", "small", "interfering", "rnas", "chromosome", ...	2019	Cul4-Ddb1 ubiquitin ligases facilitate DNA replication-coupled sister chromatid cohesion through regulation of cohesin acetyltransferase Esco2
Examples of metabolic rhythms have recently emerged from studies of budding yeast . High density microarray analyses have produced a remarkably detailed picture of cycling gene expression that could be clustered according to metabolic functions . We developed a model-based approach for the decomposition of expression t...	In bacterial and eukaryotic cells , gene expression is regulated at both the transcriptional and translational levels . In eukaryotes these two processes cannot be directly coupled because the nuclear membrane separates the chromosomes from the ribosomes . Although the transcription levels in different cellular conditi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/genomics", "computational", "biology/transcriptional", "regulation" ]	2009	Spatio-Temporal Dynamics of Yeast Mitochondrial Biogenesis: Transcriptional and Post-Transcriptional mRNA Oscillatory Modules
Escherichia coli cyclic AMP Receptor Protein ( CRP ) undergoes conformational changes with cAMP binding and allosterically promotes CRP to bind specifically to the DNA . In that , the structural and dynamic properties of apo CRP prior to cAMP binding are of interest for the comprehension of the activation mechanism . H...	Protein dynamics are central in allosteric communication . The cooperative character of atomic motions is key in the propagation of the allosteric signal and in the protein functioning . Here , we explored the dynamics of cAMP Receptor Protein ( CRP ) as an apo unbound monomer/dimer and a holo dimer by molecular dynami...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology" ]	2013	Dynamic Fluctuations Provide the Basis of a Conformational Switch Mechanism in Apo Cyclic AMP Receptor Protein
We used pulse-labeling with the methionine analogue homopropargylglycine ( HPG ) to investigate spatiotemporal aspects of protein synthesis during herpes simplex virus ( HSV ) infection . In vivo incorporation of HPG enables subsequent selective coupling of fluorochrome-capture reagents to newly synthesised proteins . ...	All viruses reprogram infected cells for the synthesis , modification and targeted localisation of virus-encoded and host proteins . Advances in proteomics and mass spectrometry have provided broad insight into these processes , but these approaches have limited ability to investigate spatial aspects of infected cell p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "vero", "cells", "medicine", "and", "health", "sciences", "immune", "physiology", "chemical", "compounds", "viral", "transmission", "and", "infection", "biological", "cultures", "immunology", "microbiology", "organic", "compounds", "geoinformatics", "protein", "synthesis"...	2016	Spatial and Temporal Resolution of Global Protein Synthesis during HSV Infection Using Bioorthogonal Precursors and Click Chemistry
Snakebite envenoming is a major public health problem throughout the rural tropics . Antivenom is effective in reducing mortality and remains the mainstay of therapy . This study aimed to determine the cost-effectiveness of using effective antivenoms for Snakebite envenoming in Nigeria . Economic analysis was conducted...	Snake bite is a major public health problem throughout rural communities in West Africa and leads to a significant number of deaths and disabilities per year . Even though effective antivenoms exist against the locally prevalent carpet viper and other poisonous snakes , they are generally not available in community set...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "epidemiology", "biology", "and", "life", "sciences", "tropical", "diseases", "toxicology", "health", "care" ]	2015	Cost-effectiveness of Antivenoms for Snakebite Envenoming in Nigeria
Specification of the myriad of unique neuronal subtypes found in the nervous system depends upon spatiotemporal cues and terminal selector gene cascades , often acting in sequential combinatorial codes to determine final cell fate . However , a specific neuronal cell subtype can often be generated in different parts of...	A fundamental challenge in developmental neurobiology is to understand how the great diversity of neuronal subtypes is generated during nervous system development . Neuronal subtype cell fate is established in a stepwise manner , starting with spatial and temporal cues that confer distinct identities to neural progenit...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "cell", "death", "medicine", "and", "health", "sciences", "nervous", "system", "gene", "regulation", "cell", "processes", "neuroscience", "animals", "animal", "models", "regulator", "genes", "drosophila", "melanogaster", "model", "organisms", "neuronal"...	2016	Neuronal Cell Fate Specification by the Convergence of Different Spatiotemporal Cues on a Common Terminal Selector Cascade
This communication reports on the Mycetoma Research Centre of the University of Khartoum , Sudan experience on 6 , 792 patients seen during the period 1991–2014 . The patients were predominately young ( 64% under 30 years old ) males ( 76% ) . The majority ( 68% ) were from the Sudan mycetoma belt and 28% were students...	Many researchers consider the Sudan as the mycetoma homeland . The first report on mycetoma was at the turn of the eighteenth century , and since then many documents on mycetoma have been reported . However , there is no recent report on mycetoma in the country . In 1977 Mahgoub published data on mycetoma in Sudan , bu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Mycetoma in the Sudan: An Update from the Mycetoma Research Centre, University of Khartoum, Sudan
Killed oral cholera vaccines ( OCVs ) are available but not used routinely for cholera control except in Vietnam , which produces its own vaccine . In 2007–2008 , unprecedented cholera outbreaks occurred in the capital , Hanoi , prompting immunization in two districts . In an outbreak investigation , we assessed the ef...	Simple measures such as adequate sanitation and clean water stops the spread of cholera; however , in areas where these are not available , cholera spreads quickly and may lead to death in a few hours if treatment is not initiated immediately . The use of life-saving rehydration therapy is the mainstay in cholera contr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "cholera", "neglected", "tropical", "diseases", "infectious", "disease", "control" ]	2011	Use of Oral Cholera Vaccines in an Outbreak in Vietnam: A Case Control Study
Chikungunya virus ( CHIKV ) belongs to a group of mosquito-borne alphaviruses associated with acute and chronic arthropathy , with peripheral and limb joints most commonly affected . Using a mouse model of CHIKV infection and arthritic disease , we show that CHIKV replication and the ensuing foot arthropathy were drama...	Chikungunya virus ( CHIKV ) and Ross River virus are mosquito-borne alphaviruses that cause epidemics of human arthritic disease that usually last from weeks to months . Arthropathy predominantly manifests in the joints of limbs and the joints at the extremities ( e . g . hand and feet ) . Herein we show a surprisingly...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "legs", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "tropical", "diseases", "microbiology", "limbs", "(anatomy)", "alphaviruses", "viruses", "animal", "models", "model", "...	2017	Lower temperatures reduce type I interferon activity and promote alphaviral arthritis
Chikungunya virus ( CHIKV ) is a re-emerging alphavirus that has caused significant disease in the Indian Ocean region since 2005 . During this outbreak , in addition to fever , rash and arthritis , severe cases of CHIKV infection have been observed in infants . Challenging the notion that the innate immune response in...	Type I interferon plays a critical role in the host defense to viral infection . Signaling through the type I IFN receptor allows for the induction of hundreds of interferon stimulated genes ( ISGs ) that generate an antiviral state within host cells . The ubiquitin-like molecule ISG15 has been shown to play an importa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	ISG15 Is Critical in the Control of Chikungunya Virus Infection Independent of UbE1L Mediated Conjugation
Retroviruses and retrotransposons are vulnerable to a suicidal pathway known as autointegration , which occurs when the 3′-ends of the reverse transcript are activated by integrase and then attack sites within the viral DNA . Retroelements have diverse strategies for suppressing autointegration , but how HIV-1 protects...	When HIV-1 infects a cell , its genomic RNA is copied into DNA . The ends of the viral DNA are then activated by the viral integrase enzyme to enable DNA insertion into a host cell chromosome . However , the activated ends can alternately insert into the virus itself by a process called autointegration , which is a sui...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/hiv", "infection", "and", "aids", "virology/viral", "replication", "and", "gene", "regulation", "virology/host", "antiviral", "responses" ]	2009	The SET Complex Acts as a Barrier to Autointegration of HIV-1
Recent advances in mathematical modeling and inference methodologies have enabled development of systems capable of forecasting seasonal influenza epidemics in temperate regions in real-time . However , in subtropical and tropical regions , influenza epidemics can occur throughout the year , making routine forecast of ...	Influenza causes high levels of morbidity , mortality , and economic burden . Accurate forecasts of epidemic timing and magnitude would provide public health sectors valuable advance information in support of the planning and deployment of intervention measures . Such forecast systems have been developed for temperate ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Forecasting Influenza Epidemics in Hong Kong
