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Autosomal recessive retinal degenerative diseases cause visual impairment and blindness in both humans and dogs . Currently , no standard treatment is available , but pioneering gene therapy-based canine models have been instrumental for clinical trials in humans . To study a novel form of retinal degeneration in Labra...	Stargardt disease ( STGD ) is the most common inherited retinal disease causing visual impairment and blindness in children and young adults , affecting 1 in 8–10 thousand people . For other inherited retinal diseases , the dog has become an established comparative animal model , both for identifying the underlying gen...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "diagnostic", "radiology", "ocular", "anatomy", "vertebrates", "social", "sciences", "neuroscience", "dogs", "animals", "mammals", "macular", "disorders", "animal", "models", "retinal", "disorders", "model", "organisms", "experim...	2019	An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease
In Toxoplasma gondii , cis-acting elements present in promoter sequences of genes that are stage-specifically regulated have been described . However , the nuclear factors that bind to these cis-acting elements and regulate promoter activities have not been identified . In the present study , we performed affinity puri...	Apicomplexa including Toxoplasma gondii are responsible for a variety of deadly infections . These intracellular parasites have complex life cycles within different hosts and their infectivity relies on their capacity to regulate gene expression in response to different environments . However , to date , little is know...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "molecular", "biology/nucleolus", "and", "nuclear", "bodies", "molecular", "biology/chromatin", "structure" ]	2011	A Novel Toxoplasma gondii Nuclear Factor TgNF3 Is a Dynamic Chromatin-Associated Component, Modulator of Nucleolar Architecture and Parasite Virulence
We have previously demonstrated that B cells can shape the immune response to Mycobacterium tuberculosis , including the level of neutrophil infiltration and granulomatous inflammation at the site of infection . The present study examined the mechanisms by which B cells regulate the host neutrophilic response upon expo...	Mycobacterium tuberculosis poses a serious threat to public health globally . It has been well established that T cells are critical in protection against M . tuberculosis . The role of B cells and humoral immunity in the process is less well understood . We previously showed that B cells and humoral immunity regulate ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "immune", "cells", "immunology", "host-pathogen", "interaction", "microbiology", "bacterial", "diseases", "emerging", "infectious", "diseases", "immunologic", "techniques", "immunomodulation", "infectious", "diseases", "microbial", "pathogens", "bi...	2013	B Cells Regulate Neutrophilia during Mycobacterium tuberculosis Infection and BCG Vaccination by Modulating the Interleukin-17 Response
Disease surveillance in rural regions of many countries is poor , such that prolonged delays ( months ) may intervene between appearance of disease and its recognition by public health authorities . For infectious disorders , delayed recognition and intervention enables uncontrolled disease spread . We tested the feasi...	Absence of health monitoring of rural populations in low-income countries allows diseases to emerge and spread for months before their detection by public health authorities . We tested the feasibility of using smartphones operated by lay villagers to report health information in real time from the populations in which...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "geographical", "locations", "uganda", "cell", "phones", "pediatrics", "research", "design", "surveys", "infectious", "disease", "control", "africa", "research", "and", "analysis", "methods", ...	2018	A real-time medical cartography of epidemic disease (Nodding syndrome) using village-based lay mHealth reporters
Compartment boundary formation plays an important role in development by separating adjacent developmental fields . Drosophila imaginal discs have proven valuable for studying the mechanisms of boundary formation . We studied the boundary separating the proximal A1 segment and the distal segments , defined respectively...	During development , boundary formation between adjacent developmental fields is important to maintain the integrity of complex organs and tissues . We examined how boundaries become established between adjacent developmental fields—which are defined by expression of distinct selector genes and developmental fates—usin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "cloning", "cell", "disruption", "animals", "notch", "signaling", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimenta...	2017	Notch-dependent epithelial fold determines boundary formation between developmental fields in the Drosophila antenna
Gene regulatory circuits drive the development , physiology , and behavior of organisms from bacteria to humans . The phenotypes or functions of such circuits are embodied in the gene expression patterns they form . Regulatory circuits are typically multifunctional , forming distinct gene expression patterns in differe...	Many essential biological processes , ranging from embryonic patterning to circadian rhythms , are driven by gene regulatory circuits , which comprise small sets of genes that turn each other on or off to form a distinct pattern of gene expression . Gene regulatory circuits often have multiple functions . This means th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "computer", "science", "genetics", "biology", "computational", "biology", "computerized", "simulations", "gene", "networks" ]	2013	Constraint and Contingency in Multifunctional Gene Regulatory Circuits
The type III receptor tyrosine kinase ( RTK ) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states . D816V KIT mutation is associated with various pathologies including mastocyt...	Protein kinases are involved in a huge amount of cellular processes through phosphorylation , a crucial mechanism in cell signaling , and their misregulation often results in disease . The deactivation of protein tyrosine kinases ( PTKs ) or their oncogenic activation arises from mutations which affect the protein prim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology", "biophysics" ]	2011	Mutation D816V Alters the Internal Structure and Dynamics of c-KIT Receptor Cytoplasmic Region: Implications for Dimerization and Activation Mechanisms
We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone . These signatures were based on a new method reported herein – Identification of Structured Signatures and Classifiers ( ISSAC ) – ...	From a multi-study , integrated transcriptomic dataset , we identified a marker panel for differentiating major human brain cancers at the gene-expression level . The ISSAC molecular signatures for brain cancers , composed of 44 unique genes , are based on comparing expression levels of pairs of genes , and phenotype p...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "computational", "biology" ]	2013	Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures
Rabies is a zoonotic disease that is endemic in many parts of the developing world , especially in Africa and Asia . However its epidemiology remains largely unappreciated in much of these regions , such as in Nepal , where limited information is available about the spatiotemporal dynamics of the main etiological agent...	Rabies is endemic in most Asian countries and represents a serious public health issue , with an estimated 31 , 000 people dying each year of this disease . The majority of human cases are transmitted by domestic dogs , which act as the principal reservoir host and vector . However , molecular epidemiology and evolutio...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2013	Recent Emergence and Spread of an Arctic-Related Phylogenetic Lineage of Rabies Virus in Nepal
The Cop9 signalosome ( CSN ) is an evolutionarily conserved multifunctional complex that controls ubiquitin-dependent protein degradation in eukaryotes . We found seven CSN subunits in Neurospora crassa in a previous study , but only one subunit , CSN-2 , was functionally characterized . In this study , we created knoc...	Protein degradation is precisely controlled in cells . The ubiquitin-mediated protein degradation pathway is highly conserved in eukaryotes , and the activity of ubiquitin ligases is regulated by the Cop9 signalosome ( CSN ) , a multisubunit complex that is evolutionarily conserved from yeast to humans . Determining ho...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/microbial", "growth", "and", "development", "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "microbiology/microbial", "growth", "and", "development", "biochemistry/protein", "chemistry" ]	2010	Role of Individual Subunits of the Neurospora crassa CSN Complex in Regulation of Deneddylation and Stability of Cullin Proteins
Diabetic kidney disease ( DKD ) is the most common etiology of chronic kidney disease ( CKD ) in the industrialized world and accounts for much of the excess mortality in patients with diabetes mellitus . Approximately 45% of U . S . patients with incident end-stage kidney disease ( ESKD ) have DKD . Independent of gly...	Type 2 diabetes is the most common cause of severe kidney disease worldwide and diabetic kidney disease ( DKD ) associates with premature death . Individuals of non-European ancestry have the highest burden of type 2 DKD; hence understanding the causes of DKD remains critical to reducing health disparities . Family stu...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Genome-Wide Association and Trans-ethnic Meta-Analysis for Advanced Diabetic Kidney Disease: Family Investigation of Nephropathy and Diabetes (FIND)
Meiosis is a specialized eukaryotic cell division that generates haploid gametes required for sexual reproduction . During meiosis , homologous chromosomes pair and undergo reciprocal genetic exchange , termed crossover ( CO ) . Meiotic CO frequency varies along the physical length of chromosomes and is determined by h...	The majority of eukaryotes reproduce via a specialized cell division called meiosis , which generates gametes with half the number of chromosomes . During meiosis , homologous chromosomes pair and undergo a process of reciprocal exchange , called crossing-over ( CO ) , which generates new combinations of genetic variat...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "meiosis", "plant", "biology", "centromeres", "plant", "science", "model", "organisms", "epigenetics", "linkage", "(genetics)", "chromatin", "arabidopsis", "thaliana", "chromosomal", "inheritance", "chromosome", "biology", "plant", "genetics", "biology", "dna", "modificat...	2012	Epigenetic Remodeling of Meiotic Crossover Frequency in Arabidopsis thaliana DNA Methyltransferase Mutants
The emergence following gene duplication of a large repertoire of Hox paralogue proteins underlies the importance taken by Hox proteins in controlling animal body plans in development and evolution . Sequence divergence of paralogous proteins accounts for functional specialization , promoting axial morphological divers...	Animal body plan diversity is controlled by transcription factors that select within each cell of a multi-cellular organism the set of genes to be expressed , eventually allowing distinct fate to emerge according to spatial coordinates . Transcription factors can be grouped based on their DNA binding domains in a few c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "genetics", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2013	Distinct Molecular Strategies for Hox-Mediated Limb Suppression in Drosophila: From Cooperativity to Dispensability/Antagonism in TALE Partnership
Most epithelial tubes arise as small buds and elongate by regulated morphogenetic processes including oriented cell division , cell rearrangements , and changes in cell shape . Through live analysis of Drosophila renal tubule morphogenesis we show that tissue elongation results from polarised cell intercalations around...	Many of the tissues in our bodies are built up around complex arrays of elongated cellular tubes , which permit the entry , exit , and transport of essential molecules such as oxygen , glucose , and water . These tubes often arise as short buds , which elongate dramatically as the organ grows . We sought to understand ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "tube", "morphogenesis", "morphogenesis", "biology", "and", "life", "sciences", "developmental", "biology" ]	2014	Epidermal Growth Factor Signalling Controls Myosin II Planar Polarity to Orchestrate Convergent Extension Movements during Drosophila Tubulogenesis
Trypanosoma cruzi is exposed during its life to exogenous and endogenous oxidative stress , leading to damage of several macromolecules such as DNA . There are many DNA repair pathways in the nucleus and mitochondria ( kinetoplast ) , where specific protein complexes detect and eliminate damage to DNA . One group of th...	Exposure of Trypanosome cruzi to oxidative stress leads to damage of several macromolecules such as DNA . DNA polymerases play a very important role in DNA repair after oxidative damage . One of them is Tc DNA polymerase β . In this work , two form of this DNA polymerase were identified and overexpressed in T . cruzi c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "phosphorylation", "oxidative", "stress", "messenger", "rna", "dna-binding", "proteins", "microbiology", "parasitic", "protozoans", "protozoan", "life", "cycles", "developmental", "biology", "trypomastigotes", "protozoans", "polymerases", "dna", "epimastigotes", "proteins", ...	2018	Endogenous overexpression of an active phosphorylated form of DNA polymerase β under oxidative stress in Trypanosoma cruzi
Streptococcus pyogenes , also known as Group A Streptococcus ( GAS ) , is an important human bacterial pathogen that can cause invasive infections . Once it colonizes its exclusively human host , GAS needs to surmount numerous innate immune defense mechanisms , including opsonization by complement and consequent phagoc...	Streptococcus pyogenes is an important cause of human infections worldwide , ranging from mild and superficial disease to life-threatening invasive infections . Development of new and efficient therapies for infections requires animal models that faithfully recapitulate infection in humans . Humans are the only natural...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Virulence of Group A Streptococci Is Enhanced by Human Complement Inhibitors
