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Allosteric regulation is a key component of cellular communication , but the way in which information is passed from one site to another within a folded protein is not often clear . While backbone motions have long been considered essential for long-range information conveyance , side-chain motions have rarely been con...	Allosteric regulation occurs when the function of one part of a protein changes in response to a signal recognized by another part of the protein . Such intra-protein communication is essential for many biochemical processes , allowing the cell to adapt its behavior to a dynamic environment . Most studies of the inform...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "protein", "chemistry", "entropy", "chemical", "biology", "thermodynamics", "chemistry", "biology", "computational", "chemistry", "biophysics", "simulations", "biophysics", "theoretical", "chemistry", "physical", "chemistry" ]	2011	Long-Range Intra-Protein Communication Can Be Transmitted by Correlated Side-Chain Fluctuations Alone
Schistosomiasis is a debilitating disease that affects over 240 million people worldwide and is considered the most important neglected tropical disease following malaria . Free-swimming freshwater cercariae , one of the six morphologically distinct schistosome life stages , infect humans by directly penetrating throug...	Parasitic schistosome worms cause morbid disease in over 240 million individuals worldwide . Acute infections with these worms can lead to Katayama fever , while chronic infections can lead to portal hypertension , enlarged abdomen , and liver damage . The infective larval stage , called cercariae , are free-swimming a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "skin", "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "cellular", "stress", "responses", "swimming", "integumentary", "system", "pathology", "and", "laboratory", "medicine", "helminths", "cell", "processes", "parasitic", "diseases", "biomechanic...	2016	Hsp70 May Be a Molecular Regulator of Schistosome Host Invasion
Identifying key reservoirs for zoonoses is crucial for understanding variation in incidence . Plague re-emerged in Mahajanga , Madagascar in the 1990s but there has been no confirmed case since 1999 . Here we combine ecological and genetic data , from during and after the epidemics , with experimental infections to exa...	The reemergence of plague is related to the persistence and dynamics of its reservoirs and vectors . During the human plague outbreaks that re-occurred in Mahajanga harbor , Madagascar in the 1990s , the shrew Suncus murinus was found infected with Yersinia pestis . Combining field surveys , experimental infections and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "plagues", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "shrews", "spleen", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "animals", "mammals", "bacterial", "dise...	2017	The Asian house shrew Suncus murinus as a reservoir and source of human outbreaks of plague in Madagascar
Local weather influences the transmission of the dengue virus . Most studies analyzing the relationship between dengue and climate are based on relatively coarse aggregate measures such as mean temperature . Here , we include both mean temperature and daily fluctuations in temperature in modelling dengue transmission i...	The sensitivity of mosquito vector and dengue virus biology to diurnal temperature variability has been established , but this study is the first analyzing these relations with dengue occurrence . We show that Dhaka’s tropical hot monsoon climate and small variation in daily temperature enhance dengue transmission one ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Interaction of Mean Temperature and Daily Fluctuation Influences Dengue Incidence in Dhaka, Bangladesh
Ivermectin ( IVM ) is a widely-used anthelmintic that works by binding to and activating glutamate-gated chloride channel receptors ( GluClRs ) in nematodes . The resulting chloride flux inhibits the pharyngeal muscle cells and motor neurons of nematodes , causing death by paralysis or starvation . IVM resistance is an...	IVM is a gold standard anti-parasitic drug that is used extensively to control invertebrate parasites pest species . The drug targets the glutamate-gated chloride channel receptor ( GluClR ) found on neurons and muscle cells of these organisms , causing paralysis and death . However , IVM resistance is becoming a serio...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "single", "channel", "recording", "neurochemistry", "chemical", "compounds", "aliphatic", "amino", "acids", "social", "sciences", "species", "delimitation", "neuroscience", "organic", "compounds", "mutation", "substitution", "mutation", "membrane", "electrophysiology", "spe...	2017	Effects of glutamate and ivermectin on single glutamate-gated chloride channels of the parasitic nematode H. contortus
Reinitiation is a gene-specific translational control mechanism characterized by the ability of some short upstream uORFs to retain post-termination 40S subunits on mRNA . Its efficiency depends on surrounding cis-acting sequences , uORF elongation rates , various initiation factors , and the intercistronic distance . ...	Protein synthesis is a fundamental mechanism capturing the rejuvenation of DNA–encoded genetic information by its translation into molecular effectors—proteins . Its regulation can be used to change the protein content and thus to adapt a cell to changing environmental conditions . Translation requires mRNAs delivering...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "gene", "regulation", "gene", "function", "protein", "synthesis", "molecular", "genetics", "sequence", "analysis", "proteins", "gene", "expression", "biology", "molecular", "biology", "mutagenesis", "biochemistry", "rna", "nucleic", "acids", "prot...	2011	Translation Reinitiation Relies on the Interaction between eIF3a/TIF32 and Progressively Folded cis-Acting mRNA Elements Preceding Short uORFs
We analyze the problem of obstacle avoidance from a Bayesian decision-theoretic perspective using an experimental task in which reaches around a virtual obstacle were made toward targets on an upright monitor . Subjects received monetary rewards for touching the target and incurred losses for accidentally touching the ...	In everyday , cluttered environments , moving to reach or grasp an object can result in unintended collisions with other objects along the path of movement . Depending on what we run into ( a priceless Ming vase , a crotchety colleague ) we can suffer serious monetary or social consequences . It makes sense to choose m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "biology", "neuroscience", "genetics", "and", "genomics" ]	2012	Speeded Reaching Movements around Invisible Obstacles
RNA pseudoknots are a kind of minimal RNA tertiary structural motifs , and their three-dimensional ( 3D ) structures and stability play essential roles in a variety of biological functions . Therefore , to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions . In the wor...	RNA pseudoknotted structures and their stability can play important roles in RNA cellular functions such as transcription , splicing and translation . Due to the polyanionic nature of RNAs , metal ions such as Na+ and Mg2+ in solutions can play an essential role in RNA folding . Although several computational models ha...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "rna", "structure", "prediction", "condensed", "matter", "physics", "rna", "stability", "sequence", "motif", "analysis", "thermodynamics", "research", "and", "analysis", "methods", "sequence", "analysis", "rna", "structure", "bioinformatics", "gene", "expression", "melt...	2018	Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions
Altered metabolism is one of the hallmarks of cancers . Deregulation of ribose-5-phosphate isomerase A ( RPIA ) in the pentose phosphate pathway ( PPP ) is known to promote tumorigenesis in liver , lung , and breast tissues . Yet , the molecular mechanism of RPIA-mediated colorectal cancer ( CRC ) is unknown . Our stud...	The pentose phosphate pathway generates NADPH , pentose , and ribose-5-phosphate by RPIA for nucleotide synthesis . Deregulation of RPIA is known to promote tumorigenesis in liver , lung , and breast tissues; however , the molecular mechanism of RPIA-mediated CRC is unknown . Here , we demonstrate a role of RPIA in CRC...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "fish", "immune", "cells", "gene", "regulation", "antigen-presenting", "cells", "biological", "cultures", "cell", "processes", "cancers", "and", "neoplasms", "vertebrates", "immunology", "animals", "oncology", "animal", "models",...	2018	Identification of a noncanonical function for ribose-5-phosphate isomerase A promotes colorectal cancer formation by stabilizing and activating β-catenin via a novel C-terminal domain
Cornelia de Lange Syndrome ( CdLS ) is a multi-organ system birth defects disorder linked , in at least half of cases , to heterozygous mutations in the NIPBL gene . In animals and fungi , orthologs of NIPBL regulate cohesin , a complex of proteins that is essential for chromosome cohesion and is also implicated in DNA...	Cornelia de Lange Syndrome ( CdLS ) is a genetic disease marked by growth retardation , cognitive and neurological problems , and structural defects in many organ systems . The majority of CdLS cases are due to mutation of one copy of the Nipped B-like ( NIPBL ) gene , the product of which regulates a complex of chromo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "developmental", "biology/developmental", "molecular", "mechanisms", "molecular", "biology/chromatin", "structure", "genetics", "and", "genomics/gene", "expression" ]	2009	Multiple Organ System Defects and Transcriptional Dysregulation in the Nipbl+/− Mouse, a Model of Cornelia de Lange Syndrome
The complement system is key to innate immunity and its activation is necessary for the clearance of bacteria and apoptotic cells . However , insufficient or excessive complement activation will lead to immune-related diseases . It is so far unknown how the complement activity is up- or down- regulated and what the ass...	The complement system , which is the frontline immune defense , constitutes proteins that flow freely in the blood . It quickly detects invading microbes and alerts the host by sending signals into immune responsive cells to eliminate the hostile substances . Inadequate or excessive complement activities harm the host ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "computational", "biology/systems", "biology", "immunology/innate", "immunity" ]	2011	A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System
Pyrethroid insecticides are widely utilized in dengue control . However , the major vector , Aedes aegypti , is becoming increasingly resistant to these insecticides and this is impacting on the efficacy of control measures . The near complete transcriptome of two pyrethroid resistant populations from the Caribbean was...	Dengue is the most rapidly spreading arboviral infection of humans and each year there are 50–100 million cases of dengue fever . There is no vaccine or drug to prevent dengue infection so control of the mosquitoes that transmit this virus is the only option to reduce transmission . Removing mosquito habitats close to ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "global", "health", "genetics", "biology", "genetics", "and", "genomics", "toxicology" ]	2012	Gene Amplification, ABC Transporters and Cytochrome P450s: Unraveling the Molecular Basis of Pyrethroid Resistance in the Dengue Vector, Aedes aegypti