The functional structure of all biologically active molecules is dependent on intra- and inter-molecular interactions . This is especially evident for RNA molecules whose functionality , maturation , and regulation require formation of correct secondary structure through encoded base-pairing interactions . Unfortunatel...	At the heart of RNA functionality , maturation , and regulation is the formation of intricate secondary structures that are dependent on specific nucleotide base-pairing interactions encoded within their sequences . These interactions can either be within ( intra-molecular ) or between ( inter-molecular ( heteroduplex ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "genomes", "and", "evolution", "evolutionary", "biology/plant", "genomes", "and", "evolution", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/molecular", "genetics", "evolutionary", "biology/genomics", "molecu...	2010	Genome-Wide Double-Stranded RNA Sequencing Reveals the Functional Significance of Base-Paired RNAs in Arabidopsis
We have characterized the biological functions of the chromatin remodeling protein Bptf ( Bromodomain PHD-finger Transcription Factor ) , the largest subunit of NURF ( Nucleosome Remodeling Factor ) in a mammal . Bptf mutants manifest growth defects at the post-implantation stage and are reabsorbed by E8 . 5 . Histolog...	While the chromatin of eukaryotes provides an efficient means to compact large amounts of DNA into a small nucleus , it renders the DNA relatively inaccessible . ATP-dependent chromatin remodeling complexes mobilize nucleosomes and provide a means to gain access to DNA in chromatin . While the biochemical functions of ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/embryology", "genetics", "and", "genomics/animal", "genetics", "developmental", "biology/stem", "cells", "developmental", "biology/morphogenesis", "and", "cell", "biology", "cell", "biology/cell", "signaling", "cell", "biology/nuclear", "structure", ...	2008	Essential Role of Chromatin Remodeling Protein Bptf in Early Mouse Embryos and Embryonic Stem Cells
We have identified and characterized a Macrophage Migration Inhibitory Factor ( MIF ) family member in the Lophotrochozoan invertebrate , Biomphalaria glabrata , the snail intermediate host of the human blood fluke Schistosoma mansoni . In mammals , MIF is a widely expressed pleiotropic cytokine with potent pro-inflamm...	Schistosoma mansoni , a parasitic blood fluke that causes intestinal schistosomiasis in humans , requires an intermediate host , a freshwater snail of the genus Biomphalaria for its transmission . Infection of the snail triggers marked cellular and humoral immune responses , but the molecular mechanisms of these respon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/helminth", "infections", "immunology/innate", "immunity" ]	2010	Involvement of the Cytokine MIF in the Snail Host Immune Response to the Parasite Schistosoma mansoni
RAD51 recombinase polymerizes at the site of double-strand breaks ( DSBs ) where it performs DSB repair . The loss of RAD51 causes extensive chromosomal breaks , leading to apoptosis . The polymerization of RAD51 is regulated by a number of RAD51 mediators , such as BRCA1 , BRCA2 , RAD52 , SFR1 , SWS1 , and the five RA...	Mutations in BRCA1 and BRCA2 predispose hereditary breast and ovarian cancer . Such mutations sensitize to chemotherapeutic agents , including camptothecin , cisplatin , and poly ( ADP-ribose ) polymerase ( PARP ) inhibitor , since RAD51 mediators including both BRCA proteins promote repair of DNA lesions induced by th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	The Epistatic Relationship between BRCA2 and the Other RAD51 Mediators in Homologous Recombination
Cell-cell recognition is a fundamental process that allows cells to coordinate multicellular behaviors . Some microbes , such as myxobacteria , build multicellular fruiting bodies from free-living cells . However , how bacterial cells recognize each other by contact is poorly understood . Here we show that myxobacteria...	How individual cells recognize each other to cooperate and assemble functional tissues is a fundamental question in biology . Although multicellularity is a trait that is typically associated with eukaryotes , certain groups of bacteria also exhibit complex multicellular behaviors , which are perhaps best exemplified b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Molecular Recognition by a Polymorphic Cell Surface Receptor Governs Cooperative Behaviors in Bacteria
Membrane-embedded prenyltransferases from the UbiA family catalyze the Mg2+-dependent transfer of a hydrophobic polyprenyl chain onto a variety of acceptor molecules and are involved in the synthesis of molecules that mediate electron transport , including Vitamin K and Coenzyme Q . In humans , missense mutations to th...	The biosynthesis of Vitamin K and Coenzyme Q requires the transfer of a long , hydrophobic moiety known as an isoprenyl onto an aromatic acceptor compound . This process is catalyzed by a family of proteins known as the UbiA proteins , which are embedded in the hydrophobic environment of cell membranes . To understand ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "membrane", "proteins", "biochemistry", "enzyme", "structure", "lipids", "transmembrane", "proteins", "cell", "biology", "enzymes", "transferases", "biology", "and", "life", "sciences", "enzymology", "isoprenoids", "cellular", "structures", "and", "organelles", "cell", ...	2014	Structure of a Membrane-Embedded Prenyltransferase Homologous to UBIAD1
Architecture of phase relationships among neural oscillations is central for their functional significance but has remained theoretically poorly understood . We use phenomenological model of delay-coupled oscillators with increasing degree of topological complexity to identify underlying principles by which the spatio-...	Functional connectivity , and in particular , phase coupling between distant brain regions may be fundamental in regulating neuronal processing and communication . However , phase relationships between the nodes of the brain and how they are confined by its spatio-temporal structure , have been mostly overlooked . We u...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "cognitive", "science", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "nervous", "system", "signal", "processing", "brain", "neuroscience", "cerebral", "hemispheres", "left", "hemisphere", "systems", "science", "mathe...	2018	Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis
The DOK1 tumor suppressor gene encodes an adapter protein that acts as a negative regulator of several signaling pathways . We have previously reported that DOK1 expression is up-regulated upon cellular stress , via the transcription factor E2F1 , and down-regulated in a variety of human malignancies due to aberrant hy...	Many oncogenic viruses exhibit cellular transforming properties , often involving oncogenes activation and tumor suppressor genes inactivation . The DOK1 gene is a newly identified tumor suppressor gene with altered expression via hypermethylation of its promoter in a variety of human cancers , including head and neck ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "virology", "viruses", "and", "cancer", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "microbiology", "molecular", "cell", "biology" ]	2014	Epstein-Barr Virus Down-Regulates Tumor Suppressor DOK1 Expression
Zika is one of the most challenging emergent vector-borne diseases , yet its future public health impact remains unclear . Zika was of little public health concern until recent reports of its association with congenital syndromes . By 3 August 2017 ∼217 , 000 Zika cases and ∼3 , 400 cases of associated congenital syndr...	In February 2016 the World Health Organisation ( WHO ) declared Zika virus infection in the Americas as a Public Health Emergency of International Concern ( PHEIC ) . By November 2016 , Zika was declared a long-term public health challenge . This change of status implies that Zika is likely to become an endemic problem...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results/Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "microcephaly", "pathology", "and", "laboratory", "medicine", "atmospheric", "science", "pathogens", "geographical", "locations", "microbiology", "social", "sciences", "animals", "health", "care", "viruses", "devel...	2017	After the epidemic: Zika virus projections for Latin America and the Caribbean
As Arabidopsis thaliana has colonized a wide range of habitats across the world it is an attractive model for studying the genetic mechanisms underlying environmental adaptation . Here , we used public data from two collections of A . thaliana accessions to associate genetic variability at individual loci with differen...	A central problem when studying adaptation to a new environment is the interplay between genetic variation and phenotypic plasticity . Arabidopsis thaliana has colonized a wide range of habitats across the world and it is therefore an attractive model for studying the genetic mechanisms underlying environmental adaptat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "genome-wide", "association", "studies", "plant", "genomes", "quantitative", "trait", "association", "studies", "quantitative", "trait", "loci", "population", "genetics", "quantitative", "traits", "statistical", "analysis", "of", "genetic", "association", ...	2014	Natural CMT2 Variation Is Associated With Genome-Wide Methylation Changes and Temperature Seasonality