When incorporated into a polypeptide chain , proline ( Pro ) differs from all other naturally occurring amino acid residues in two important respects . The φ dihedral angle of Pro is constrained to values close to −65° and Pro lacks an amide hydrogen . Consequently , mutations which result in introduction of Pro can si...	Unlike other amino acids that constitute proteins , Proline is missing a vital hydrogen atom and also bestows local structural rigidity to the three-dimensional ( 3D ) structure of proteins . In some locations , proline can be introduced with little or no detrimental effect to protein function , while at others it is d...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "eubacteria", "computational", "biology" ]	2007	Stereochemical Criteria for Prediction of the Effects of Proline Mutations on Protein Stability
The ILEP Nerve Function Impairment in Reaction ( INFIR ) is a cohort study designed to identify predictors of reactions and nerve function impairment ( NFI ) in leprosy . Antibodies to mycobacteria , nerve components and serum cytokine were measured as potential markers for their possible association with reactions and...	Leprosy is one of the oldest known diseases . In spite of the established fact that it is least infectious and a completely curable disease , the social stigma associated with it still lingers in many countries and remains a major obstacle to self reporting and early treatment . The nerve damage that occurs in leprosy ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis" ]	2011	Analysis of Antibody and Cytokine Markers for Leprosy Nerve Damage and Reactions in the INFIR Cohort in India
Target repurposing utilizes knowledge of “druggable” targets obtained in one organism and exploits this information to pursue new potential drug targets in other organisms . Here we describe such studies to evaluate whether inhibitors targeting the kinase domain of the mammalian Target of Rapamycin ( mTOR ) and human p...	In our study we describe the potency of established phosphoinositide-3-kinase ( PI3K ) and mammalian Target of Rapamycin ( mTOR ) kinase inhibitors against three trypanosomatid parasites: Trypanosoma brucei , T . cruzi , and Leishmania sp . , which are the causative agents for African sleeping sickness , Chagas disease...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "medicinal", "chemistry", "african", "trypanosomiasis", "parasitic", "diseases", "neglected", "tropical", "diseases", "protein", "kinase", "signaling", "cascade", "infectious", "diseases", "chemistry", "biology", "molecular", "biology", "signal", "transduction",...	2011	The Susceptibility of Trypanosomatid Pathogens to PI3/mTOR Kinase Inhibitors Affords a New Opportunity for Drug Repurposing
Stimulus-induced perturbations from the steady state are a hallmark of signal transduction . In some signaling modules , the steady state is characterized by rapid synthesis and degradation of signaling proteins . Conspicuous among these are the p53 tumor suppressor , its negative regulator Mdm2 , and the negative feed...	Eukaryotic cells constantly synthesize new proteins and degrade old ones . While most proteins are degraded within 24 hours of being synthesized , some proteins are short-lived and exist for only minutes . Using mathematical models , we asked how rapid turnover , or flux , of signaling proteins might regulate the activ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cellular", "stress", "responses", "signaling", "networks", "mathematics", "stress", "signaling", "cascade", "regulatory", "networks", "biology", "nonlinear", "dynamics", "systems", "biology", "biochemical", "simulations", "signal", "transduction", "cell", "biology", "com...	2013	A Protein Turnover Signaling Motif Controls the Stimulus-Sensitivity of Stress Response Pathways
Northeast Africa has a long history of human habitation , with fossil-finds from the earliest anatomically modern humans , and housing ancient civilizations . The region is also the gate-way out of Africa , as well as a portal for migration into Africa from Eurasia via the Middle East and the Arabian Peninsula . We inv...	Northeast Africa has geographic and historical links to Eurasia via the Middle East and the Arabian Peninsula , but the demographic history of the region itself has been more elusive . We investigate genomic diversity of northeast African populations and found a clear bimodal distribution of variation , correlated with...	[ "Abstract", "Introduction", "Results/Discussion", "Conclusion", "Methods" ]	[ "africans", "linguistics", "population", "genetics", "geographical", "locations", "sudan", "social", "sciences", "south", "sudan", "sociolinguistics", "ethnicities", "population", "biology", "africa", "homozygosity", "people", "and", "places", "languages", "heredity", "ge...	2017	Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations
This article can also be viewed as an enhanced version in which the text of the article is integrated with interactive 3-D representations and animated transitions . Please note that a Web plugin is required to access this enhanced functionality . Instructions for the installation and use of the web plugin are availabl...	Cyclophilins are proteins that catalyze the isomerization of prolines , interconverting this structurally important amino acid between cis and trans isomers . Although there are 17 cyclophilins in the human genome , the function of most cyclophilin isoforms is unknown . At least some members of this protein family are ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "biophysics/structural", "genomics", "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/structural", "genomics", "biophysics" ]	2010	Structural and Biochemical Characterization of the Human Cyclophilin Family of Peptidyl-Prolyl Isomerases
σ factors endow RNA polymerase with promoter specificity in bacteria . Extra-Cytoplasmic Function ( ECF ) σ factors represent the largest and most diverse family of σ factors . Most ECF σ factors must be activated in response to an external signal . One mechanism of activation is the stepwise proteolytic destruction of...	All cells sense and respond to changes in their environments by transmitting information across the membrane . In bacteria , σ factors provide promoter specificity to RNA polymerase . Bacteria encode Extra-Cytoplasmic Function ( ECF ) σ factors , which often respond to extracellular signals . Activation of some ECF σ f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "bacillus", "microbiology", "prokaryotic", "models", "model", "organisms", "molecular", "genetics", "bacterial", "pathogens", "research", "and", ...	2014	Evidence of a Bacterial Receptor for Lysozyme: Binding of Lysozyme to the Anti-σ Factor RsiV Controls Activation of the ECF σ Factor σV
The activities of the Global Programme for the Elimination of Lymphatic Filariasis have been in operation since the year 2000 , with Mass Drug Administration ( MDA ) undertaken yearly in disease endemic communities . Information collected during MDA–such as population demographics , age , sex , drugs used and remaining...	The Global Programme for the Elimination of Lymphatic Filariasis has been conducting yearly treatment of entire communities in endemic countries since the year 2000 . During the treatments various information is collected on the populations , number of medicine tablets distributed and remaining , the number of people t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussions" ]	[ "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "data", "management", "filariasis", "pharmaceutics", "neglected", "tropical", "diseases", "pharmacology", "lymphatic", "filariasis", "africa", "public", ...	2016	Assessing Lymphatic Filariasis Data Quality in Endemic Communities in Ghana, Using the Neglected Tropical Diseases Data Quality Assessment Tool for Preventive Chemotherapy