Unmodified or as a poly[lactide-co-glycolide] nanoparticle , tetraiodothyroacetic acid ( tetrac ) acts at the integrin αvβ3 receptor on human cancer cells to inhibit tumor cell proliferation and xenograft growth . To study in vitro the pharmacodynamics of tetrac formulations in the absence of and in conjunction with ot...	Clinical treatment protocols for specific solid cancers have favorable response rates of 20%–25% . Cancer cells frequently become resistant to treatment . Therefore , novel anti-cancer drugs and combination regimens need to be developed . Conducting enough clinical trials to evaluate combinations of anti-cancer agents ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "oncology/breast", "cancer", "oncology/oncology", "agents", "oncology/neuro-oncology" ]	2011	Pharmacodynamic Modeling of Anti-Cancer Activity of Tetraiodothyroacetic Acid in a Perfused Cell Culture System
RNA-DNA hybrids are naturally occurring obstacles that must be overcome by the DNA replication machinery . In the absence of RNase H enzymes , RNA-DNA hybrids accumulate , resulting in replication stress , DNA damage and compromised genomic integrity . We demonstrate that Mph1 , the yeast homolog of Fanconi anemia prot...	DNA damage can either occur exogenously through DNA damaging agents such as UV light and exposure to chemotherapeutics , or endogenously via metabolic , cellular processes . The RNA product of transcription , for example , can engage in the formation of RNA-DNA hybrids . Such RNA-DNA hybrids can impede replication fork...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chromosome", "structure", "and", "function", "nucleases", "molecular", "probe", "techniques", "enzymes", "dna-binding", "proteins", "enzymology", "dna-rna", "hybridization", "dna", "damage", "telomeres", "fungi", "dna", "replication", "molecular", "biology", "techniques"...	2017	The Smc5/6 complex regulates the yeast Mph1 helicase at RNA-DNA hybrid-mediated DNA damage
Metabolic homeostasis in metazoans is regulated by endocrine control of insulin/IGF signaling ( IIS ) activity . Stress and inflammatory signaling pathways—such as Jun-N-terminal Kinase ( JNK ) signaling—repress IIS , curtailing anabolic processes to promote stress tolerance and extend lifespan . While this interaction...	Metabolism of multicellular organisms has to adjust to environmental changes . Insulin signaling plays an important role in this regulation . Stress signals can repress Insulin signaling , curtailing growth to promote stress tolerance and extend lifespan . While this interaction allows managing energy resources under s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "diabetes", "and", "endocrinology/obesity", "genetics", "and", "genomics/gene", "function", "diabetes", "and", "endocrinology/type", "2", "diabetes" ]	2009	Control of Metabolic Homeostasis by Stress Signaling Is Mediated by the Lipocalin NLaz
Based on previous studies , historical records and risk factors , trachoma was suspected to be endemic in 31 health districts ( HDs ) in Guinea . To facilitate planning for the elimination of trachoma as a public health problem , national trachoma surveys were conducted between 2011 and 2016 to determine the prevalence...	Trachoma is the leading infectious cause of blindness worldwide . The World Health Organization ( WHO ) recommends that endemic countries implement the SAFE strategy ( surgery for trichiasis , antibiotic treatment , facial cleanliness and environmental improvement ) to achieve trachoma elimination by the year 2020 . Tr...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "guinea", "antimicrobials", "medicine", "and", "health", "sciences", "european", "union", "drugs", "tropical", "diseases", "geographical", "locations", "microbiology", "surgical", "and", "invasive", "medical", "procedures", "health", "care", "bacterial", "diseases", "re...	2018	Baseline trachoma prevalence in Guinea: Results of national trachoma mapping in 31 health districts
Mendelian disorders are often caused by mutations in genes that are not lethal but induce functional distortions leading to diseases . Here we study the extent of gene duplicates that might compensate genes causing monogenic diseases . We provide evidence for pervasive functional redundancy of human monogenic disease g...	Duplicated genes , as opposed to singletons , are genes that have additional copies in a genome due to evolutionary mechanisms such as whole genome duplication , homologous recombination or retrotransposition events . Duplicates can have similar functions and thus mask the phenotypic consequences when one copy is mutat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "molecular", "genetics", "biology", "computational", "biology", "evolutionary", "biology", "genetics", "of", "disease", "evolutionary", "genetics" ]	2013	Human Monogenic Disease Genes Have Frequently Functionally Redundant Paralogs
Retinal vascular caliber provides information about the structure and health of the microvascular system and is associated with cardiovascular and cerebrovascular diseases . Compared to European Americans , African Americans tend to have wider retinal arteriolar and venular caliber , even after controlling for cardiova...	Retinal vessels provide a window to microvascular systems elsewhere in the body . The diameter of retinal vessels varies between racial/ethnic groups , being generally wider in African Americans compared to European Americans . To determine whether genetic background may contribute to this observed difference , we scan...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "ophthalmology/retinal", "disorders", "genetics", "and", "genomics/complex", "traits", "evolutionary", "biology/genomics", "cardiovascular", "disorders/peripheral", "vascular", "disease", "ophthalmology", "public", "health", "and", "epidemiology/epidemiology", "cardiovascular", "...	2010	Admixture Mapping Scans Identify a Locus Affecting Retinal Vascular Caliber in Hypertensive African Americans: the Atherosclerosis Risk in Communities (ARIC) Study
The World Health Organization ( WHO ) has targeted trachoma for elimination as a public health concern by 2020 . Mathematical modelling is used for a range of infectious diseases to assess the impact of different intervention strategies on the prevalence of infection or disease . Here we evaluate the performance of fou...	Trachoma is the world’s leading infectious cause of blindness . Mathematical models are used by researchers to examine the spread of infectious diseases and understand how they can be controlled . Such models are developed based on the natural history of infection . For trachoma we identify four different model structu...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "mathematical", "models", "bacterial", "diseases", "age", "groups", "eye", "diseases", "neglected", "tropical", "dis...	2017	Improving our forecasts for trachoma elimination: What else do we need to know?
We consider the feasibility of reusing existing control data obtained in genetic association studies in order to reduce costs for new studies . We discuss controlling for the population differences between cases and controls that are implicit in studies utilizing external control data . We give theoretical calculations...	This paper discusses and provides unique insight into an important problem raised by the current state of genetic studies into disease susceptibility , namely whether we can reuse genetic data from participants genotyped as controls in one study when cases ( people with a disease of interest ) are obtained from other s...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics", "genetics", "and", "genomics/population", "genetics" ]	2010	The Potential for Enhancing the Power of Genetic Association Studies in African Americans through the Reuse of Existing Genotype Data
NK cells are enriched in the liver , constituting around a third of intrahepatic lymphocytes . We have previously demonstrated that they upregulate the death ligand TRAIL in patients with chronic hepatitis B virus infection ( CHB ) , allowing them to kill hepatocytes bearing TRAIL receptors . In this study we investiga...	Hepatitis B virus ( HBV ) infection is responsible for more than a million deaths annually as a result of the immune-mediated chronic liver damage it induces . One of the key immune players in the liver is the natural killer ( NK ) cell , which we have recently found can cause liver damage in HBV infection . Here we ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "antiviral", "responses", "infectious", "diseases/viral", "infections", "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "immunology/innate", "immunity" ]	2010	Blockade of Immunosuppressive Cytokines Restores NK Cell Antiviral Function in Chronic Hepatitis B Virus Infection
Achieving facile specific recognition is essential for intrinsically disordered proteins ( IDPs ) that are involved in cellular signaling and regulation . Consideration of the physical time scales of protein folding and diffusion-limited protein-protein encounter has suggested that the frequent requirement of protein f...	Intrinsically disordered proteins ( IDPs ) are key components of regulatory networks that dictate various aspects of cellular decision-making . They are over-represented in major disease pathways , and are considered novel albeit currently difficult drug targets . Recognition of IDPs has extended the traditional protei...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Electrostatically Accelerated Encounter and Folding for Facile Recognition of Intrinsically Disordered Proteins
Between 20 and 30 bacteriologically confirmed cases of leprosy are diagnosed each year at the French National Reference Center for mycobacteria . Patients are mainly immigrants from various endemic countries or living in French overseas territories . We aimed at expanding data regarding the geographical distribution of...	Leprosy is an old disease that is nearly eradicated from the European continent but not worldwide . The infectious agent , Mycobacterium leprae , has a highly conserved genome , and this property has been used to elucidate the route of its dissemination all over the world . At the French National Reference Center for m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	New Insights into the Geographic Distribution of Mycobacterium leprae SNP Genotypes Determined for Isolates from Leprosy Cases Diagnosed in Metropolitan France and French Territories
In a screen for RNA mutagen resistance , we isolated a high fidelity RNA dependent RNA polymerase ( RdRp ) variant of Coxsackie virus B3 ( CVB3 ) . Curiously , this variant A372V is also resistant to amiloride . We hypothesize that amiloride has a previously undescribed mutagenic activity . Indeed , amiloride compounds...	RNA viruses have extreme mutation frequencies , due in large part to the erroneous nature of the viral RNA dependent RNA polymerases ( RdRp ) that replicate their genomes . Since RdRp lack proofreading and repair mechanisms , the use of base analogs as RNA mutagens to increase lethal mutations and extinguish the virus ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology/new", "therapies,", "including", "antivirals", "and", "immunotherapy", "virology/antivirals,", "including", "modes", "of", "action", "and", "resistance", "virology", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "genetic...	2010	Fidelity Variants of RNA Dependent RNA Polymerases Uncover an Indirect, Mutagenic Activity of Amiloride Compounds