Antimicrobial resistance of infectious agents is a growing problem worldwide . To prevent the continuing selection and spread of drug resistance , rational design of antibiotic treatment is needed , and the question of aggressive vs . moderate therapies is currently heatedly debated . Host immunity is an important , bu...	The evolution and spread of antimicrobial resistance is a major global problem , and a cause of substantial human mortality . As the discovery of new antibiotics does not follow the rate at which new resistances develop , a more judicial use of available drugs is needed . Here we develop a mathematical model of within-...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "immunology", "microbiology", "antibiotic", "resistance", "pharmaceutics", "antibiotics", "pharmacology", "antimicrobial", "resistance", "pathogenesi...	2016	Integrating Antimicrobial Therapy with Host Immunity to Fight Drug-Resistant Infections: Classical vs. Adaptive Treatment
Several components of the mosquito immune system including the RNA interference ( RNAi ) , JAK/STAT , Toll and IMD pathways have previously been implicated in controlling arbovirus infections . In contrast , the role of the phenoloxidase ( PO ) cascade in mosquito antiviral immunity is unknown . Here we show that condi...	Arboviruses are transmitted to vertebrates by arthropod vectors such as mosquitoes . Infection of mosquitoes with arboviruses activates immune defence responses including the RNA interference pathway . Another component of the insect immune system is the phenoloxidase ( PO ) cascade , which produces melanin that accumu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mosquitoes", "immunity", "vector", "biology", "innate", "immunity", "virology", "biology", "microbiology" ]	2012	Phenoloxidase Activity Acts as a Mosquito Innate Immune Response against Infection with Semliki Forest Virus
ClinicalTrials . gov 2013-0047 . Protozoan parasites of the genus Leishmania are the causative agents of leishmaniasis , a neglected disease with worldwide distribution . With 350 million people at risk and 300 000 estimated cases , the visceral form of leishmaniasis ( VL ) can be fatal if not treated . The symptoms co...	Visceral leishmaniasis is a chronic disease caused by the life-threatening parasite Leishmania donovani . This chronicity character is a major concern in experimental models of visceral leishmaniasis , since infected animals do not develop any visible sign or symptom before one/two months after infection . Consequently...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "liver", "immune", "physiology", "spleen", "microbiology", "vertebrates", "parasitic", "diseases", "protozoan", "life", "cycles", "mammals", "animals", "electromagnetic", "radiation", "parasitic", "protozoans", "developmental", "bi...	2017	New insights into experimental visceral leishmaniasis: Real-time in vivo imaging of Leishmania donovani virulence
Epithelial–mesenchymal transition ( EMT ) is a normal cell differentiation event during development and contributes pathologically to carcinoma and fibrosis progression . EMT often associates with increased transforming growth factor-β ( TGF-β ) signaling , and TGF-β drives EMT , in part through Smad-mediated reprogram...	TGF-β family proteins control cell differentiation and various cell functions . Increased TGF-β signaling , acting through heteromeric receptor complexes , contributes to carcinoma progression and fibrosis . TGF-β drives epithelial–mesenchymal transdifferentiation ( EMT ) , which enables cell migration and invasion . U...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	ShcA Protects against Epithelial–Mesenchymal Transition through Compartmentalized Inhibition of TGF-β-Induced Smad Activation
Elimination of blinding trachoma by 2020 can only be achieved if affected areas have effective control programs in place before the target date . Identifying risk factors for active disease that are amenable to intervention is important to successfully design such programs . Previous studies have linked sleeping by a c...	Trachoma remains the leading preventable cause of infectious blindness in the world . Identifying risk factors for active disease that are amenable to intervention is key to successfully designing effective control programs to eliminate blinding trachoma . Association between cooking fire and eye inflammation makes bio...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Exposure to an Indoor Cooking Fire and Risk of Trachoma in Children of Kongwa, Tanzania
Thosea asigna virus ( TaV ) , an insect virus belonging to the Permutatetraviridae family , has a positive-sense single-stranded RNA ( ssRNA ) genome with two overlapping open reading frames , encoding for the replicase and capsid proteins . The particular TaV replicase includes a structurally unique RNA-dependent RNA ...	RNA dependent RNA polymerases ( RdRPs ) are the catalytic components of the RNA replication and transcription machineries , and thus central players in the life cycle of RNA viruses . The in-depth understanding of both the structure and regulation of viral RdRPs displaying different replication-transcription strategies...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases
Telomeres are protein–DNA structures found at the ends of linear chromosomes and are crucial for genome integrity . Telomeric DNA length is primarily maintained by the enzyme telomerase . Cells lacking telomerase will undergo senescence when telomeres become critically short . In Saccharomyces cerevisiae , a very small...	Homologous recombination is a means for an organism or a cell to repair damaged DNA in its genome . Eukaryotic chromosomes have a linear configuration with two ends that are special DNA–protein structures called telomeres . Telomeres can be recognized by the cell as DNA double-strand breaks and subjected to repair by h...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology", "gene", "function", "telomeres", "model", "organisms", "molecular", "genetics", "dna", "mycology", "chromosome", "biology", "biology", "molecular", "biology", "yeast", "cell", "biology", "nucleic", "acids", "genetic", "screens", "gene", "identification",...	2013	Telomerase-Null Survivor Screening Identifies Novel Telomere Recombination Regulators
The wheat pathogen Stagonospora nodorum produces multiple necrotrophic effectors ( also called host-selective toxins ) that promote disease by interacting with corresponding host sensitivity gene products . SnTox1 was the first necrotrophic effector identified in S . nodorum , and was shown to induce necrosis on wheat ...	In this manuscript we describe the cloning of SnTox1 from Stagonospora nodorum , the gene encoding the first host selective toxin ( SnTox1 ) identified in this fungus . SnTox1 induces necrosis and promotes disease on wheat lines harboring the Snn1 gene . We verified the function of the SnTox1 gene by expressing it in a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology", "gene", "function", "plant", "science", "pest", "control", "plant", "pathology", "molecular", "genetics", "gene", "expression", "plant", "genetics", "biology", "agriculture", "gene", "identification", "and", "analysis", "plant", "pathogens", "genet...	2012	The Cysteine Rich Necrotrophic Effector SnTox1 Produced by Stagonospora nodorum Triggers Susceptibility of Wheat Lines Harboring Snn1
The heavily methylated vertebrate genomes are punctuated by stretches of poorly methylated DNA sequences that usually mark gene regulatory regions . It is known that the methylation state of these regions confers transcriptional control over their associated genes . Given its governance on the transcriptome , cellular ...	The genomes of vertebrate animals are naturally and extensively modified by methylation . The DNA methylation is essential to normal functions of cells , hence the whole animal , since it governs gene expression . Defects in the establishment and maintenance of proper methylation pattern are commonly associated with va...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "vertebrates", "animals", "blastulas", "developmental", "biology", "genome", "analysis", "sequence", "motif", "analysis", "epigenetics", "dna", "embryos", "molecular", "biology", "techniques", "dna", "methylation", "chromatin", "research", "and...	2017	Unlinking the methylome pattern from nucleotide sequence, revealed by large-scale in vivo genome engineering and methylome editing in medaka fish
The subtle effects of DNA-protein recognition are illustrated in the homeodomain fold . This is one of several small DNA binding motifs that , in spite of limited DNA binding specificity , adopts crucial , specific roles when incorporated in a transcription factor . The homeodomain is composed of a 3-helix domain and a...	All organisms require the capability to control gene expression . In eukaryotes , transcription factors play an important role in gene regulation by recognizing specific DNA control regions associated with each gene . The DNA binding domains of transcription factors belong to evolutionarily conserved families with diff...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "chemistry", "biology" ]	2013	Binding Polymorphism in the DNA Bound State of the Pdx1 Homeodomain
Most arthropod-borne viruses ( arboviruses ) are RNA viruses , which are maintained in nature by replication cycles that alternate between arthropod and vertebrate hosts . Arboviruses appear to experience lower rates of evolution than RNA viruses that replicate in a single host . This genetic stability is assumed to re...	Arthropod-borne viruses are transmitted among vertebrate hosts by insect vectors . Unusually , Rift Valley fever virus ( RVFV ) can also be transmitted by direct contacts of animals/humans with infectious tissues . What are the molecular mechanisms and evolutionary events leading to adopt one mode of transmission rathe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "veterinary", "virology", "veterinary", "science" ]	2011	Host Alternation Is Necessary to Maintain the Genome Stability of Rift Valley Fever Virus