A major challenge in computational biology is constraining free parameters in mathematical models . Adjusting a parameter to make a given model output more realistic sometimes has unexpected and undesirable effects on other model behaviors . Here , we extend a regression-based method for parameter sensitivity analysis ...	Mathematical models of biological processes generally contain many free parameters that are not known from experiments . Choosing values for these parameters , although an important step in the construction of realistic computational models , is frequently performed using an ad hoc approach that is a combination of int...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cardiovascular", "disorders/arrhythmias,", "electrophysiology,", "and", "pacing", "computational", "biology/systems", "biology", "physiology/cardiovascular", "physiology", "and", "circulation" ]	2010	Regression Analysis for Constraining Free Parameters in Electrophysiological Models of Cardiac Cells
Zika virus ( ZIKV ) infection causes diseases ranging from acute self-limiting febrile illness to life-threatening Guillain–Barré Syndrome and other neurological disorders in adults . Cumulative evidence suggests an association between ZIKV infection and microcephaly in newborn infants . Given the host-range restrictio...	Mosquito-borne Zika virus ( ZIKV ) is an emerging threat to human health worldwide . In 2007 , a ZIKV outbreak was reported in the Yap Island of Micronesia and was the first outbreak outside Africa and Asia . In 2013 and 2014 , another ZIKV outbreak was reported in French Polynesia , and more than 28 , 800 people were ...	[ "Abstract", "Introduction", "Result", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "body", "weight", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "immunology", "microbiology", "animal", "models", "viruses", "model", "org...	2018	ICR suckling mouse model of Zika virus infection for disease modeling and drug validation
Leishmania protozoan parasites ( Trypanosomatidae family ) are the causative agents of cutaneous , mucocutaneous and visceral leishmaniasis worldwide . While these diseases are associated with significant morbidity and mortality , there are few adequate treatments available . Sterol 14alpha-demethylase ( CYP51 ) in the...	Visceral leishmaniasis is the second most lethal parasitic infection after malaria . Other forms of leishmaniasis also cause significant morbidity . However , there are few treatments available , and many cause severe side effects or are associated with the development of resistance . A key difference between mammalian...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Targeting Ergosterol Biosynthesis in Leishmania donovani: Essentiality of Sterol 14alpha-demethylase
Ym1 and RELMα are established effector molecules closely synonymous with Th2-type inflammation and associated pathology . Here , we show that whilst largely dependent on IL-4Rα signaling during a type 2 response , Ym1 and RELMα also have IL-4Rα-independent expression patterns in the lung . Notably , we found that Ym1 h...	Immune cells produce molecules that limit infections , attract other immune cells or repair tissue damage . Two such molecules , Ym1 and RELMα , are abundantly produced in mice during infection and injury . Related human molecules are strongly associated with many chronic diseases and yet we know very little about thei...	[ "Abstract", "Introduction", "Results", "Ym1", "during", "adaptive", "immunity", "is", "required", "for", "lung", "tissue", "repair", "Discussion", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "diagnostic", "radiology", "cytokines", "immune", "cells", "immunology", "parasitic", "diseases", "nematode", "infections", "physiological", "processes", "de...	2018	Ym1 induces RELMα and rescues IL-4Rα deficiency in lung repair during nematode infection
Theoretical and empirical investigations of search strategies typically have failed to distinguish the distinct roles played by density versus patchiness of resources . It is well known that motility and diffusivity of organisms often increase in environments with low density of resources , but thus far there has been ...	Understanding how animals search for food is crucial for animal ecology . Although much has been learned about the main aspects of the so-called foraging problem , some important questions still remain unanswered . In this work we address the issue of the relevance of heterogeneity in the resources distribution to effi...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "theoretical", "biology", "biology" ]	2011	How Landscape Heterogeneity Frames Optimal Diffusivity in Searching Processes
Identifying the source of transmission using pathogen genetic data is complicated by numerous biological , immunological , and behavioral factors . A large source of error arises when there is incomplete or sparse sampling of cases . Unsampled cases may act as either a common source of infection or as an intermediary i...	Molecular data from pathogens may be useful for identifying the source of infection and identifying pairs of individuals such that one host transmitted to the other . Inference of who acquired infection from whom is confounded by incomplete sampling , and given genetic data only , it is not possible to infer the direct...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Inferring the Source of Transmission with Phylogenetic Data
The co-evolutionary dynamics of competing populations can be strongly affected by frequency-dependent selection and spatial population structure . As co-evolving populations grow into a spatial domain , their initial spatial arrangement and their growth rate differences are important factors that determine the long-ter...	Evolutionary public good ( PG ) games capture the essence of production of growth-beneficial factors that are vulnerable to exploitation by free-riders who do not carry the cost of production . PGs emerge in cellular populations , for example in growing bacteria and cancer cells . We study the eco-evolutionary dynamics...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "cell", "processes", "endocrine", "physiology", "systems", "science", "mathematics", "phase", "diagrams", "growth", "factors", "waves", "traveling", "waves", "compu...	2019	Time scales and wave formation in non-linear spatial public goods games
Helicobacter pylori , a human pathogen infecting about half of the world population , is characterised by its large intraspecies variability . Its genome plasticity has been invoked as the basis for its high adaptation capacity . Consistent with its small genome , H . pylori possesses only two bona fide DNA polymerases...	Helicobacter pylori is the main cause of ulcers and gastric cancers . One the characteristics of this bacterial species is that it displays an amazing capacity to change its genetic information . This genetic variability provides H . pylori with an adaptation potential that allows it to successfully colonise the stomac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "microbiology", "dna", "replication", "dna", "bacterial", "pathogens", "biology", "mutagenesis", "biochemistry", "gram", "negative", "nucleic", "acids", "genetics", "dna", "repair", "genetics", "and", "genomics" ]	2011	Unexpected Role for Helicobacter pylori DNA Polymerase I As a Source of Genetic Variability