Transposable elements ( TEs ) account for a large portion of the genome in many eukaryotic species . Despite their reputation as “junk” DNA or genomic parasites deleterious for the host , TEs have complex interactions with host genes and the potential to contribute to regulatory variation in gene expression . It has be...	Transposable elements are mobile DNA elements that are a prevalent component of many eukaryotic genomes . While transposable elements can often have deleterious effects through insertions into protein-coding genes they may also contribute to regulatory variation of gene expression . There are a handful of examples in w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "plant", "genetics", "biology", "and", "life", "sciences" ]	2015	Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress
A better description of the clinical and laboratory manifestations of fatal patients with dengue hemorrhagic fever ( DHF ) is important in alerting clinicians of severe dengue and improving management . Of 309 adults with DHF , 10 fatal patients and 299 survivors ( controls ) were retrospectively analyzed . Regarding c...	Fatality rate and causes of fatality in dengue-affected patients greatly varied from one reported series to another . A better understanding of the clinical and laboratory manifestations of fatal patients with dengue hemorrhagic fever ( DHF ) is important in alerting clinicians of severe dengue and improving management...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2012	Fatal Dengue Hemorrhagic Fever in Adults: Emphasizing the Evolutionary Pre-fatal Clinical and Laboratory Manifestations
The production of antimicrobial reactive oxygen species by the nicotinamide dinucleotide phosphate ( NADPH ) oxidase complex is an important mechanism for control of invading pathogens . Herein , we show that the gastrointestinal pathogen Vibrio parahaemolyticus counteracts reactive oxygen species ( ROS ) production us...	The marine bacterium Vibrio parahaemolyticus is the world’s leading cause of food poisoning associated with the consumption of contaminated raw seafood . We recently discovered that during infection , V . parahaemolyticus invades cells from the host and uses a suite of effector proteins to convert the invaded cell into...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "viral", "transmission", "and", "infection", "chemical", "compounds", "oxides", "pathogens", "biological", "cultures", "microbiology", "caco-2", "cells", ...	2017	T3SS effector VopL inhibits the host ROS response, promoting the intracellular survival of Vibrio parahaemolyticus
Schistosomes are trematode parasites of global importance , causing infections in millions of people , livestock , and wildlife . Most studies on schistosomiasis , involve human subjects; as such , there is a paucity of longitudinal studies investigating parasite dynamics in the absence of intervention . As a consequen...	Schistosomes are a parasite of global importance , affecting over 200 million people worldwide , while also infecting livestock and wildlife . Despite decades of research on schistosomiasis in humans , little is known about what drives patterns of infection in untreated naturally occurring populations . We took advanta...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "helminths", "immunology", "vertebrates", "parasitic", "diseases", "animals", "nematode", "infections", "reptiles", "infectious", "diseases", "epidemiology", "crocodiles", "immune", "response", "eukary...	2017	Host immunity, nutrition and coinfection alter longitudinal infection patterns of schistosomes in a free ranging African buffalo population
RNA viruses exploit host cells by co-opting host factors and lipids and escaping host antiviral responses . Previous genome-wide screens with Tomato bushy stunt virus ( TBSV ) in the model host yeast have identified 18 cellular genes that are part of the actin network . In this paper , we show that the p33 viral replic...	The actin network , which is a central node in cellular pathways , is frequently targeted by various pathogens to modulate cellular responses . In this paper , the authors show that TBSV interacts with cofilin actin depolymerization factor leading to inhibition of the dynamic function of the actin network in infected c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "motility", "plant", "anatomy", "actin", "filaments", "plant", "cell", "biology", "microbiology", "membrane", "proteins", "fungi", "plant", "science", "cellular", "structures", "and", "organelles", "dynamic", "actin", "filaments", "contractile", "proteins", "a...	2016	Viral Replication Protein Inhibits Cellular Cofilin Actin Depolymerization Factor to Regulate the Actin Network and Promote Viral Replicase Assembly
In prokaryotes , clustered regularly interspaced short palindromic repeats ( CRISPRs ) and their associated ( Cas ) proteins constitute a defence system against bacteriophages and plasmids . CRISPR/Cas systems acquire short spacer sequences from foreign genetic elements and incorporate these into their CRISPR arrays , ...	Bacteria have evolved mechanisms that provide protection from continual invasion by viruses and other foreign elements . Resistance systems , known as CRISPR/Cas , were recently discovered and equip bacteria and archaea with an “adaptive immune system . ” This adaptive immunity provides a highly evolvable sequence-spec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "bacterial", "physiology", "microbial", "mutation", "microbial", "physiology", "microbial", "evolution", "microbial", "pathogens", "biology", "microbiology", "bacterial", "evolution" ]	2013	Cytotoxic Chromosomal Targeting by CRISPR/Cas Systems Can Reshape Bacterial Genomes and Expel or Remodel Pathogenicity Islands
Bardet-Biedl Syndrome ( BBS ) is a heterogeneous syndromic form of retinal degeneration . We have identified a novel transcript of a known BBS gene , BBS3 ( ARL6 ) , which includes an additional exon . This transcript , BBS3L , is evolutionally conserved and is expressed predominantly in the eye , suggesting a speciali...	Retinitis pigmentosa ( RP ) , a disorder of retinal degeneration resulting in blindness , occurs due to mutations in dozens of different genes encoding proteins with highly diverse functions . To date , there are no effective therapies to delay or arrest retinal degeneration . RP places a large burden on affected famil...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "ophthalmology/retinal", "disorders", "developmental", "biology/morphogenesis", "and", "cell", "biology", "genetics", "and", "genomics/gene", "expression", "cell", "biology", "molecular", "biology/rna", "splicing", "genetics", "and", "genomics/dise...	2010	Identification and Functional Analysis of the Vision-Specific BBS3 (ARL6) Long Isoform
The segmentation of the vertebrate body is laid down during early embryogenesis . The formation of signaling gradients , the periodic expression of genes of the Notch- , Fgf- and Wnt-pathways and their interplay in the unsegmented presomitic mesoderm ( PSM ) precedes the rhythmic budding of nascent somites at its anter...	Somitogenesis is a process in embryonic development establishing the segmentation of the vertebrate body by the periodic separation of small balls of epithelialized cells called somites from a growing mesenchymal tissue , the presomitic mesoderm ( PSM ) . The basic mechanisms are often discussed in terms of the clock-a...	[ "Abstract", "Introduction", "Model", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "developmental", "biology", "embryology", "biology", "computational", "biology", "signaling", "networks", "pattern", "formation" ]	2012	From Dynamic Expression Patterns to Boundary Formation in the Presomitic Mesoderm
Multiple Sclerosis ( MS ) is an autoimmune disease associated with abnormal expression of a subset of cytokines , resulting in inappropriate T-lymphocyte activation and uncontrolled immune response . A key issue in the field is the need to understand why these cytokines are transcriptionally activated in the patients ....	In patients suffering from Multiple Sclerosis ( MS ) , T lymphocytes express abnormally high levels of a subset of cytokines . The same cells also transcribe a series of vestigial retroviral sequences normally silenced by chromatin factors . In this study , we have searched for regulatory mechanisms shared between the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Citrullination of Histone H3 Interferes with HP1-Mediated Transcriptional Repression
Computational models of classical conditioning have made significant contributions to the theoretic understanding of associative learning , yet they still struggle when the temporal aspects of conditioning are taken into account . Interval timing models have contributed a rich variety of time representations and provid...	How does the time of events affect the way we learn about associations between these events ? Computational models have made great contributions to our understanding of associative learning , but they usually do not perform very well when time is taken into account . Models of timing have reached high levels of accurac...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "learning", "classical", "conditioning", "conditioned", "response", "social", "sciences", "neuroscience", "learning", "and", "memory", "simulation", "and", "modeling", "cognitive", "psychology", "cognition", "memory", "research", "and", "analysis", "methods", "learning", ...	2017	A Rescorla-Wagner drift-diffusion model of conditioning and timing
Sporotrichosis is a polymorphic chronic infection of humans and animals classically acquired after traumatic inoculation with soil and plant material contaminated with Sporothrix spp . propagules . An alternative and successful route of transmission is bites and scratches from diseased cats , through which Sporothrix y...	Sporotrichosis is polymorphic infection that is acquired after traumatic implantation of Sporothrix propagules into host tissues . In Brazil , large epizooties occur in domestic cats and consequently massive zoonotic transmission has been observed since the 2000s without signs of decreasing over time . In this study , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "humoral", "immunity", "body", "weight", "medicine", "and", "health", "sciences", "yeast", "infections", "pathology", "and", "laboratory", "medicine", "weight", "loss", "molecular", "probe", "techniques", "pathogens", "immunology", "microbiology", "immunoblotting", "ani...	2017	Exploring virulence and immunogenicity in the emerging pathogen Sporothrix brasiliensis
Multi-drug tolerance is a key phenotypic property that complicates the sterilization of mammals infected with Mycobacterium tuberculosis . Previous studies have established that iniBAC , an operon that confers multi-drug tolerance to M . bovis BCG through an associated pump-like activity , is induced by the antibiotics...	Understanding the cellular processes stimulated when Mycobacterium tuberculosis is treated with antibiotics may provide clues as to why months of therapy and use of several drugs simultaneously are required to prevent antibiotic resistance . Antibiotic treatment “turns on” or induces certain M . tuberculosis genes . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "in", "vitro", "microbiology", "molecular", "biology", "genetics", "and", "genomics", "eubacteria" ]	2007	Transcriptional Regulation of Multi-Drug Tolerance and Antibiotic-Induced Responses by the Histone-Like Protein Lsr2 in M. tuberculosis
Positive-strand RNA viruses are the largest genetic class of viruses and include many serious human pathogens . All positive-strand RNA viruses replicate their genomes in association with intracellular membrane rearrangements such as single- or double-membrane vesicles . However , the exact sites of RNA synthesis and c...	Whereas cells store and replicate their genomes as DNA , most viruses have RNA genomes that replicate by using virus-specific pathways in the host cell . The largest class of RNA viruses , the positive-strand RNA viruses , replicate their genomes on intracellular membranes . However , little is understood about how and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "viruses", "virology" ]	2007	Three-Dimensional Analysis of a Viral RNA Replication Complex Reveals a Virus-Induced Mini-Organelle
Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish–borne gastroenteritis and traveler's diarrhea . The complete genome sequence of L . hongkongensis HLHK9 , recovered from an immunocompetent patient with severe gastroenteritis , consists of ...	Laribacter hongkongensis is a recently discovered bacterium associated with gastroenteritis and traveler's diarrhea . Freshwater fish is the reservoir of L . hongkongensis . In order to achieve a rapid understanding on the mechanisms by which the bacterium adapts to different habitats and its potential virulence factor...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genome", "projects", "microbiology" ]	2009	The Complete Genome and Proteome of Laribacter hongkongensis Reveal Potential Mechanisms for Adaptations to Different Temperatures and Habitats
Patterns of social mixing are key determinants of epidemic spread . Here we present the results of an internet-based social contact survey completed by a cohort of participants over 9 , 000 times between July 2009 and March 2010 , during the 2009 H1N1v influenza epidemic . We quantify the changes in social contact patt...	Changes in patterns of social mixing can result in changes in epidemic behaviour; this was observed during the 2009 influenza pandemic , in which the epidemic declined during school holidays and grew during term time . Until now , little information has been available to quantify how people's mixing patterns change ove...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "computer", "science", "public", "health", "and", "epidemiology", "mathematics", "epidemiology", "applied", "mathematics", "biology", "computational", "biology", "population", "biology", "computerized", "simulations", "viral", "diseases...	2012	Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza
Olfactory neuropiles across different phyla organize into glomerular structures where afferents from a single olfactory receptor class synapse with uniglomerular projecting interneurons . In adult Drosophila , olfactory projection interneurons , partially instructed by the larval olfactory system laid down during embry...	The mechanisms underlying the patterning of connectivity in the insect olfactory system are radically different from those found in vertebrates , but to date most studies in insects have focused on the development of the adult olfactory network . Here , for the first time , we report how larval olfactory circuitry is f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "biology", "neuroscience" ]	2012	Embryonic Origin of Olfactory Circuitry in Drosophila: Contact and Activity-Mediated Interactions Pattern Connectivity in the Antennal Lobe
In all sexual organisms , adaptations exist that secure the safe reassortment of homologous alleles and prevent the intrusion of potentially hazardous alien DNA . Some bacteria engage in a simple form of sex known as transformation . In the human pathogen Neisseria meningitidis and in related bacterial species , transf...	Through computational and biological methods , this work analyzes the function and evolution of short DNA sequences called DNA uptake sequences ( DUS ) that regulate genetic transformation of bacteria in the family Neisseriaceae . Previous studies show that DUS affects transformation favourably . Here , for the first t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "organismal", "evolution", "genome", "evolution", "population", "genetics", "microbiology", "gene", "function", "prokaryotic", "models", "model", "organisms", "microbial", "evolution", "divergent", "evolution", "bacterial", "pathogens", "sequence", "analysis...	2013	Dialects of the DNA Uptake Sequence in Neisseriaceae
The over-replicating wMelPop strain of the endosymbiont Wolbachia pipientis has recently been shown to be capable of inducing immune upregulation and inhibition of pathogen transmission in Aedes aegypti mosquitoes . In order to examine whether comparable effects would be seen in the malaria vector Anopheles gambiae , t...	Malaria is one of the world's most devastating diseases , particularly in Africa , and new control strategies are desperately needed . Here we show that the presence of Wolbachia bacteria inhibits the development of a malaria parasite in the most important Anopheles mosquito species of Africa . In addition we show that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system" ]	2010	Wolbachia Stimulates Immune Gene Expression and Inhibits Plasmodium Development in Anopheles gambiae
Is visual cortex made up of general-purpose information processing machinery , or does it consist of a collection of specialized modules ? If prior knowledge , acquired from learning a set of objects is only transferable to new objects that share properties with the old , then the recognition system’s optimal organizat...	Domain-specific regions , like the fusiform face area , are a prominent feature of ventral visual cortex organization . Despite decades of interest from a large number of investigators employing diverse methods , there has been surprisingly little theoretical work on “why” the ventral stream may adopt this modular orga...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Invariance Hypothesis Implies Domain-Specific Regions in Visual Cortex
A literature survey and analysis was conducted to describe the epidemiology of dengue disease in Brazil reported between 2000 and 2010 . The protocol was registered on PROSPERO ( CRD42011001826: http://www . crd . york . ac . uk/prospero/display_record . asp ? ID=CRD42011001826 ) . Between 31 July and 4 August 2011 , t...	Dengue disease is the most prevalent arthropod-borne viral disease in humans and is a global and national public health concern in Brazil . We conducted this review to consolidate and describe the existing evidence on the epidemiology of dengue disease in Brazil , between 2000 and 2011 , to gauge the recent national an...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[]	2013	Epidemiological Trends of Dengue Disease in Brazil (2000–2010): A Systematic Literature Search and Analysis
The ability to find and consume nutrient-rich diets for successful reproduction and survival is fundamental to animal life . Among the nutrients important for all animals are polyamines , a class of pungent smelling compounds required in numerous cellular and organismic processes . Polyamine deficiency or excess has de...	Animals , including humans , evaluate food by its smell and taste . Odors and tastes not only signal the presence of food , they also reveal details about the type and amount of nutrients contained in it . A preference for certain foods frequently reflects the specific metabolic needs of an animal . Among the important...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "smell", "invertebrates", "medicine", "and", "health", "sciences", "legs", "social", "sciences", "limbs", "(anatomy)", "neuroscience", "animals", "reproductive", "physiology", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "drosophila", "research"...	2016	Ionotropic Chemosensory Receptors Mediate the Taste and Smell of Polyamines
One outcome of interspecific hybridization and subsequent effects of evolutionary forces is introgression , which is the integration of genetic material from one species into the genome of an individual in another species . The evolution of several groups of eukaryotic species has involved hybridization , and cases of ...	Hybridization is the mating between individuals from two different species . While hybridization introduces genetic material into a host genome , this genetic material may be transient and is purged from the population within a few generations after hybridization . However , in other cases , the introduced genetic mate...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion", "Conclusions" ]	[ "genetics", "biology", "and", "life", "sciences", "genomics", "evolutionary", "biology", "computational", "biology" ]	2014	An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes
Although the SLX4 complex , which includes structure-specific nucleases such as XPF , MUS81 , and SLX1 , plays important roles in the repair of several kinds of DNA damage , the function of SLX1 in the germline remains unknown . Here we characterized the endonuclease activities of the Caenorhabditis elegans SLX-1-HIM-1...	Crossover formation between homologous chromosomes is important for generating genetic diversity in subsequent generations , as well as for promoting accurate chromosome segregation during meiosis , which is a specialized cell division program that results in the formation of haploid gametes ( sperm and eggs ) from dip...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	SLX-1 Is Required for Maintaining Genomic Integrity and Promoting Meiotic Noncrossovers in the Caenorhabditis elegans Germline
Cardiovascular disease ( CVD ) is the leading cause of death worldwide . Recent genome-wide association ( GWA ) studies have pinpointed many loci associated with CVD risk factors in adults . It is unclear , however , if these loci predict trait levels at all ages , if they are associated with how a trait develops over ...	We have studied the association between genetic factors on a whole genome level and cardiovascular disease ( CVD ) risk factors in a population of individuals studied from childhood through adulthood . The longitudinal study design has enabled the investigation of genetic variation influencing trait values over time . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "cardiovascular", "disorders" ]	2010	Longitudinal Genome-Wide Association of Cardiovascular Disease Risk Factors in the Bogalusa Heart Study
Mechanistic mathematical modeling of biochemical reaction networks using ordinary differential equation ( ODE ) models has improved our understanding of small- and medium-scale biological processes . While the same should in principle hold for large- and genome-scale processes , the computational methods for the analys...	In this manuscript , we introduce a scalable method for parameter estimation for genome-scale biochemical reaction networks . Mechanistic models for genome-scale biochemical reaction networks describe the behavior of thousands of chemical species using thousands of parameters . Standard methods for parameter estimation...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "applied", "mathematics", "simulation", "and", "modeling", "algorithms", "optimization", "genomic", "databases", "mathematics", "genome", "analysis", "research", "and", "analysis", "methods", "genome", "complexity", "biological", "databases", "differential", "equations", ...	2017	Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks
Chromatin insulators are genetic elements implicated in the organization of chromatin and the regulation of transcription . In Drosophila , different insulator types were characterized by their locus-specific composition of insulator proteins and co-factors . Insulators mediate specific long-range DNA contacts required...	Chromatin insulators mediate specific long-range DNA interactions required for the three dimensional organization of the interphase nucleus and for transcription regulation , but the mechanisms underlying the formation of these interactions is currently unknown . In this manuscript , we investigate the molecular associ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "biochemistry", "genomics", "cell", "biology", "nucleic", "acids", "chromosome", "biology", "genome", "analysis", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "epigenetics", "computational", "biology", ...	2014	Chromatin Insulator Factors Involved in Long-Range DNA Interactions and Their Role in the Folding of the Drosophila Genome