Annual incidence rates of varicella infection in the general population in France have been rather stable since 1991 when clinical surveillance started . Rates however show a statistically significant increase over time in children aged 0–3 years , and a decline in older individuals . A significant increase in day-care...	During the last decades , an increasing circulation of varicella in the early childhood has been observed in France . A plausible explanation of this trend may rely on the progressive increase of day-care attendance in the past years , which could have anticipated the exposure of young children to the infection . We pr...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "children", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "european", "union", "education", "infectious", "disease", "epidemiology", "pathogens", "sociology", "geographical", "locations", "microbiology", "social",...	2018	Modeling the impact of changes in day-care contact patterns on the dynamics of varicella transmission in France between 1991 and 2015
While infectious agents have typical host preferences , the noninvasive enteric bacterium Vibrio cholerae is remarkable for its ability to survive in many environments , yet cause diarrheal disease ( cholera ) only in humans . One key V . cholerae virulence factor is its neuraminidase ( VcN ) , which releases host inte...	Ingestion of food or water contaminated with the bacterium Vibrio cholerae can cause fatal diarrheal disease ( cholera ) in humans , but not in other mammals exposed to the bacterium . This unusual pathogen uses a specialized enzyme V . cholerae neuraminidase ( VcN ) to cleave sugars called sialic acids and thereby rem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "small", "intestine", "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "sialic", "acids", "sphingolipids", "pathogens", "vibrio", "tropical", "diseases", "microbiology", "carbohydrates", "organic", "compounds"...	2018	Human evolutionary loss of epithelial Neu5Gc expression and species-specific susceptibility to cholera
Dynamic modification of histone proteins plays a key role in regulating gene expression . However , histones themselves can also be dynamic , which potentially affects the stability of histone modifications . To determine the molecular mechanisms of histone turnover , we developed a parallel screening method for epigen...	Packaging of eukaryotic genomes by the histone proteins influences many processes that use the DNA , such as transcription , repair , and replication . One well-known mechanism of regulation of histone function is the covalent modification of histone proteins . Replacement of modified histones by new histones has recen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "chromosome", "structure", "and", "function", "microbiology", "histone", "modification", "model", "organisms", "epigenetics", "chromatin", "chromosome", "biology", "gene", "expression", "biology", "molecular", "biology", "cell", "biology", "genet...	2011	A Barcode Screen for Epigenetic Regulators Reveals a Role for the NuB4/HAT-B Histone Acetyltransferase Complex in Histone Turnover
Cooperativity is one of the most important properties of molecular interactions in biological systems . It is the ability to influence ligand binding at one site of a macromolecule by previous ligand binding at another site of the same molecule . As a consequence , the affinity of the macromolecule for the ligand is ei...	The binding of a ligand to a protein is one of the most important steps in determining the function of these two interactive biological partners . In many cases , successive binding steps occur at multiple sites such that binding at one site influences ligand binding at other sites . This concept is called cooperative ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biophysics", "neuroscience" ]	2007	Resolving the Fast Kinetics of Cooperative Binding: Ca2+ Buffering by Calretinin
Computational biology is replete with high-dimensional ( high-D ) discrete prediction and inference problems , including sequence alignment , RNA structure prediction , phylogenetic inference , motif finding , prediction of pathways , and model selection problems in statistical genetics . Even though prediction and inf...	Sequence alignment is the cornerstone capability used by a multitude of computational biology applications , such as phylogeny reconstruction and identification of common regulatory mechanisms . Sequence alignment methods typically seek a high-scoring alignment between a pair of sequences , and assign a statistical sig...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular", "biology/bioinformatics", "mathematics/statistics", "computational", "biology/sequence", "motif", "analysis" ]	2008	Measuring Global Credibility with Application to Local Sequence Alignment
Molecular determinants and mechanisms of arthropod-borne flavivirus transmission to the vertebrate host are poorly understood . In this study , we show for the first time that a cell line from medically important arthropods , such as ticks , secretes extracellular vesicles ( EVs ) including exosomes that mediate transm...	In this study we have demonstrated that cells from the medically important vector tick , secretes exosomes that mediate transmission of tick-borne Langat ( LGTV ) viruses from arthropod to human and other vertebrate host cells . This study not only provides evidence that suggest tick-borne pathogens use arthropod-deriv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "vesicles", "viral", "transmission", "and", "infection", "molecular", "probe", "techniques", "endothelial", "cells", "rna", "extraction", "immunoblotting", "microbiology", "vertebrates", "neuroscience", "animals", ...	2018	Exosomes serve as novel modes of tick-borne flavivirus transmission from arthropod to human cells and facilitates dissemination of viral RNA and proteins to the vertebrate neuronal cells
Characterization of Human Endogenous Retrovirus ( HERV ) expression within the transcriptomic landscape using RNA-seq is complicated by uncertainty in fragment assignment because of sequence similarity . We present Telescope , a computational software tool that provides accurate estimation of transposable element expre...	Almost half of the human genome is composed of Transposable elements ( TEs ) , but their contribution to the transcriptome , their cell-type specific expression patterns , and their role in disease remains poorly understood . Recent studies have found many elements to be actively expressed and involved in key cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "engineering", "and", "technology", "astronomical", "sciences", "astronomical", "instruments", "genome", "analysis", "genetic", "elements", "optical", "equipment", "molecular", "biology", "techniques", "rna", "sequencing", "research", "and", "a...	2019	Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
Selective sweeps are at the core of adaptive evolution . We study how the shape of coalescent trees is affected by recent selective sweeps . To do so we define a coarse-grained measure of tree topology . This measure has appealing analytical properties , its distribution is derived from a uniform , and it is easy to es...	It is one of the major interests in population genetics to contrast the properties and consequences of neutral and non-neutral modes of evolution . As is well-known , positive Darwinian selection and genetic hitchhiking drastically change the profile of genetic diversity compared to neutral expectations . The present-d...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "modeling", "genetics", "population", "genetics", "biology", "computational", "biology" ]	2013	Coalescent Tree Imbalance and a Simple Test for Selective Sweeps Based on Microsatellite Variation
Mice expressing a Cre recombinase from the lysozyme M-encoding locus ( Lyz2 ) have been widely used to dissect gene function in macrophages and neutrophils . Here , we show that while naïve resident tissue macrophages from IL-4Rαflox/deltaLysMCre mice almost completely lose IL-4Rα function , a large fraction of macroph...	Chronic injury and inflammation lead to irreversible fibrosis in a range of diseases and infections . Macrophages alternatively activated by the immune system are capable of regulating inflammation and fibrosis , but our understanding of the source and function of these cells is incomplete . Mice genetically engineered...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "gastroenterology", "and", "hepatology", "biology", "and", "life", "sciences", "immunology" ]	2014	Incomplete Deletion of IL-4Rα by LysMCre Reveals Distinct Subsets of M2 Macrophages Controlling Inflammation and Fibrosis in Chronic Schistosomiasis
Human papillomaviruses ( HPV ) have genotype-specific disease associations , with high-risk alpha types causing at least 5% of all human cancers . Despite these conspicuous differences , our data show that high- and low- risk HPV types use similar approaches for genome maintenance and persistence . During the maintenan...	Human papillomavirus research has been prioritised towards understanding the progression of high-risk HPV infections to malignant cancer , rather than the regulation of the HPV productive cycle . Low-risk HPV types are often considered as a ‘less effective’ version of their high-risk counterparts . To date , they have ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "keratinocytes", "pathology", "and", "laboratory", "medicine", "pathogens", "hpv-11", "microbiology", "cell", "differentiation", "epithelial", "cells", "viruses", "developmental", "biology", "dna", "replication", "dna", "viruses", ...	2019	Roles for E1-independent replication and E6-mediated p53 degradation during low-risk and high-risk human papillomavirus genome maintenance