The apicomplexans are a large group of parasitic protozoa , many of which are important human and animal pathogens , including Plasmodium falciparum and Toxoplasma gondii . These parasites cause disease only when they replicate , and their replication is critically dependent on the proper assembly of the parasite cytos...	Toxoplasma gondii is one of the most prevalent parasites in warm-blooded animals and a highly important human pathogen . It is the most common cause of congenital neurological defects in humans and also causes devastating opportunistic infections in immuno-compromised patients . Many of its 5 , 000 relatives in phylum ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "cell", "biology", "infectious", "diseases", "eukaryotes" ]	2008	Organizational Changes of the Daughter Basal Complex during the Parasite Replication of Toxoplasma gondii
The recent emergence of artemisinin resistance in the Greater Mekong Subregion poses a major threat to the global effort to control malaria . Tracking the spread and evolution of artemisinin-resistant parasites is critical in aiding efforts to contain the spread of resistance . A total of 417 patient samples from the y...	The Plasmodium falciparum parasites that cause malaria are evolving resistance to our most effective and potent anti-malarial drugs available , called artemisinins . Currently , artemisinin resistance is emerging in a number of countries in the Greater Mekong Subregion , including Cambodia , Thailand , Myanmar , and Vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Selection and Spread of Artemisinin-Resistant Alleles in Thailand Prior to the Global Artemisinin Resistance Containment Campaign
The cyclic GMP-AMP synthase ( cGAS ) , upon cytosolic DNA stimulation , catalyzes the formation of the second messenger 2′3′-cGAMP , which then binds to stimulator of interferon genes ( STING ) and activates downstream signaling . It remains to be elucidated how the cGAS enzymatic activity is modulated dynamically . He...	Ubiquitination has been demonstrated to serve as an effective means to catalyze the rapid , dynamic and versatile regulatory processes that are activated when hosts face microbes . Given the critical functions of cytosolic DNA sensing pathway in anti-viral innate immune responses and the pathogenesis of autoimmune dise...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "transfection", "phosphorylation", "rheumatology", "medicine", "and", "health", "sciences", "gene", "regulation", "enzymes", "biological", "cultures", "immunology", "enzymology", "ubiquitin", "ligases", "clinical", "medicine", "immunoprecipitation", "molecular", "biology", ...	2017	The E3 ubiquitin ligase RNF185 facilitates the cGAS-mediated innate immune response
HIV and related primate lentiviruses possess single-stranded RNA genomes . Multiple regions of these genomes participate in critical steps in the viral replication cycle , and the functions of many RNA elements are dependent on the formation of defined structures . The structures of these elements are still not fully u...	Human immunodeficiency virus ( HIV ) is a persistent and critical threat to human health . Replication and pathogenesis of HIV is governed by information encoded in its single-stranded RNA genome . In addition to coding for viral proteins , the HIV genomic RNA forms base paired and higher-order structures that are crit...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Structure-Based Alignment and Consensus Secondary Structures for Three HIV-Related RNA Genomes
Early diagnosis of reactivated Chagas disease in HIV patients could be lifesaving . In Latin America , the diagnosis is made by microscopical detection of the T . cruzi parasite in the blood; a diagnostic test that lacks sensitivity . This study evaluates if levels of T . cruzi antigens in urine , determined by Chunap ...	Reactivation of Chagas disease in people living with HIV is a serious clinical condition that is associated with high mortality . Hence , early diagnosis and treatment can be lifesaving . Although there are not well accepted criteria to identify patients at risk of reactivation , parasitemia levels are usually consider...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "tropical", "diseases", "microbiology", "parasitic", "diseases", "parasitic", "protozoans", "parasito...	2016	Use of a Chagas Urine Nanoparticle Test (Chunap) to Correlate with Parasitemia Levels in T. cruzi/HIV Co-infected Patients
At the imprinted Rasgrf1 locus in mouse , a cis-acting sequence controls DNA methylation at a differentially methylated domain ( DMD ) . While characterizing epigenetic marks over the DMD , we observed that DNA and H3K27 trimethylation are mutually exclusive , with DNA and H3K27 methylation limited to the paternal and ...	Methylation of DNA and histones exert profound and inherited effects on gene expression . These occur without changes to the underlying DNA sequence and are considered epigenetic effects . Disrupting epigenetic states can cause developmental abnormalities and cancer . Very little is known about how locations in the mam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/epigenetics", "molecular", "biology/histone", "modification", "molecular", "biology/dna", "methylation" ]	2008	Antagonism between DNA and H3K27 Methylation at the Imprinted Rasgrf1 Locus
The O-acetylation of the essential cell wall polymer peptidoglycan occurs in most Gram-positive bacterial pathogens , including species of Staphylococcus , Streptococcus and Enterococcus . This modification to peptidoglycan protects these pathogens from the lytic action of the lysozymes of innate immunity systems and ,...	Multi-drug resistance amongst important human pathogens , such as methicillin-resistant Staphylococcus aureus ( MRSA ) , vancomycin-resistant Enterococcus ( VRE ) and drug-resistant Streptococcus pneumoniae ( DRSP ) , continues to challenge clinicians and threaten the lives of infected patients . Of the several approac...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pneumococcus", "chemical", "compounds", "phosphates", "enzymes", "pathogens", "enzymology", "microbiology", "staphylococcus", "aureus", "sodium", "phosphate", "bacteria", "bacterial", ...	2017	In vitro characterization of the antivirulence target of Gram-positive pathogens, peptidoglycan O-acetyltransferase A (OatA)
Lyme disease spirochetes demonstrate strain- and species-specific differences in tissue tropism . For example , the three major Lyme disease spirochete species , Borrelia burgdorferi sensu stricto , B . garinii , and B . afzelii , are each most commonly associated with overlapping but distinct spectra of clinical manif...	Lyme disease , the most common vector-borne disease in the United States , is caused by a bacterium , Borrelia burgdorferi . This bacterium infects the skin at the site of the tick bite and then can spread to other tissues , such as the heart , joints or nervous system , causing carditis , arthritis or neurologic disea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dermatology", "rheumatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "immunology", "microbiology", "bacterial", "diseases", "rheumatoid", "arthritis", "skin", "infections", "emerging", "infectious", "diseases", "bacterial", ...	2014	Strain-Specific Variation of the Decorin-Binding Adhesin DbpA Influences the Tissue Tropism of the Lyme Disease Spirochete