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection . We introduce an inference method based on the joint frequency spectrum of genetic variants within and between populations . For candidate models we numerically ...	The demographic history of our species is reflected in patterns of genetic variation within and among populations . We developed an efficient method for calculating the expected distribution of genetic variation , given a demographic model including such events as population size changes , population splits and joins ,...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/genomics", "genetics", "and", "genomics/population", "genetics" ]	2009	Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data
To characterize the repair pathways of chromosome double-strand breaks ( DSBs ) , one approach involves monitoring the repair of site-specific DSBs generated by rare-cutting endonucleases , such as I-SceI . Using this method , we first describe the roles of Ercc1 , Msh2 , Nbs1 , Xrcc4 , and Brca1 in a set of distinct r...	A deleterious lesion in DNA is a break of both strands , or a chromosome double-strand break ( DSB ) . DSBs can arise during normal cellular metabolism , but are also a consequence of many forms of cancer therapy . If DSBs are not repaired prior to cell division , entire segments of a chromosome can be lost . Several p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/dna", "repair", "molecular", "biology/recombination", "genetics", "and", "genomics/chromosome", "biology" ]	2009	Limiting the Persistence of a Chromosome Break Diminishes Its Mutagenic Potential
Ellis-van Creveld ( EvC ) syndrome is a skeletal dysplasia , characterized by short limbs , postaxial polydactyly , and dental abnormalities . EvC syndrome is also categorized as a ciliopathy because of ciliary localization of proteins encoded by the two causative genes , EVC and EVC2 ( aka LIMBIN ) . While recent stud...	Ellis-van Creveld ( EvC ) syndrome is a congenital skeleton disorder characterized by short limbs . Recent studies indicated that EVC and EVC2 , the proteins encoded by two causative genes of EvC syndrome , play important function in transducing Hedgehog signaling , a signaling pathway critical for embryonic developmen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "growth", "plate", "tibia", "medicine", "and", "health", "sciences", "chondrocytes", "dwarfism", "achondroplasia", "developmental", "biology", "bone", "connective", "tissue", "cells", "skeleton", "cartilage", "morphogenesis", "cellular", "structures", "and", "organelles",...	2016	Elevated Fibroblast Growth Factor Signaling Is Critical for the Pathogenesis of the Dwarfism in Evc2/Limbin Mutant Mice
Drug-drug interactions ( DDIs ) are a common cause of adverse drug events . In this paper , we combined a literature discovery approach with analysis of a large electronic medical record database method to predict and evaluate novel DDIs . We predicted an initial set of 13197 potential DDIs based on substrates and inhi...	Drug-drug interactions are a common cause of adverse drug events . In this paper , we developed an automated search algorithm which can predict new drug interactions based on published literature . Using a large electronic medical record database , we then analyzed the correlation between concurrent use of these potent...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "clinical", "pharmacology", "pharmacoepidemiology", "drugs", "and", "devices", "statistics", "text", "mining", "drug", "information", "mathematics", "pharmacology", "biostatistics", "information", "technology", "drug", "metabolism", "adverse", "reactions", "phar...	2012	Literature Based Drug Interaction Prediction with Clinical Assessment Using Electronic Medical Records: Novel Myopathy Associated Drug Interactions
The ILEP Nerve Function Impairment in Reaction ( INFIR ) is a cohort study designed to identify predictors of reactions and nerve function impairment in leprosy . The aim was to study correlations between clinical and histological diagnosis of reactions . Three hundred and three newly diagnosed patients with World Heal...	Leprosy affects skin and peripheral nerves . Although we have antibiotics to treat the mycobacterial infection , the accompanying inflammation is a major part of the disease process . This can worsen after starting antibacterial treatment with episodes of immune mediated inflammation , so called reactions . These are a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "bacterial", "diseases", "infectious", "diseases", "leprosy" ]	2012	Comparing the Clinical and Histological Diagnosis of Leprosy and Leprosy Reactions in the INFIR Cohort of Indian Patients with Multibacillary Leprosy
The Mi-2/nucleosome remodeling and histone deacetylase ( NuRD ) complex is a multiprotein machine proposed to regulate chromatin structure by nucleosome remodeling and histone deacetylation activities . Recent reports describing localization of NuRD provide new insights that question previous models on NuRD action , bu...	Chromatin structure is tightly regulated by multiple mechanisms; its dysregulation is associated with developmental abnormalities and disease . The Mi-2/nucleosome remodeling and histone deacetylase ( NuRD ) complex is proposed to regulate chromatin structure by changing the location and/or the chemical properties of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	MBD3 Localizes at Promoters, Gene Bodies and Enhancers of Active Genes
Insecticide-based methods represent the most effective means of blocking the transmission of vector borne diseases . However , insecticide resistance poses a serious threat and there is a need for tools , such as diagnostic tests for resistance detection , that will improve the sustainability of control interventions ....	Aedes mosquitoes transmit many human viral pathogens including dengue , yellow fever and chikungunya . Most of these pathogens have no specific treatment or vaccine and hence their control is reliant on controlling the mosquito vectors , which usually involves the use of insecticides . In order to prevent the alarming ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/viral", "infections", "ecology/population", "ecology", "biochemistry/experimental", "biophysical", "methods" ]	2010	A Simple Colorimetric Assay for Specific Detection of Glutathione-S Transferase Activity Associated with DDT Resistance in Mosquitoes
The family Arenaviridae comprises three genera , Mammarenavirus , Reptarenavirus and the most recently added Hartmanivirus . Arenaviruses have a bisegmented genome with ambisense coding strategy . For mammarenaviruses and reptarenaviruses the L segment encodes the Z protein ( ZP ) and the RNA-dependent RNA polymerase ,...	From the 1930s to 2015 arenaviruses were known as mainly rodent-borne viruses , which occasionally infect humans , causing a severe disease . After isolation of novel arenaviruses from snakes , the family Arenaviridae now comprises three genera , Mammarenavirus , Reptarenavirus , and Hartmanivirus . Here we characteriz...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "blood", "serum", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "biological", "cultures", "microbiology", "vertebrates", "animals", "viruses...	2018	Characterization of Haartman Institute snake virus-1 (HISV-1) and HISV-like viruses—The representatives of genus Hartmanivirus, family Arenaviridae
Gene expression data has been used in lieu of phenotype in both classical and quantitative genetic settings . These two disciplines have separate approaches to measuring and interpreting epistasis , which is the interaction between alleles at different loci . We propose a framework for estimating and interpreting epist...	Epistasis has long had two slightly different meanings depending on the context in which it is discussed . The classical definition describes an allele at one locus completely masking the effect of an allele at a second locus . Such relationships can be interpreted as hierarchical , and they can be combined to infer ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "computational", "biology/systems", "biology", "genetics", "and", "genomics/gene", "expression" ]	2008	From Classical Genetics to Quantitative Genetics to Systems Biology: Modeling Epistasis
Dendrites of pyramidal cells exhibit complex morphologies and contain a variety of ionic conductances , which generate non-trivial integrative properties . Basal and proximal apical dendrites have been shown to function as independent computational subunits within a two-layer feedforward processing scheme . The outputs...	Pyramidal neurons are the principal cell type in the cerebral cortex . Revealing how these cells operate is key to understanding the dynamics and computations of cortical circuits . However , it is still a matter of debate how pyramidal neurons transform their synaptic inputs into spike outputs . Recent studies have pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "control", "theory", "action", "potentials", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "nervous", "system", "depolarization", "membrane", "potential", "electrophysiology", "neuroscience", "control", "engineering", "systems", "science", "...	2019	Tuft dendrites of pyramidal neurons operate as feedback-modulated functional subunits
Mutations accumulate during all stages of growth , but only germ line mutations contribute to evolution . While meiosis contributes to evolution by reassortment of parental alleles , we show here that the process itself is inherently mutagenic . We have previously shown that the DNA synthesis associated with repair of ...	Meiosis , the cellular division that gives rise to germ cells , contributes to evolution by reassortment of parental alleles . This process involves recombination initiated by Spo11-induced double-strand breaks early in meiosis . The result is that germ cells from a single meiosis are different from either parent . Her...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2015	Elevated Mutation Rate during Meiosis in Saccharomyces cerevisiae
A major goal in translational cancer research is to identify biological signatures driving cancer progression and metastasis . A common technique applied in genomics research is to cluster patients using gene expression data from a candidate prognostic gene set , and if the resulting clusters show statistically signifi...	A major goal in biomedical research is to identify sets of genes ( or “biological signatures” ) associated with patient survival , as these genes could be targeted to aid in diagnosing and treating disease . A major challenge in using prognostic associations to identify biologically informative signatures is that in so...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "medicine", "breast", "tumors", "mathematics", "gynecological", "tumors", "statistics", "biostatistics", "cancers", "and", "neoplasms", "statistical", "methods" ]	2013	Significance Analysis of Prognostic Signatures
Drugs currently available for leishmaniasis treatment often show parasite resistance , highly toxic side effects and prohibitive costs commonly incompatible with patients from the tropical endemic countries . In this sense , there is an urgent need for new drugs as a treatment solution for this neglected disease . Here...	Every year , more than 2 million people worldwide suffer from leishmaniasis , a neglected tropical disease present in 88 countries . The disease is caused by the single-celled protozoan parasite species of the genus Leishmania , which is transmitted to humans by the bite of the sandfly . The disease manifests itself in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Antileishmanial High-Throughput Drug Screening Reveals Drug Candidates with New Scaffolds