Lifespan is influenced by a large number of conserved proteins and gene-regulatory pathways . Here , we introduce a strategy for systematically finding such longevity factors in Saccharomyces cerevisiae and scoring the genetic interactions ( epistasis ) among these factors . Specifically , we developed an automated com...	The budding yeast Saccharomyces cerevisiae has emerged as an important model for the genetic analysis of aging , and insights gained about this process in yeast cells enhance our understanding of aging in other organisms , including humans . Even in yeast , our knowledge of the number and identity of the genes that det...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "epistasis", "aging", "developmental", "biology", "genome", "analysis", "tools", "genetic", "networks", "functional", "genomics", "organism", "development", "model", "organisms", "genetic", "screens", "heredity", "genetics", "yeast", "and", "fungal", "models", "biology"...	2014	High-Resolution Profiling of Stationary-Phase Survival Reveals Yeast Longevity Factors and Their Genetic Interactions
The mosquito midgut microbiota has been shown to influence vector competence for multiple human pathogens . The microbiota is highly variable in the field , and the sources of this variability are not well understood , which limits our ability to understand or predict its effects on pathogen transmission . In this work...	The mosquito midgut microbiota plays an important role in mosquito susceptibility to human pathogens and therefore is an important component of mosquito disease transmission . The microbiota can be highly variable , however , and the sources of this variation are not well understood . In this work , we aimed to improve...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "microbiome", "chemical", "compounds", "disaccharides", "metabolic", "processes", "microbiology", "carbohydrates", "organic", "compounds", "animals", "molecular", "biology", "techniques", "insect", ...	2017	Amino acid metabolic signaling influences Aedes aegypti midgut microbiome variability
Sexual reproduction is essential for the life cycle of most angiosperms . However , pseudovivipary is an important reproductive strategy in some grasses . In this mode of reproduction , asexual propagules are produced in place of sexual reproductive structures . However , the molecular mechanism of pseudovivipary still...	Sexual reproduction is essential for the life cycle of most flowering plants . However , pseudovivipary , in which floral organs are replaced by bulbils or plantlets , provides an asexual means for many grasses to reproduce in extreme environments . Although the molecular mechanism of pseudovivipary is still unknown , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "genetics", "and", "genomics/gene", "expression", "genetics", "and", "genomics/functional", "genomics", "developmental", "biology/plant", "growth", "and", "development", "plant", "biology/plant", "growth", "and", "development...	2010	DEP and AFO Regulate Reproductive Habit in Rice
Human menopause is an unsolved evolutionary puzzle , and relationships among the factors that produced it remain understood poorly . Classic theory , involving a one-sex ( female ) model of human demography , suggests that genes imparting deleterious effects on post-reproductive survival will accumulate . Thus , a ‘dea...	The origin and evolution of menopause is understood poorly and explanations remain contentious . Virtually ignored among explanations is the effect that mate choice can exert on an evolving population . We designed and used a computational model and computer simulation to show that male mating preference for younger fe...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "computer", "science", "theoretical", "biology", "genetics", "population", "biology", "biology", "computational", "biology", "evolutionary", "biology", "computerized", "simulations" ]	2013	Mate Choice and the Origin of Menopause
Malaria and schistosomiasis are major parasitic diseases causing morbidity and mortality in the tropics . Epidemiological surveys have revealed coinfection rates of up to 30% among children in Sub-Saharan Africa . To investigate the impact of coinfection of these two parasites on disease epidemiology and pathology , we...	Malaria and schistosomiasis are parasitic infectious diseases that cause severe morbidity and mortality in the tropics . Chronic schistosomiasis causes malnutrition and impaired intellectual development to children while malaria can cause fatal acute infections . Since coinfection of these two parasites is common in th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "helminths", "plasmodium", "yoelii", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "animals", "parasitology",...	2018	Schistosoma mansoni infection suppresses the growth of Plasmodium yoelii parasites in the liver and reduces gametocyte infectivity to mosquitoes
Bubonic plague ( a fatal , flea-transmitted disease ) remains an international public health concern . Although our understanding of the pathogenesis of bubonic plague has improved significantly over the last few decades , researchers have still not been able to define the complete set of Y . pestis genes needed for di...	In order to understand and combat infectious diseases , it is essential to characterize the full set of genes required by pathogenic bacteria to overcome the many immunological and physiological challenges encountered during infection . Here , we used a genome-scale approach to identify genes required by the bacterium ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "bacteriology", "microbial", "mutation", "genomics", "functional", "genomics", "microbial", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "genetic", "screens", "genome", "analysis", "g...	2014	New Insights into How Yersinia pestis Adapts to Its Mammalian Host during Bubonic Plague
Negative-sense RNA viruses assemble large ribonucleoprotein ( RNP ) complexes that direct replication and transcription of the viral genome . Influenza virus RNPs contain the polymerase , genomic RNA and multiple copies of nucleoprotein ( NP ) . During RNP assembly , monomeric NP oligomerizes along the length of the ge...	Replication and transcription by negative-sense RNA viruses occurs in large macromolecular complexes . These complexes contain the viral polymerase , genomic RNA , and multiple copies of nucleoprotein that bind RNA and oligomerize to coat the genome . For influenza virus , nucleoprotein ( NP ) non-specifically binds nu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phosphorylation at the Homotypic Interface Regulates Nucleoprotein Oligomerization and Assembly of the Influenza Virus Replication Machinery
S6 kinases ( S6Ks ) act to integrate nutrient and insulin signaling pathways and , as such , function as positive effectors in cell growth and organismal development . However , they also have been shown to play a key role in limiting insulin signaling and in mediating the autophagic response . To identify novel regula...	In biological systems , the execution of morphogenic programs requires coordinated integration of the essential processes of growth , proliferation , and differentiation . Signaling networks embedded within these processes include the insulin and nutrient pathways required for cell growth and the steroid hormone-regula...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/cell", "growth", "and", "division", "cell", "biology/developmental", "molecular", "mechanisms", "cell", "biology/cell", "signaling" ]	2010	The Nuclear Receptor DHR3 Modulates dS6 Kinase–Dependent Growth in Drosophila
In eukaryotic cells , surface expression of most type I transmembrane proteins requires translation and simultaneous insertion of the precursor protein into the endoplasmic reticulum ( ER ) membrane for subsequent routing to the cell surface . This co-translational translocation pathway is initiated when a hydrophobic ...	All cells are highly crowded with proteins that , once synthesized , have to reach their proper subcellular location in order to maintain the cellular homeostasis . Approximately 30% of the proteome needs to be sorted from the cytosol and inserted into , or transported through , biological membranes . For proteins sort...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "protein", "synthesis", "protein", "synthesis", "inhibitors", "proteins", "biology", "and", "life", "sciences", "transmembrane", "receptors", "cell-free", "protein", "synthesis" ]	2014	Signal Peptide-Binding Drug as a Selective Inhibitor of Co-Translational Protein Translocation
The surface HIV-1 exterior envelope glycoprotein , gp120 , binds to CD4 on the target cell surface to induce the co-receptor binding site on gp120 as the initial step in the entry process . The binding site is comprised of a highly conserved region on the gp120 core , as well as elements of the third variable region ( ...	A major goal of HIV-1 vaccine research is to design novel candidates capable of neutralizing the vast array of viruses circulating in the human population . One approach is to base the vaccine upon the HIV-1 outer surface envelope glycoproteins to generate antibodies . However , during persistent infection in humans , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/antigen", "processing", "and", "recognition", "virology/immune", "evasion" ]	2008	B Cell Recognition of the Conserved HIV-1 Co-Receptor Binding Site Is Altered by Endogenous Primate CD4