Defining the complex dynamics of Zika virus ( ZIKV ) infection in pregnancy and during transmission between vertebrate hosts and mosquito vectors is critical for a thorough understanding of viral transmission , pathogenesis , immune evasion , and potential reservoir establishment . Within-host viral diversity in ZIKV i...	Understanding the complex dynamics of Zika virus ( ZIKV ) infection during pregnancy and during transmission to and from vertebrate host and mosquito vector is critical for a thorough understanding of viral transmission , pathogenesis , immune evasion , and reservoir establishment . We sought to develop a virus model s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "pathogens", "microbiology", "vertebrates", "animals", "mammals", "primates",...	2018	Molecularly barcoded Zika virus libraries to probe in vivo evolutionary dynamics
The complement system plays a key role in host defense against pneumococcal infection . Three different pathways , the classical , alternative and lectin pathways , mediate complement activation . While there is limited information available on the roles of the classical and the alternative activation pathways of compl...	Streptococcus pneumoniae is a major human pathogen that causes pneumonia , septicemia and meningitis . The host defense against pneumococci is largely dependent on complement , a system of blood proteins which , when activated , attach to bacteria , targeting them for clearance by phagocytes . There are three routes of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "humoral", "immunity", "medicine", "complement", "system", "pneumococcus", "immune", "activation", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "animal", "models", "bacterial", "diseases", "adaptive", "immunity", "model", "...	2012	The Lectin Pathway of Complement Activation Is a Critical Component of the Innate Immune Response to Pneumococcal Infection
The psychological impact of snakebite on its victims , especially possible late effects , has not been systematically studied . To assess delayed somatic symptoms , depressive disorder , post-traumatic stress disorder ( PTSD ) , and impairment in functioning , among snakebite victims . The study had qualitative and qua...	Snakebite envenoming is a neglected public health problem , especially in rural areas of tropical and sub-tropical countries . Little is known about the long term effects , and even less about the possible psychological effects , of snakebites and envenoming . We investigated the possible psychological impact of snakeb...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "socioeconomic", "aspects", "of", "health", "public", "health", "and", "epidemiology", "mental", "health", "behavioral", "and", "social", "aspects", "of", "health", "global", "health", "anxiety", "disorders", "public", "health", "psychiatry" ]	2011	Delayed Psychological Morbidity Associated with Snakebite Envenoming
Mammalian CST ( CTC1-STN1-TEN1 ) participates in multiple aspects of telomere replication and genome-wide recovery from replication stress . CST resembles Replication Protein A ( RPA ) in that it binds ssDNA and STN1 and TEN1 are structurally similar to RPA2 and RPA3 . Conservation between CTC1 and RPA1 is less apparen...	Mammalian CST ( CTC1/STN1/TEN1 ) is a three protein complex that aids in several steps during telomere replication and has genome-wide roles during recovery from replication fork stalling . Loss of CST leads to abnormalities in telomere structure , genomic instability and defects in chromosome segregation . Currently ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "bonding", "chemical", "characterization", "chromosome", "structure", "and", "function", "anaphase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna-binding", "proteins", "nucleotides", "telomeres", "dna", "replication", "dna", "physica...	2016	STN1 OB Fold Mutation Alters DNA Binding and Affects Selective Aspects of CST Function
The HIV envelope ( Env ) glycoprotein mediates membrane fusion through sequential interactions with CD4 and coreceptors , followed by the refolding of the transmembrane gp41 subunit into the stable 6-helix bundle ( 6HB ) conformation . Synthetic peptides derived from the gp41 C-terminal heptad repeat domain ( C-peptide...	The human immunodeficiency virus ( HIV ) envelope glycoprotein ( Env ) mediates fusion between the viral and cell membranes . The fusion is initiated by Env-receptor interactions and is followed by coreceptor binding and refolding of the transmembrane gp41 subunit . The gp41 refolding proceeds through several distinct ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "virology/host", "invasion", "and", "cell", "entry" ]	2009	Early Steps of HIV-1 Fusion Define the Sensitivity to Inhibitory Peptides That Block 6-Helix Bundle Formation
The role of rodents in Leptospira epidemiology and transmission is well known worldwide . Rats are known to carry different pathogenic serovars of Leptospira spp . capable of causing disease in humans and animals . Wild rats ( Rattus spp . ) , especially the Norway/brown rat ( Rattus norvegicus ) and the black rat ( R ...	The role of rodents in the transmission of many diseases , including leptospirosis , is widely known . Rats abundant in urban and peridomestic environments are the most important reservoirs and sources of Leptospira infection in humans and animals . Leptospirosis is a significant but neglected disease of humans and ani...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion", "Conclusions", "and", "recommendations" ]	[ "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "dynamics", "tropical", "diseases", "microbiology", "vertebrates", "animals", "mammals", "animal"...	2019	Leptospira infection in rats: A literature review of global prevalence and distribution
Tumor cells develop different strategies to cope with changing microenvironmental conditions . A prominent example is the adaptive phenotypic switching between cell migration and proliferation . While it has been shown that the migration-proliferation plasticity influences tumor spread , it remains unclear how this par...	Controlling tumor growth remains a major medical challenge . Current clinical therapies focus on strategies to reduce tumor cell proliferation . However , during tumor progression , tumor cells may switch between proliferative and migratory behaviors , thereby allowing adaptation to microenvironmental changes that resu...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	An Emerging Allee Effect Is Critical for Tumor Initiation and Persistence