Integrins have emerged as key sensory molecules that translate chemical and physical cues from the extracellular matrix ( ECM ) into biochemical signals that regulate cell behavior . Integrins function by clustering into adhesion plaques , but the molecular mechanisms that drive integrin clustering in response to inter...	Critical cell decisions , including whether to live , proliferate , or assemble into tissue structures , are directed by cues from the extracellular matrix , the external protein scaffold that surrounds cells . Integrin receptors on the cell surface bind to the extracellular matrix and cluster into complexes that trans...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "cell", "biology/cell", "signaling", "biophysics/theory", "and", "simulation", "cell", "biology/extra-cellular", "matrix", "computational", "biology", "cell", "biology/cell", "adhesion" ]	2009	Integrin Clustering Is Driven by Mechanical Resistance from the Glycocalyx and the Substrate
Specification of the dorsal-ventral axis in the highly regulative sea urchin embryo critically relies on the zygotic expression of nodal , but whether maternal factors provide the initial spatial cue to orient this axis is not known . Although redox gradients have been proposed to entrain the dorsal-ventral axis by act...	A key event during development of bilaterians is specification of the anterior-posterior and dorsal-ventral axes of the embryo . In some species , such as the fly Drosophila , this process relies on the activity of maternal determinants localized into the egg during oogenesis . However , in other animals , such as mamm...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Maternal Maverick/GDF15-like TGF-β Ligand Panda Directs Dorsal-Ventral Axis Formation by Restricting Nodal Expression in the Sea Urchin Embryo
Changes in the locations and boundaries of heterochromatin are critical during development , and de novo assembly of silent chromatin in budding yeast is a well-studied model for how new sites of heterochromatin assemble . De novo assembly cannot occur in the G1 phase of the cell cycle and one to two divisions are need...	Heterochromatin , characterized by the repression of transcription , is a specialized chromatin structure that plays both structural and functional roles on chromosomes . Heterochromatic domains are dynamic , switching between active and inactive states , and this property is used by cells during developmental switches...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Competition between Heterochromatic Loci Allows the Abundance of the Silencing Protein, Sir4, to Regulate de novo Assembly of Heterochromatin
Hospital-acquired pneumonia is associated with high rates of morbidity and mortality , and dissemination to the bloodstream is a recognized risk factor for particularly poor outcomes . Yet the mechanism by which bacteria in the lungs gain access to the bloodstream remains poorly understood . In this study , we used a m...	Dissemination to the bloodstream is a poor prognostic sign in patients with hospital-acquired pneumonia , yet the mechanism by which this occurs is poorly understood . To begin to address this issue , we have used a mouse model of P . aeruginosa pneumonia to study the mechanism by which the type-III-secreted effector p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Role of ExoS in Dissemination of Pseudomonas aeruginosa during Pneumonia
Toxoplasma gondii is an obligate intracellular parasite for which the discharge of apical organelles named rhoptries is a key event in host cell invasion . Among rhoptry proteins , ROP2 , which is the prototype of a large protein family , is translocated in the parasitophorous vacuole membrane during invasion . The ROP...	Apicomplexa are unicellular eukaryotes that cause a number of diseases , including malaria . Most of them are obligate intracellular parasites , developing in a parasitophorous vacuole ( PV ) within their host cell . PV formation during invasion is associated with the exocytosis of parasite secretory organelles named r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "eukaryotes", "cell", "biology", "microbiology" ]	2007	ROP18 Is a Rhoptry Kinase Controlling the Intracellular Proliferation of Toxoplasma gondii
Environmental and anthropogenic changes are expected to promote emergence and spread of pathogens worldwide . Since 2013 , human urogenital schistosomiasis is established in Corsica island ( France ) . Schistosomiasis is a parasitic disease affecting both humans and animals . The parasite involved in the Corsican outbr...	There is an increasing interest on the effect of global changes on the transmission of infectious diseases . Both environmental and anthropogenic changes are expected to promote outbreaks and spread of pathogens . In particular , tropical infectious diseases are expected to move towards more temperate latitudes . Until...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "livestock", "medicine", "and", "health", "sciences", "ruminants", "helminths", "vertebrates", "parasitic", "diseases", "animals", "mammals", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "research", "and"...	2019	Epidemiological surveillance of schistosomiasis outbreak in Corsica (France): Are animal reservoir hosts implicated in local transmission?
Oscillations are omnipresent in neural population signals , like multi-unit recordings , EEG/MEG , and the local field potential . They have been linked to the population firing rate of neurons , with individual neurons firing in a close-to-irregular fashion at low rates . Using a combination of mean-field and linear r...	Recordings of brain activity show multiple coexisting oscillations . The generation of these oscillations has so far only been investigated in generic one- and two-population networks , neglecting their embedment into larger systems . We introduce a method that determines the mechanisms and sub-circuits generating osci...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "engineering", "and", "technology", "electrical", "circuits", "population", "dynamics", "membrane", "potential", "electrophysiology", "neuroscience", "mathematics", "algebra", "population...	2016	Identifying Anatomical Origins of Coexisting Oscillations in the Cortical Microcircuit
Snake envenoming is a significant public health problem in underdeveloped and developing countries . In sub-Saharan Africa , it is estimated that 90 , 000–400 , 000 envenomations occur each year , resulting in 3 , 500–32 , 000 deaths . Envenomings are caused by snakes from the Viperidae ( Bitis spp . and Echis spp . ) ...	Snake envenoming has long been a serious public health problem in underdeveloped and developing countries . In sub-Saharan Africa , the number of bites can be as high as 400 , 000 and result in up to 32 , 000 deaths . As accidents involving snakes are most common among young men in rural areas , complications and amput...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	Development of Equine IgG Antivenoms against Major Snake Groups in Mozambique
Hierarchical processing is pervasive in the brain , but its computational significance for learning under uncertainty is disputed . On the one hand , hierarchical models provide an optimal framework and are becoming increasingly popular to study cognition . On the other hand , non-hierarchical ( flat ) models remain in...	Learning and predicting in every-day life is made difficult by the fact that our world is both uncertain ( e . g . will it rain tonight ? ) and changing ( e . g . climate change shakes up weather ) . When a change occurs , what has been learned must be revised: learning should therefore be flexible . One possibility th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[]	2019	Confidence resets reveal hierarchical adaptive learning in humans
High throughput measurement of gene expression at single-cell resolution , combined with systematic perturbation of environmental or cellular variables , provides information that can be used to generate novel insight into the properties of gene regulatory networks by linking cellular responses to external parameters ....	Decades ago , Waddington , and later Kauffman , likened the dynamics of a differentiating cell to a marble rolling downhill on bumpy terrain—the epigenetic landscape . In this metaphor , the valleys of the landscape represent the paths that cells can follow towards a stable cell type , and the fate of the cell is deter...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/bioinformatics", "computational", "biology/systems", "biology" ]	2010	Estimating the Stochastic Bifurcation Structure of Cellular Networks
Annual mass treatment with ivermectin and albendazole is used to treat lymphatic filariasis in many African countries , including Tanzania . In areas where both diseases occur , it is unclear whether HIV co-infection reduces treatment success . In a general population study in Southwest Tanzania , individuals were test...	Parasite infections and HIV show large geographical overlap in sub-Saharan Africa and could hence potentially interact in co-infected individuals . In a general-population study conducted in Southwest Tanzania , we found high prevalence of both , lymphatic filariasis and HIV , with 42 . 5% of the adult population infec...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "hiv", "infections", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "geographical", "locations", "parasitic", "diseases", "animals", "retroviruses", "viruses", "i...	2016	Prevalence of Lymphatic Filariasis and Treatment Effectiveness of Albendazole/ Ivermectin in Individuals with HIV Co-infection in Southwest-Tanzania
Eukaryotic positive-strand RNA [ ( + ) RNA] viruses are intracellular obligate parasites replicate using the membrane-bound replicase complexes that contain multiple viral and host components . To replicate , ( + ) RNA viruses exploit host resources and modify host metabolism and membrane organization . Phospholipase D...	All characterized eukaryotic positive-strand RNA [ ( + ) RNA] viruses replicate their genomes using the viral replication complexes ( VRCs ) , which contain multiple viral and host components , on intracellular membranes . Phospholipids are major constituents of cellular membranes; however , the function ( s ) of phosp...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Phosphatidic Acid Produced by Phospholipase D Promotes RNA Replication of a Plant RNA Virus
During early meiotic prophase , homologous chromosomes are connected along their entire lengths by a proteinaceous tripartite structure known as the synaptonemal complex ( SC ) . Although the components that comprise the SC are predominantly studied in this canonical ribbon-like structure , they can also polymerize int...	Mistakes that occur during meiotic chromosome segregation can lead to fetal death or various disorders in offspring , hence proper chromosome segregation is crucial . To ensure optimal execution of this process , crossing over must occur between homologous chromosomes . Crossovers form only in the presence of a large p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "plant", "anatomy", "medicine", "and", "health", "sciences", "homologous", "chromosomes", "reproductive", "system", "chromosome", "structure", "and", "function", "centromeres", "animals", "germ", "cells", "animal", "models", "oocytes", "drosophila", "me...	2019	The E3 ubiquitin ligase Sina regulates the assembly and disassembly of the synaptonemal complex in Drosophila females