In Latin America , Bothrops snakes account for most snake bites in humans , and the recommended treatment is administration of multispecific Bothrops antivenom ( SAB – soro antibotrópico ) . However , Bothrops snakes are very diverse with regard to their venom composition , which raises the issue of which venoms should...	Snakebite envenomation is a serious health issue in Latin America , particularly in the Amazon , where antivenom administration may be delayed due to logistic constraints . Bothrops snakes are involved in most of the snakebite-related accidents in Brazil . This work reports a comparative study of the toxin composition ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[]	2013	Comparison of Phylogeny, Venom Composition and Neutralization by Antivenom in Diverse Species of Bothrops Complex
Parameters predicting the evolution of leptospirosis would be useful for clinicians , as well as to better understand severe leptospirosis , but are scarce and rarely validated . Because severe leptospirosis includes septic shock , similarities with predictors evidenced for sepsis and septic shock were studied in a ham...	Leptospirosis is a widespread bacterial infection that is transmitted by soil or water contaminated by the urine of infected animals , or directly from these animals . It has highly diverse clinical presentations , making its differential diagnosis difficult . Though most cases are minor and self-resolving , there are ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "evidence-based", "healthcare/clinical", "decision-making", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "critical", "care", "and", "emergency", "medicine/sepsis", "and", "multiple", "orga...	2010	Differential Cytokine Gene Expression According to Outcome in a Hamster Model of Leptospirosis
A female’s reproductive state influences her perception of odors and tastes along with her changed behavioral state and physiological needs . The mechanism that modulates chemosensory processing , however , remains largely elusive . Using Drosophila , we have identified a behavioral , neuronal , and genetic mechanism t...	Food choices often correlate with nutritional needs or physiological states of an animal . For instance , during pregnancy , women frequently report that their food preferences change—sometimes dramatically . In part , this change in preference is brought about by a change in the perception of smells and tastes . Resea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "decision", "making", "social", "sciences", "neuroscience", "reproductive", "physiology", "cognition", "epigenetics", "animal", "cells", "taste", "genetic", "interference", "gene", "expression", "olfactory", ...	2016	Neuropeptides Modulate Female Chemosensory Processing upon Mating in Drosophila
The term heterochromatin has been long considered synonymous with gene silencing , but it is now clear that the presence of transcribed genes embedded in pericentromeric heterochromatin is a conserved feature in the evolution of eukaryotic genomes . Several studies have addressed the epigenetic changes that enable the ...	This study concerns the evolutionary dynamics underlying the emergence of heterochromatic single-copy genes in D . melanogaster heterochromatin . By combining genome annotation analysis and high-resolution cytology , we have performed a comparative mapping of the orthologs of 53 single-copy genes of D . melanogaster he...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "animals", "invertebrate", "genomics", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "epigenetics", "molecular", "biology", "techniques", "chromatin", "drosophila", "polytene", "chromosomes", "heterochromatin", "research", "and", "...	2016	Comparative Genomic Analyses Provide New Insights into the Evolutionary Dynamics of Heterochromatin in Drosophila
Buruli Ulcer ( BU ) is one of the most neglected debilitating tropical diseases caused by Mycobacterium ulcerans , which causes considerable morbidity and disability . Building on earlier findings that community-based interventions could enhance case detection and reduce treatment dropout and defaulter rates , we estab...	The study revealed that it is feasible to train periphery health workers and community-based volunteers to implement a community-based active surveillance–response system for early buruli ulcer ( BU ) case detection , diagnosis and treatment at outpatient clinics . At the end of 12 months follow-up , there were 36084 s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "geographical", "locations", "parasitic", "diseases", "health", "care", "bacterial", "diseases", "health", "services", "administration", "and", "management", "...	2018	Implementing active community-based surveillance-response system for Buruli ulcer early case detection and management in Ghana
Prions are a group of proteins that can adopt a spectrum of metastable conformations in vivo . These alternative states change protein function and are self-replicating and transmissible , creating protein-based elements of inheritance and infectivity . Prion conformational flexibility is encoded in the amino acid comp...	Protein misfolding and assembly into ordered aggregates known as amyloid has emerged as a novel mechanism for regulation of protein function . In the case of prion proteins , the resulting amyloid is transmissible , creating protein-based elements of infectivity and inheritance . These unusual properties are linked to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "luciferase", "molecular", "probe", "techniques", "prions", "enzymes", "enzymology", "immunoblotting", "nucleotides", "chaperone", "proteins", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "artificial", "gene", ...	2016	Distinct Prion Domain Sequences Ensure Efficient Amyloid Propagation by Promoting Chaperone Binding or Processing In Vivo
During vertebrate early embryogenesis , the ventral development is directed by the ventral-to-dorsal activity gradient of the bone morphogenetic protein ( BMP ) signaling . As secreted ligands , the extracellular traffic of BMP has been extensively studied . However , it remains poorly understood that how BMP ligands a...	Bone morphogenetic proteins ( BMPs ) are extracellular proteins which belong to the transforming growth factor-β ( TGF-β ) superfamily . BMP signaling is essential for embryonic development , organogenesis , and tissue regeneration and homeostasis , and tightly linked to various diseases and tumorigenesis . However , a...	[ "Abstract", "Introduction", "Result", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "medicine", "and", "health", "sciences", "fish", "molecular", "probe", "techniques", "cell", "processes", "immunoblotting", "vertebrates", "animals", "animal", "models", "organisms", "physiological", "processes", "developmental", "biology", "osteichthyes"...	2019	Marcksb plays a key role in the secretory pathway of zebrafish Bmp2b
Infection with Leishmania parasites causes mainly cutaneous lesions at the site of the sand fly bite . Inflammatory metastatic forms have been reported with Leishmania species such as L . braziliensis , guyanensis and aethiopica . Little is known about the factors underlying such exacerbated clinical presentations . Le...	Leishmania RNA virus ( LRV ) has been detected in Leishmania ( Viannia ) braziliensis and guyanensis species , parasites causing not only cutaneous but also mucosal and disseminated leishmaniases . In a mouse model , the viral dsRNA genome within L . guyanensis parasites is recognized by host Toll-like receptor 3 ( TLR...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "protozoans", "leishmania", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "parasitology", "protozoology", "biology", "and", "life", "sciences", "microbiology", "pathogenesis", "parasitic", "protozoans...	2014	Leishmania aethiopica Field Isolates Bearing an Endosymbiontic dsRNA Virus Induce Pro-inflammatory Cytokine Response
Since divergence ∼50 Ma ago from their terrestrial ancestors , cetaceans underwent a series of adaptations such as a ∼10–20 fold increase in myoglobin ( Mb ) concentration in skeletal muscle , critical for increasing oxygen storage capacity and prolonging dive time . Whereas the O2-binding affinity of Mbs is not signif...	In this work , we identify positive selection in cetacean myoglobins and an early , significant divergence event . While O2-binding is nearly unchanged , positive selection acts to introduce and later maintain stability . Stability correlates with abundance across the species , supporting that selection for increased s...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "physics", "biochemistry", "protein", "chemistry", "biochemistry", "simulations", "proteins", "biophysic", "al", "simulations", "evolutionary", "modeling", "protein", "structure", "evolutionary", "biology", "biology", "hemoproteins", "biophysics", "computational", "biology" ]	2013	Positively Selected Sites in Cetacean Myoglobins Contribute to Protein Stability
One major consequence of economic development in South-East Asia has been a rapid expansion of rubber plantations , in which outbreaks of dengue and malaria have occurred . Here we explored the difference in risk of exposure to potential dengue , Japanese encephalitis ( JE ) , and malaria vectors between rubber workers...	Rapid economic development in South-East Asia has resulted in a high demand for rubber , leading to the felling of natural forest and the expansion of rubber plantations . Hundred-thousands of people work in these man-made forests throughout the region , with some studies showing a higher risk of vector-borne diseases ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusion" ]	[ "invertebrates", "rubber", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "elastomers", "infectious", "disease", "epidemiology", "tropical", "diseases", "parasitic", "diseases", "animals", "parasitic", "protozoans", "protozoans", "...	2017	Risk of exposure to potential vector mosquitoes for rural workers in Northern Lao PDR