Schistosoma japonicum , which remains a major public health problem in the Philippines and mainland China , is the only schistosome species for which zoonotic transmission is considered important . While bovines are suspected as the main zoonotic reservoir in parts of China , the relative contributions of various non-h...	Schistosomiasis is a disease caused by parasitic worms known as schistosomes , which infect about 200 million people worldwide . In the Philippines , as in China , the species of schistosome ( Schistosoma japonicum ) which causes the disease infects not only humans , but also many other species of mammals . In China , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/helminth", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases/epidemiology", "and", "...	2008	Population Genetics of Schistosoma japonicum within the Philippines Suggest High Levels of Transmission between Humans and Dogs
The malaria parasite Plasmodium falciparum has evolved an unusual genome structure . The majority of the genome is relatively stable , with mutation rates similar to most eukaryotic species . However , some regions are very unstable with high recombination rates , driving the generation of new immune evasion-associated...	Human malaria is caused by Plasmodium parasites , with most of the mortality ( almost half a million deaths each year ) being caused by one species , Plasmodium falciparum . This parasite has an unusual genome: it is exceptionally biased towards A and T nucleotides rather than G and C , and it contains specific areas r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "parasite", "groups", "plasmodium", "chromosome", "structure", "and", "function", "enzymes", "enzymology", "cloning", "parasitic", "protozoans", "parasitology", "dna", "transcription", "telomeres", "apicomplexa", "protozoans", "dna", "replication", "dna", "molecular", "bi...	2018	RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics
Chlamydiae are intracellular bacteria that commonly cause infections of the respiratory and genital tracts , which are major clinical problems . Infections are also linked to the aetiology of diseases such as asthma , emphysema and heart disease . The clinical management of infection is problematic and antibiotic resis...	Chlamydial infections are a common cause of respiratory , genital tract and eye diseases , and infections are clinically associated with the aetiology of asthma , emphysema , heart disease and Alzheimer's . However , it is not known what immune factors regulate enhanced susceptibility to infection and immunopathology ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/reproductive", "immunology", "microbiology/immunity", "to", "infections", "respiratory", "medicine/respiratory", "infections", "microbiology/innate", "immunity", "immunology/immunity", "to", "infections", "immunology/innate", "immunity", "respiratory", "medicine/asthma", ...	2011	Interleukin-13 Promotes Susceptibility to Chlamydial Infection of the Respiratory and Genital Tracts
Mammalian sleep varies widely , ranging from frequent napping in rodents to consolidated blocks in primates and unihemispheric sleep in cetaceans . In humans , rats , mice and cats , sleep patterns are orchestrated by homeostatic and circadian drives to the sleep–wake switch , but it is not known whether this system is...	The field of sleep physiology has made huge strides in recent years , uncovering the neurological structures which are critical to sleep regulation . However , given the small number of species studied in such detail in the laboratory , it remains to be seen how universal these mechanisms are across the whole mammalian...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "marine", "and", "aquatic", "sciences/evolutionary", "biology", "biophysics/theory", "and", "simulation", "computational", "biology/computational", "neuroscience", "physiology", "evolutionary", "biology", "computational", "biology/systems", "biology" ]	2010	Mammalian Sleep Dynamics: How Diverse Features Arise from a Common Physiological Framework
Alternative polyadenylation ( APA ) can for example occur when a protein-coding gene has several polyadenylation ( polyA ) signals in its last exon , resulting in messenger RNAs ( mRNAs ) with different 3′ untranslated region ( UTR ) lengths . Different 3′UTR lengths can give different microRNA ( miRNA ) regulation suc...	Variants in DNA that affect gene expression—so-called regulatory variants—are thought to play important roles in common complex diseases , such as cancer . In contrast to variants in protein-coding regions , regulatory variants do not affect protein sequence and function . Instead , regulatory variants affect the amoun...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "expression", "analysis", "rna", "interference", "gene", "regulation", "genome", "analysis", "tools", "molecular", "genetics", "sequence", "analysis", "gene", "expression", "biology", "rna", "processing", "genetics", "g...	2012	Single Nucleotide Polymorphisms Can Create Alternative Polyadenylation Signals and Affect Gene Expression through Loss of MicroRNA-Regulation
Peroxisome proliferator activated receptor gamma 2 ( PPARg2 ) is the nutritionally regulated isoform of PPARg . Ablation of PPARg2 in the ob/ob background , PPARg2−/− Lepob/Lepob ( POKO mouse ) , resulted in decreased fat mass , severe insulin resistance , β-cell failure , and dyslipidaemia . Our results indicate that ...	It is known that obesity is linked to type 2 diabetes , however how obesity causes insulin resistance and diabetes is not well understood . Some extremely obese people are not diabetic , while other less obese people develop severe insulin resistance and diabetes . We believe diabetes occurs when adipose tissue becomes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "nutrition", "diabetes", "and", "endocrinology", "mus", "(mouse)", "molecular", "biology" ]	2007	PPAR gamma 2 Prevents Lipotoxicity by Controlling Adipose Tissue Expandability and Peripheral Lipid Metabolism
Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations . To determine the forces that cause increased evolutionary rates in certain genes , we analyzed alignments of 10 , 238 human genes to their orthologues in...	Regions of the human genome that appear to evolve rapidly may have been under strong positive selection and could contain the genetic changes responsible for the uniqueness of our species . However , neutral ( nonadaptive ) evolutionary processes can give rise to signals that can be mistaken as signs of selection . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2009	Hotspots of Biased Nucleotide Substitutions in Human Genes
Development in the central nervous system is highly dependent on the regulation of the switch from progenitor cell proliferation to differentiation , but the molecular and cellular events controlling this process remain poorly understood . Here , we report that ablation of Crb1 and Crb2 genes results in severe impairme...	Mutations in the human CRB1 gene lead to one of the most severe forms of retinal dystrophies , called Leber congenital amaurosis . Here , we report that ablation of CRB1 and the second family member CRB2 are crucial for proper retinal development . These mice display severe impairment of retinal function , abnormal lam...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Targeted Ablation of Crb1 and Crb2 in Retinal Progenitor Cells Mimics Leber Congenital Amaurosis