Courtship is a widespread behavior in which one gender conveys to the other a series of cues about their species identity , gender , and suitability as mates . In many species , females decode these male displays and either accept or reject them . Despite the fact that courtship has been investigated for a long time , ...	Males of the fruit fly Drosophila melanogaster generate a series of courtship displays that convey visual , auditory , and olfactory information that females must decode in order to accept or reject mating . Despite the central role of female decision in sexual selection , relatively little is known about how genes and...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "invertebrates", "animal", "genetics", "rna", "interference", "nervous", "system", "neuroscience", "animals", "gene", "function", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "epigenetics", "drosophila", "research", "and", "analysis", "methods",...	2014	The KRÜPPEL-Like Transcription Factor DATILÓGRAFO Is Required in Specific Cholinergic Neurons for Sexual Receptivity in Drosophila Females
Efficient and highly organized regulation of transcription is fundamental to an organism’s ability to survive , proliferate , and quickly respond to its environment . Therefore , precise mapping of transcriptional units and understanding their regulation is crucial to determining how pathogenic bacteria cause disease a...	The canonical relationship between a bacterial operon and the mRNA transcript produced from the operon has become significantly more complex as numerous regulatory mechanisms that impact the stability , translational efficiency , and early termination rates for mRNA transcripts have been described . With the rise of an...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "nucleobases", "gene", "regulation", "pathogens", "microbiology", "operons", "nucleotides", "dna", "transcription", "regulator", "genes", "ur...	2018	The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence
Altered metabolism in cancer cells has been viewed as a passive response required for a malignant transformation . However , this view has changed through the recently described metabolic oncogenic factors: mutated isocitrate dehydrogenases ( IDH ) , succinate dehydrogenase ( SDH ) , and fumarate hydratase ( FH ) that ...	Cancer and metabolism have been considered to be associated for a long period since Otto Warburg observed that tumor cells consume glucose and convert most of it to lactate , despite the presence of oxygen . However , the role of the Warburg effect in oncogenesis had been under doubt because no solid links between gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "and", "life", "sciences", "computational", "biology" ]	2014	A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks
African trypanosomiasis is a severe parasitic disease that affects both humans and livestock . Several different species may cause animal trypanosomosis and although Trypanosoma vivax ( sub-genus Duttonella ) is currently responsible for the vast majority of debilitating cases causing great economic hardship in West Af...	While most research efforts have focused on T . b . brucei trypanosomosis , infections caused by T . vivax and T . congolense which predominate in livestock and small ruminants have been subject to little study . In order to circumvent the major constraints inherent to studying T . vivax/host interactions in the field ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/leukocyte", "development", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immune", "response", "immunology/genetics", "of", "the", "immune", "system", "infectious", "diseases/protozoal", "infections" ]	2010	Trypanosoma vivax Infections: Pushing Ahead with Mouse Models for the Study of Nagana. I. Parasitological, Hematological and Pathological Parameters
Bacteria encounter sub-inhibitory concentrations of antibiotics in various niches , where these low doses play a key role for antibiotic resistance selection . However , the physiological effects of these sub-lethal concentrations and their observed connection to the cellular mechanisms generating genetic diversificati...	Bacteria can remodel their genome in order to adapt to new environments . This genomic plasticity can be mediated by horizontal gene transfer , genome rearrangements , and mutations . One important factor is the bacterial SOS response , induced upon DNA damaging stress conditions . SOS response induction leads to incre...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "flow", "cytometry", "microbial", "mutation", "cellular", "stress", "responses", "genetic", "mutation", "gene", "regulation", "microbiology", "mutational", "hypotheses", "dna", "transcription", "gene", "function", "escherichia", "coli", "emerging", "infectious", "diseases...	2013	RpoS Plays a Central Role in the SOS Induction by Sub-Lethal Aminoglycoside Concentrations in Vibrio cholerae
Paracoccidioides brasiliensis is a dimorphic fungus that is the causative agent of paracoccidioidomycosis , the most important prevalent systemic mycosis in Latin America . Recently , the existence of three genetically isolated groups in P . brasiliensis was demonstrated , enabling comparative studies of molecular evol...	The fungus Paracoccidioides brasiliensis is the causative agent of paracoccidioidomycosis , a severe pulmonary mycosis that is endemic to Latin America , where an estimated 10 million people are infected with the fungus . Despite the importance of this disease , we know little about the ecological and evolutionary hist...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "evolutionary", "biology", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2008	Evidence for Positive Selection in Putative Virulence Factors within the Paracoccidioides brasiliensis Species Complex
Bacterial sepsis is a major killer in hospitalized patients . Coagulase-negative staphylococci ( CNS ) with the leading species Staphylococcus epidermidis are the most frequent causes of nosocomial sepsis , with most infectious isolates being methicillin-resistant . However , which bacterial factors underlie the pathog...	Coagulase-negative staphylococci ( CNS ) are the leading cause of sepsis in hospitalized patients , causing a significant number of deaths . This situation is further worsened by a limitation of therapeutic options due to the fact that most CNS infectious isolates are resistant to methicillin . CNS sepsis has been assu...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "toxins", "body", "fluids", "pathology", "and", "laboratory", "medicine", "immune", "cells", "gene", "regulation", "pathogens", "immunology", "microbiology", "staphylococcus", "aureus", "toxicology", "toxic", ...	2017	Toxin Mediates Sepsis Caused by Methicillin-Resistant Staphylococcus epidermidis
Major depression is a common and severe psychiatric disorder with a highly polygenic genetic architecture . Genome-wide association studies have successfully identified multiple independent genetic loci that harbour variants associated with major depression , but the exact causal genes and biological mechanisms are lar...	Although genome-wide association studies have identified genetic risk variants associated with major depression , our understanding of the mechanisms through which they influence disease susceptibility remains largely unknown . Genetic risk variants are highly enriched in non-coding regions of the genome and affect gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "genetic", "networks", "volcanology", "magma", "body", "fluids", "neural", "networks", "brain", "neuroscience", "network", "analysis", "genome", "analysis", "geology", "mood", "disorders",...	2019	A gene co-expression network-based analysis of multiple brain tissues reveals novel genes and molecular pathways underlying major depression
In October 2012 , the Haitian Ministry of Health and the US CDC were notified of 25 recent dengue cases , confirmed by rapid diagnostic tests ( RDTs ) , among non-governmental organization ( NGO ) workers . We conducted a serosurvey among NGO workers in Léogane and Port-au-Prince to determine the extent of and risk fac...	Dengue is the most common mosquito-borne viral disease in the world , and caused an estimated 390 million infections and 96 million cases in the tropics and subtropics in 2010 . Over the last decade , the number of cases of dengue and the severity of dengue virus infections have increased in the Americas , including th...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "infectious", "disease", "epidemiology", "immunology", "vector-borne", "diseases", "microbiology", "tropical", "diseases", "geographical", "locations", "animals", "epidemi...	2014	Dengue Virus Infections among Haitian and Expatriate Non-governmental Organization Workers — Léogane and Port-au-Prince, Haiti, 2012
Health planners use forecasts of key metrics associated with influenza-like illness ( ILI ) ; near-term weekly incidence , week of season onset , week of peak , and intensity of peak . Here , we describe our participation in a weekly prospective ILI forecasting challenge for the United States for the 2016-17 season and...	It is estimated that there are between 3 and 5 million worldwide annual seasonal cases of severe influenza illness , and between 290 000 and 650 000 respiratory deaths . Influenza-like illness ( ILI ) describes a set of symptoms and is a practical way for health-care workers to easily estimate likely influenza cases . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "statistics", "atmospheric", "science", "influenza", "pathogens", "biological", "locomotion", "health", "care", "seasons", "mathematics", "forecasting", "patients", "humidity", "researc...	2019	Forecasting national and regional influenza-like illness for the USA
Sleep is an ancient animal behavior that is regulated similarly in species ranging from flies to humans . Various genes that regulate sleep have been identified in invertebrates , but whether the functions of these genes are conserved in mammals remains poorly explored . Drosophila insomniac ( inc ) mutants exhibit sev...	Sleep is ubiquitous among animals and is regulated in a similar manner across phylogeny , but whether conserved molecular mechanisms govern sleep is poorly defined . The Insomniac protein is vital for sleep in Drosophila and is a putative adaptor for the Cul3 ubiquitin ligase . We show that two mammalian orthologs of I...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "asses", "nervous", "system", "sleep", "vertebrates", "electrophysiology", "neuroscience", "animals", "mammals", "sleep", "disorders", "animal", "models", "physiological", "processes", "drosophila", "melanogaster", ...	2017	Conserved properties of Drosophila Insomniac link sleep regulation and synaptic function
P-glycoprotein ( P-gp ) is an ATP-dependent transport protein that is selectively expressed at entry points of xenobiotics where , acting as an efflux pump , it prevents their entering sensitive organs . The protein also plays a key role in the absorption and blood-brain barrier penetration of many drugs , while its ov...	With many drugs failing in the preclinical stages of drug discovery due to undesirable ADMETox ( absorption , distribution , metabolism , excretion and toxicity ) properties , improvement of these properties early on in the process , alongside the optimization of the compound activity , is emerging as a new focus in th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biomacromolecule-ligand", "interactions", "biochemistry", "biology", "computational", "biology", "drug", "discovery" ]	2011	Predicting Binding to P-Glycoprotein by Flexible Receptor Docking