The organ of Corti in the cochlea is a two-cell layered epithelium: one cell layer of mechanosensory hair cells that align into one row of inner and three rows of outer hair cells interdigitated with one cell layer of underlying supporting cells along the entire length of the cochlear spiral . These two types of epithe...	Auditory sensory hair cells and surrounding supporting cells are derived from common prosensory progenitors , which undergo rearrangements through intercalation to achieve extension and establish the mosaic structure between hair and supporting cells . Hair cells are susceptible to damage from a variety of insults and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "ears", "precursor", "cells", "neuroscience", "cell", "differentiation", "outer", "hair", "cells", "developmental", "biology", "organ", "of", "corti", "inner", "ear", "embryos", "embryology", "animal", "cells", "biological", ...	2017	Six1 is essential for differentiation and patterning of the mammalian auditory sensory epithelium
The spikes on virus surfaces bind receptors on host cells to propagate infection . High spike densities ( SDs ) can promote infection , but spikes are also targets of antibody-mediated immune responses . Thus , diverse evolutionary pressures can influence virus SDs . HIV’s SD is about two orders of magnitude lower than...	The spike protein on the virus surface mediates its entry to the host cell and a high spike density promotes infection . HIV has a spike density that is almost two orders of magnitude lower than other viruses . This unique feature of HIV has defied explanation since it was first observed . By bringing together theory a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "organismal", "evolution", "hiv", "infections", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "evolutionary", "biology", "pathogens", "immunol...	2018	The low spike density of HIV may have evolved because of the effects of T helper cell depletion on affinity maturation
Helminth infections can negatively affect the immunologic host control , which may increase the risk of progression from latent Mycobacterium tuberculosis infection to tuberculosis ( TB ) disease and alter the clinical presentation of TB . We assessed the prevalence and determined the clinical relevance of helminth co-...	Tuberculosis ( TB ) , caused by the bacterium Mycobacterium tuberculosis , and parasitic worm infections are typical diseases of poverty . They often overlap geographically , and can occur in the same individual . Parasitic worm infections contribute to the down-regulation of the essential immune response against TB , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "helminths", "pathogens", "tropical", "diseases", "microbiology", "parasitic", "diseases", "animals", "retrov...	2017	Prevalence and clinical relevance of helminth co-infections among tuberculosis patients in urban Tanzania
Human polymorphonuclear leucocytes , PMN , are highly motile cells with average 12-15 µm diameters and prominent , loboid nuclei . They are produced in the bone marrow , are essential for host defense , and are the most populous of white blood cell types . PMN also participate in acute and chronic inflammatory processe...	Human white blood cells , polymorphonuclear leucocytes ( PMN ) , were microscopically imaged and analyzed as single living cells . PMN are generally observed in a spheroid Idling state transitioning to an activated , egg-shaped , translocating state when triggered by the body's signals of infection or inflammation . Oc...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology", "computational", "biology" ]	2011	A Third Measure-Metastable State in the Dynamics of Spontaneous Shape Change in Healthy Human's White Cells
In muscle , force emerges from myosin binding with actin ( forming a cross-bridge ) . This actomyosin binding depends upon myofilament geometry , kinetics of thin-filament Ca2+ activation , and kinetics of cross-bridge cycling . Binding occurs within a compliant network of protein filaments where there is mechanical co...	Striated muscle is highly structured , and the molecular organization of muscle filaments varies within individuals ( by fiber type ) and taxonomically . The consequences of filament arrangement on muscle contraction , however , remain largely unknown . We explore how filament arrangement affects force production in mu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "spatially-explicit", "model", "thin", "filament", "regulation", "physiology", "myosin", "biophysics", "muscle", "contraction" ]	2007	Sarcomere Lattice Geometry Influences Cooperative Myosin Binding in Muscle
Two components of integrin containing attachment complexes , UNC-97/PINCH and UNC-112/MIG-2/Kindlin-2 , were recently identified as negative regulators of muscle protein degradation and as having decreased mRNA levels in response to spaceflight . Integrin complexes transmit force between the inside and outside of muscl...	Muscle is a dynamic tissue that grows in response to use and nutrition and shrinks in response to lack of use , poor nutrition , or disease . Loss of muscle mass is an important public health problem , but we understand little of the genes that regulate muscle shrinkage . We have found that , in adult worm muscle , att...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "space", "exploration", "astronomical", "sciences", "anatomy", "and", "physiology", "muscle", "animal", "models", "model", "organisms", "musculoskeletal", "system", "cell", "membrane", "cytochemistry", "cell", "adhesion", "extracellular", "matrix", "biology", "biochemistr...	2012	Calpains Mediate Integrin Attachment Complex Maintenance of Adult Muscle in Caenorhabditis elegans
An epidemiological study of Ehrlichia canis infection in dogs in Peninsular Malaysia was carried out using molecular detection techniques . A total of 500 canine blood samples were collected from veterinary clinics and dog shelters . Molecular screening by polymerase chain reaction ( PCR ) was performed using genus-spe...	Canine vector-borne diseases are a worldwide concern particularly in the tropics and sub-tropics that provide favourable climatic conditions for the vectors . Malaysia , a tropical paradise , is thus home to a wide range of vectors as well as the pathogens that they harbor . Ehrlichia canis , a ubiquitous tick-borne pa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "veterinary", "science", "biology" ]	2013	Molecular Detection of Ehrlichia canis in Dogs in Malaysia
Biological systems consist of multiple organizational levels all densely interacting with each other to ensure function and flexibility of the system . Simultaneous analysis of cross-sectional multi-omics data from large population studies is a powerful tool to comprehensively characterize the underlying molecular mech...	Biological systems operate on multiple , intertwined organizational layers that can nowadays be accesses by high-throughput measurement methods , the so-called ‘omics’ technologies . A major aim in the field of systems biology is to understand the flow of biological information between the different layers at a systems...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Human Blood Metabolome-Transcriptome Interface
Speculative statements communicating experimental findings are frequently found in scientific articles , and their purpose is to provide an impetus for further investigations into the given topic . Automated recognition of speculative statements in scientific text has gained interest in recent years as systematic analy...	Published speculations about possible molecular mechanisms underlying normal and diseased biological processes provide valuable input for the generation of new scientific hypotheses . However , a systematic gathering of all scientific speculation that exists in a given context is a non-trivial task and , if done manual...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "text", "mining", "computer", "science", "natural", "language", "processing", "biology", "computational", "biology" ]	2013	‘HypothesisFinder:’ A Strategy for the Detection of Speculative Statements in Scientific Text
The niche conservatism hypothesis states that related species diverge in niche characteristics at lower rates than expected , given their lineage divergence . Here we analyze whether niche conservatism is a common pattern among vector species ( Hemiptera: Reduviidae: Triatominae ) of Trypanosoma cruzi that inhabit Nort...	Knowledge regarding the evolutionary history of insect vectors of pathogens is essential to design precise and appropriately integrated control strategies , since species' dispersal and invasive capacity are key components to prevent human-vector interaction . Given several well-known invasive or dispersal events of Tr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "medicine", "and", "health", "sciences", "tropical", "diseases", "parasitic", "diseases", "animal", "phylogenetics", "phylogenetics", "speciation", "neglected", "tropical", "diseases", "zoology", "infectious", "diseases", "ep...	2014	Phylogeny and Niche Conservatism in North and Central American Triatomine Bugs (Hemiptera: Reduviidae: Triatominae), Vectors of Chagas' Disease
Traits that are attractive to the opposite sex are often positively correlated when scaled such that scores increase with attractiveness , and this correlation typically has a genetic component . Such traits can be genetically correlated due to genes that affect both traits ( “pleiotropy” ) and/or because assortative m...	Traits that are attractive to the opposite sex are often positively correlated when scaled such that scores increase with attractiveness , and this correlation typically has a genetic component . Such traits can be genetically correlated due to genes that affect both traits and/or because assortative mating ( people ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "population", "genetics", "biology", "human", "genetics", "evolutionary", "biology", "evolutionary", "genetics" ]	2013	The Genetic Correlation between Height and IQ: Shared Genes or Assortative Mating?