Ticks salivate while feeding on their hosts . Saliva helps blood feeding through host anti-hemostatic and immunomodulatory components . Previous transcriptomic and proteomic studies revealed the complexity of tick saliva , comprising hundreds of polypeptides grouped in several multi-genic families such as lipocalins , ...	In this work , we confirm previous reports that the repertoire of tick salivary gland transcripts changes as a function of time , but in addition , we now identify transcripts that change their levels according to the mode of feeding of ticks . Implementation of membrane feeding allowed us to feed ticks on an immune-de...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "enzymes", "gene", "regulation", "regulatory", "proteins", "metalloproteases", "enzymology", "vertebrates", "rabbits", "dna-binding", "proteins", "saliva", "animals", "mammals", "animal", "models", "experimental",...	2018	Sialome diversity of ticks revealed by RNAseq of single tick salivary glands
Synthesis of ribosomal RNA by RNA polymerase I ( RNA pol I ) is an elemental biological process and is key for cellular homeostasis . In a forward genetic screen in C . elegans designed to identify DNA damage-response factors , we isolated a point mutation of RNA pol I , rpoa-2 ( op259 ) , that leads to altered rRNA sy...	Maintenance of genome integrity and tissue homeostasis is critically important for organisms to survive . For adequate responses to DNA damage or other types of stress , cells have evolved intricate surveillance mechanisms such as repair , cell cycle arrest and apoptosis . Disruption of these response pathways leads to...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Ribosome Synthesis and MAPK Activity Modulate Ionizing Radiation-Induced Germ Cell Apoptosis in Caenorhabditis elegans
Cytokinesis occurs through the coordinated action of several biochemically-mediated stresses acting on the cytoskeleton . Here , we develop a computational model of cellular mechanics , and using a large number of experimentally measured biophysical parameters , we simulate cell division under a number of different sce...	Cytokinesis , the physical separation of a mother cell into two daughter cells , requires force to deform the cell . Though there is ample evidence in many systems that myosin II provides some of this force , it is also well known that some cell types can divide in the absence of myosin II . To elucidate the mechanisms...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "computer", "science", "computer", "modeling", "biophysic", "al", "simulations", "biology", "cell", "mechanics", "computational", "biology", "biophysics", "biomechanics" ]	2012	Deconvolution of the Cellular Force-Generating Subsystems that Govern Cytokinesis Furrow Ingression
In the interest of identification of new kinase-targeting chemotypes for target and pathway analysis and drug discovery in Trypanosomal brucei , a high-throughput screen of 42 , 444 focused inhibitors from the GlaxoSmithKline screening collection was performed against parasite cell cultures and counter-screened against...	Human African trypanosomiasis , or sleeping sickness , affects 10 , 000 patients annually , yet current drugs for this disease are poor , with high toxicity and inconvenient dosing requirements . Trypanosoma brucei , the parasite that causes sleeping sickness , is sensitive to a class of compounds called kinase inhibit...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "trypanosoma", "medicinal", "chemistry", "protozoans", "biology", "and", "life", "sciences", "pharmacology", "drug", "screening", "trypanosoma", "brucei", "gambiense", "physical", "sciences", "chemistry", "parasitic", "protozoans",...	2014	Identification and Characterization of Hundreds of Potent and Selective Inhibitors of Trypanosoma brucei Growth from a Kinase-Targeted Library Screening Campaign
Clonorchis sinensis is a carcinogenic human liver fluke , prolonged infection which provokes chronic inflammation , epithelial hyperplasia , periductal fibrosis , and even cholangiocarcinoma ( CCA ) . These effects are driven by direct physical damage caused by the worms , as well as chemical irritation from their excr...	The oriental liver fluke , Clonorchis sinensis , is a biological carcinogen of humans and is the cause of death of infectious cancer patients in China and Korea . Its chronic infection promotes cholangiocarcinogenesis due to direct contact of host tissues with the worms and their excretory-secretory products ( ESPs ) ;...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biliary", "system", "invertebrates", "amorphous", "solids", "medicine", "and", "health", "sciences", "innate", "immune", "system", "liver", "immune", "physiology", "cytokines", "engineering", "and", "technology", "helminths", "gene", "regulation", "immunology", "carcin...	2019	Clonorchis sinensis excretory-secretory products increase malignant characteristics of cholangiocarcinoma cells in three-dimensional co-culture with biliary ductal plates
Dendrodendritic synaptic interactions between olfactory bulb mitral and granule cells represent a key neuronal mechanism of odor discrimination . Dendritic release of gamma-aminobutyric acid ( GABA ) from granule cells contributes to stimulus-dependent , rapid , and accurate odor discrimination , yet the physiological ...	In axonal nerve terminals , neurotransmitter release is triggered by a localized Ca2+ nanodomain generated by voltage-gated calcium channels in response to an action potential , which in turn is mediated by voltage-gated sodium channels . Dendritic neurotransmitter release has been thought to work differently , mainly ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neurochemistry", "membrane", "potential", "green", "fluorescent", "protein", "electrophysiology", "neuroscience", "histochemistry", "and", "cytochemistry", "techniques", "luminescent", "proteins", "cognition", ...	2018	Axonal sodium channel NaV1.2 drives granule cell dendritic GABA release and rapid odor discrimination
Porcine Reproductive and Respiratory Syndrome ( PRRS ) is a panzootic infectious disease of pigs , causing major economic losses to the world-wide pig industry . PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets . The causa...	Porcine Reproductive and Respiratory Syndrome is an endemic infectious disease of pigs , manifesting differently in pigs of different ages but primarily causing late-term abortions and stillbirths in sows and respiratory disease in piglets . The causative agent of the disease is the positive-strand RNA PRRS virus ( PRR...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "livestock", "medicine", "and", "health", "sciences", "immune", "cells", "body", "fluids", "immunology", "rna", "extraction", "variant", "genotypes", "vertebrates", "animals", "mammals", "genetic", "mapping", "germ", "cells", "zygotes", "molecular", ...	2017	Precision engineering for PRRSV resistance in pigs: Macrophages from genome edited pigs lacking CD163 SRCR5 domain are fully resistant to both PRRSV genotypes while maintaining biological function
Trypanosoma cruzi enters host cells by subverting the mechanism of cell membrane repair . In this process , the parasite induces small injuries in the host cell membrane leading to calcium entry and lysosomal exocytosis , which are followed by compensatory endocytosis events that drive parasites into host cells . We ha...	Trypanosoma cruzi is the etiological agent of Chagas disease , a very debilitating illness that has no efficient treatment to date . Better knowledge of the mechanisms involved with host cell infection is important to change this scenario . T . cruzi enters host cells by subverting the mechanism by which cells repair s...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "lysosomes", "medicine", "and", "health", "sciences", "viral", "transmission", "and", "infection", "cell", "processes", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "fibroblasts", "protozoans", "connective", "tissue", "cells", "cellular", "structure...	2017	LAMP-2 absence interferes with plasma membrane repair and decreases T. cruzi host cell invasion
Schistosomiasis is one of the most prevalent parasitic diseases , affecting millions of people in developing countries . Amongst the human-infective species , Schistosoma mansoni is also the most commonly used in the laboratory and here we present the systematic improvement of its draft genome . We used Sanger capillar...	Schistosomiasis is a disease caused by parasitic blood flukes of the genus Schistosoma . Human-infective species are prevalent in developing countries , where they represent a major disease burden as well as an impediment to socioeconomic development . In addition to its clinical relevance , Schistosoma mansoni is the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "genomics", "genetics", "and", "genomics" ]	2012	A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke Schistosoma mansoni
Mass vaccinations are a main strategy in the deployment of oral cholera vaccines . Campaigns avoid giving vaccine to pregnant women because of the absence of safety data of the killed whole-cell oral cholera ( rBS-WC ) vaccine . Balancing this concern is the known higher risk of cholera and of complications of pregnanc...	Pregnant women are more vulnerable to complications of cholera than other people . It would be helpful to include pregnant women in vaccination campaigns against cholera but pregnant women and their unborn children are highly vulnerable to the potential adverse effects of biological products such as vaccines . The safe...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2012	Safety of the Recombinant Cholera Toxin B Subunit, Killed Whole-Cell (rBS-WC) Oral Cholera Vaccine in Pregnancy
Since the discovery of tumour initiating cells ( TICs ) in solid tumours , studies focussing on their role in cancer initiation and progression have abounded . The biological interrogation of these cells continues to yield volumes of information on their pro-tumourigenic behaviour , but actionable generalised conclusio...	In this paper , we present a mathematical/computational model of a tumour growing according to the canonical cancer stem-cell hypothesis with a simplified microenvironment . We explore the parameters of this model and find good agreement between our model and other theoretical models in terms of the intrinsic cellular ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "complex", "systems", "medicine", "oncology", "computer", "science", "computer", "modeling", "mathematics", "applied", "mathematics", "cancers", "and", "neoplasms" ]	2014	Microenvironmental Variables Must Influence Intrinsic Phenotypic Parameters of Cancer Stem Cells to Affect Tumourigenicity
Human papillomaviruses ( HPV ) activate a number of host factors to control their differentiation-dependent life cycles . The transcription factor signal transducer and activator of transcription ( STAT ) -3 is important for cell cycle progression and cell survival in response to cytokines and growth factors . STAT3 re...	Human papillomaviruses ( HPV ) are the leading cause of viral induced cancers worldwide . HPV are the causative agents of cervical cancers and an increasing number of head and neck cancers . HPV infections are dependant on the manipulation of the host cell for their replication and this may result in diseases such as c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "and", "materials" ]	[ "phosphorylation", "urology", "keratinocytes", "medicine", "and", "health", "sciences", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "cell", "differentiation", "epithelial", "cells", "developmental", "biology", "sexually", "tran...	2018	STAT3 activation by E6 is essential for the differentiation-dependent HPV18 life cycle

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