Different pathogens share similar medical settings and rely on similar virulence strategies to cause infections . We have previously applied 3-D computational modeling and bioinformatics to discover novel antigens that target more than one human pathogen . Active and passive immunization with the recombinant N-terminus...	Different pathogens share similar medical settings and rely on similar virulence strategies to cause infections . We have applied computational modeling and bioinformatics to discover novel antigens that target organisms sharing ecological niches in the intensive care units ( ICUs ) : the fungus Candida albicans , and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biofilms", "bacteriology", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "acinetobacter", "infections", "pathogens", "immunology", "microbiology", "membrane", "proteins", "bacterial", "diseases", "fungi", "...	2018	The Hyr1 protein from the fungus Candida albicans is a cross kingdom immunotherapeutic target for Acinetobacter bacterial infection
Cyclic nucleotides are universally used as secondary messengers to control cellular physiology . Among these signalling molecules , cyclic di-adenosine monophosphate ( c-di-AMP ) is a specific bacterial second messenger recognized by host cells during infections and its synthesis is assumed to be necessary for bacteria...	Nucleotide-based second messengers play central functions in bacterial physiology and host-pathogen interactions . Among these signalling nucleotides , cyclic-di-AMP ( c-di-AMP ) synthesis was originally assumed to be essential for bacterial growth . In this study , we confirmed that the only di-adenylate cyclase enzym...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "aliphatic", "amino", "acids", "gene", "regulation", "pathogens", "microbiology", "operons", "organic", "compounds", "physiological", "processes", "mutation", ...	2018	Cyclic di-AMP regulation of osmotic homeostasis is essential in Group B Streptococcus
Pathogen expulsion from the gut is an important defense strategy against infection , but little is known about how interaction between the intestinal microbiome and host immunity modulates defecation . In Drosophila melanogaster , dual oxidase ( Duox ) kills pathogenic microbes by generating the microbicidal reactive o...	The amount and pattern of defecation are often determined by the bacterial composition in the gut , and can have a significant impact on human health . It is however unknown how changes in the bacterial community affect defecation . A chemical defense system called the Duox pathway is known to kill ill-causing bacteria...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2016	TrpA1 Regulates Defecation of Food-Borne Pathogens under the Control of the Duox Pathway
Earlier studies had suggested that epigenetic mechanisms play an important role in the control of human cytomegalovirus ( HCMV ) infection . Here we show that productive HCMV infection is indeed under the control of histone H3K27 trimethylation . The histone H3K27 methyltransferase EZH2 , and its regulators JARID2 and ...	Human cytomegalovirus ( HCMV ) is a significant pathogen that belongs to the herpesvirus family . Here we show that the histone H3K27 methyltransferase EZH2 and its regulators JARID2 and NDY1/KDM2B are required for the establishment of productive infection . Mechanistically , the EZH2-NDY1/KDM2B-JARID2 axis downregulat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "microbiology", "virology" ]	2014	The Downregulation of GFI1 by the EZH2-NDY1/KDM2B-JARID2 Axis and by Human Cytomegalovirus (HCMV) Associated Factors Allows the Activation of the HCMV Major IE Promoter and the Transition to Productive Infection
Pentavalent antimonials have been the mainstay of antileishmanial therapy for decades , but increasing failure rates under antimonial treatment have challenged further use of these drugs in the Indian subcontinent . Experimental evidence has suggested that parasites which are resistant against antimonials have superior...	The protozoan flagellate Leishmania donovani causes the neglected , life-threatening disease visceral leishmaniasis . Parasites are transmitted from man to man by the bite of the sand fly Phlebotomus argentipes , the vector of the disease . Pentavalent antimonials have been the mainstay of antileishmanial therapy for d...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "mathematics", "epidemiology", "statistics", "infectious", "disease", "epidemiology", "neglected", "tropical", "diseases", "leishmaniasis", "biostatistics", "infectious", "disease", "control", ...	2012	Treatment of Visceral Leishmaniasis: Model-Based Analyses on the Spread of Antimony-Resistant L. donovani in Bihar, India
The investigation of RNA-based regulation of cellular processes is becoming an increasingly important part of biological or medical research . For the analysis of this type of data , RNA-related prediction tools are integrated into many pipelines and workflows . In order to correctly apply and tune these programs , the...	RNA molecules are central players in many cellular processes . Thus , the analysis of RNA-based regulation has provided valuable insights and is often pivotal to biological and medical research . In order to correctly select appropriate algorithms and apply available RNA structure and RNA–RNA interaction prediction sof...	[ "Abstract", "Background", "Results", "and", "discussion", "Maximum", "expected", "accuracy", "Conclusion" ]	[ "computer", "applications", "rna", "sequences", "education", "molecular", "probe", "techniques", "applied", "mathematics", "rna", "structure", "prediction", "rna", "stem-loop", "structure", "simulation", "and", "modeling", "algorithms", "mathematics", "molecular", "biolog...	2018	Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching
Protein expression and post-translational modification levels are tightly regulated in neoplastic cells to maintain cellular processes known as ‘cancer hallmarks’ . The first Pan-Cancer initiative of The Cancer Genome Atlas ( TCGA ) Research Network has aggregated protein expression profiles for 3 , 467 patient samples...	Pan-cancer proteomic datasets from The Cancer Genome Atlas provide a unique opportunity to study the functions of proteins in human cancers . Such datasets , where proteins are measured in different conditions and where correlations are informative , can enable the discovery of potentially causal protein-protein intera...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "squamous", "cell", "lung", "carcinoma", "protein", "interactions", "applied", "mathematics", "protein", "interaction", "networks", "carcinomas", "cancers", "and", "neoplasms", "simulation", "and", "modeling", "oncology", "algori...	2016	A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers
For many decades , invertebrate immunity was believed to be non-adaptive , poorly specific , relying exclusively on sometimes multiple but germ-line encoded innate receptors and effectors . But recent studies performed in different invertebrate species have shaken this paradigm by providing evidence for various types o...	Contrary to the traditional view that immunity in invertebrates is limited to innate mechanisms , recent studies have shown that these several species of protostome invertebrates express putative immune receptors that can be somatically diversified in a way resulting in an analogy with Immunoglobulins or T Cell Recepto...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "immunology/innate", "immunity", "infectious", "diseases/helminth", "infections" ]	2010	A Large Repertoire of Parasite Epitopes Matched by a Large Repertoire of Host Immune Receptors in an Invertebrate Host/Parasite Model
Paracoccidioidomycosis ( PCM ) is a life-threatening systemic disease and is a neglected public health problem in many endemic regions of Latin America . Though several diagnostic methods are available , almost all of them present with some limitations . A latex immunoassay using sensitized latex particles ( SLPs ) wit...	Paracoccidioidomycosis is one of the most prevalent systemic mycoses in Latin America , and still poses a significant threat to the health of human hosts , especially those with an impaired immune system . Early and accurate diagnosis is mandatory for the implementation of effective treatment . Currently , most of the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Immunodiagnosis of Paracoccidioidomycosis due to Paracoccidioides brasiliensis Using a Latex Test: Detection of Specific Antibody Anti-gp43 and Specific Antigen gp43
The functional role of synchronization has attracted much interest and debate: in particular , synchronization may allow distant sites in the brain to communicate and cooperate with each other , and therefore may play a role in temporal binding , in attention or in sensory-motor integration mechanisms . In this article...	Synchronization phenomena are pervasive in biology , creating collective behavior out of local interactions between neurons , cells , or animals . On the other hand , many of these systems function in the presence of large amounts of noise or disturbances , making one wonder how meaningful behavior can arise in these h...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computer", "science/systems", "and", "control", "theory", "neuroscience/theoretical", "neuroscience" ]	2010	How Synchronization Protects from Noise
Metabolomics coupled with heavy-atom isotope-labelled glucose has been used to probe the metabolic pathways active in cultured bloodstream form trypomastigotes of Trypanosoma brucei , a parasite responsible for human African trypanosomiasis . Glucose enters many branches of metabolism beyond glycolysis , which has been...	In this work we have followed the distribution of carbon derived from glucose in bloodstream form trypanosomes , the causative agent of African trypanosomiasis , revealing it to enter a diverse range of metabolites . The work involved using 13C-labelled glucose and following the fate of the labelled carbon with an LC-M...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Probing the Metabolic Network in Bloodstream-Form Trypanosoma brucei Using Untargeted Metabolomics with Stable Isotope Labelled Glucose

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