Eukaryotic gene expression requires the coordinated action of transcription factors , chromatin remodelling complexes and RNA polymerase . The conserved nuclear protein Akirin plays a central role in immune gene expression in insects and mammals , linking the SWI/SNF chromatin-remodelling complex with the transcription...	When animals are infected , as part of their innate immune response , they switch on defence genes that encode proteins that help fight pathogens . We use the nematode Caenorhabditis elegans to understand the steps in this process . When infected , C . elegans can turn on clusters of antimicrobial peptide genes . We ha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "integumentary", "system", "caenorhabditis", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "animals", "animal", "models", "caenorhabditis", "elegans", "mo...	2018	Evolutionary plasticity in the innate immune function of Akirin
Understanding the binding mode of agonists to adrenergic receptors is crucial to enabling improved rational design of new therapeutic agents . However , so far the high conformational flexibility of G protein-coupled receptors has been an obstacle to obtaining structural information on agonist binding at atomic resolut...	G-protein coupled receptors are the largest family of membrane proteins in the human genome and they constitute the largest class of drug targets . Amongst them , beta adrenergic receptors are involved in the regulation of muscular and vascular tone and are thus molecular targets for the treatment of various diseases i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/theory", "and", "simulation", "biophysics/biomacromolecule-ligand", "interactions", "biochemistry/biomacromolecule-ligand", "interactions", "biochemistry/theory", "and", "simulation", "biophysics/membrane", "proteins", "and", "energy", "transduction", "computational", "bi...	2011	Predicting Novel Binding Modes of Agonists to β Adrenergic Receptors Using All-Atom Molecular Dynamics Simulations
Large-scale insertional mutagenesis screens can be powerful genome-wide tools if they are streamlined with efficient downstream analysis , which is a serious bottleneck in complex biological systems . A major impediment to the success of next-generation sequencing ( NGS ) -based screens for virulence factors is that th...	Insertion mutant screens are widely used to identify genotype–phenotype relationships . In negative selection screens , a major limitation is the efficient identification of mutants that are lost or retained after selection . To identify these mutants , the two genomic sequences flanking the insertion cassette must be ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "methods", "and", "resources", "ustilago", "maydis", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "pathogens", "population", "genetics", "gene", "pool", "fungi", "plant", "science", "mode...	2018	In vivo insertion pool sequencing identifies virulence factors in a complex fungal–host interaction
Glossina fuscipes fuscipes is the major vector of human African trypanosomiasis , commonly referred to as sleeping sickness , in Uganda . In western and eastern Africa , the disease has distinct clinical manifestations and is caused by two different parasites: Trypanosoma brucei rhodesiense and T . b . gambiense . Ugan...	The two types of sleeping sickness in West and East Africa are markedly distinct , require different treatments , and are caused by different parasites . The only country where both parasites are present is Uganda , where they are separated by a narrow 160 km disease-free belt . Because there is no restriction on the m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "genetics", "and", "genomics/population", "genetics", "public", "health", "and", "epidemiology/infectious", "diseases", "evolutionary", "biology/evolutionary", "ecology" ]	2008	High Levels of Genetic Differentiation between Ugandan Glossina fuscipes fuscipes Populations Separated by Lake Kyoga
Borrelia burgdorferi , the spirochetal agent of Lyme disease , is a vector-borne pathogen that cycles between a mammalian host and tick vector . This complex life cycle requires that the spirochete modulate its gene expression program to facilitate growth and maintenance in these diverse milieus . B . burgdorferi conta...	Borrelia burgdorferi is the vector-borne pathogen that causes Lyme disease . It has a complex life cycle that involves growth in a tick vector and a mammalian host — two diverse environments that present B . burgdorferi with alternative carbohydrate sources for support of growth . Previous studies suggested that glycer...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "metabolism", "emerging", "infectious", "diseases", "vector", "biology", "biology", "microbiology", "ticks", "host-pathogen", "interaction", "bacterial", "biochemistry", "bacterial", "pathogens", "microbial", "growth", "and", "development", "pat...	2011	Borrelia burgdorferi Requires Glycerol for Maximum Fitness During The Tick Phase of the Enzootic Cycle
In spite of decades-long studies , the mechanism of morphogenesis of plus-stranded RNA viruses belonging to the genus Enterovirus of Picornaviridae , including poliovirus ( PV ) , is not understood . Numerous attempts to identify an RNA encapsidation signal have failed . Genetic studies , however , have implicated a ro...	Enteroviruses are single , plus-stranded RNA viruses that contain a large number of closely related pathogens . Human enteroviruses cause altogether >3 billion human infections per year , inflicting diseases ranging from benign ( common cold ) to very serious ( poliomyelitis ) . Enterovirus replication has been studied...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2010	Direct Interaction between Two Viral Proteins, the Nonstructural Protein 2CATPase and the Capsid Protein VP3, Is Required for Enterovirus Morphogenesis
Epigenetic research has been focused on cell-type-specific regulation; less is known about common features of epigenetic programming shared by diverse cell types within an organism . Here , we report a modified method for chromatin immunoprecipitation and deep sequencing ( ChIP–Seq ) and its use to construct a high-res...	Just as a genome sequence map is indispensible to genetic studies , an epigenome map is crucial for epigenetic research . This is especially true for a sophisticated genetic model such as Drosophila melanogaster , where the wealth of information on genetics and developmental biology awaits systematic epigenetic interpr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	A High-Resolution Whole-Genome Map of Key Chromatin Modifications in the Adult Drosophila melanogaster
In a study of household contacts ( HHC ) , households were categorized into High ( HT ) and Low ( LT ) transmission groups based on the proportion of HHC with a positive tuberculin skin test . The Mycobacterium tuberculosis ( Mtb ) strains from HT and LT index cases of the households were designated Mtb-HT and Mtb-LT ,...	Mycobacterium tuberculosis ( Mtb ) , the bacteria that causes tuberculosis ( TB ) , is spread through the air from infected patients to their close contacts . In a household contact ( HHC ) study of patients with TB , we found that in some households a larger proportion of contacts were infected with Mtb compared to ot...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods", "Statistics" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "granulomas", "immunology", "tropical", "diseases", "animal", "models", "bacterial", "diseases", "model", "organisms", "signs", "and", "symptoms...	2019	Transmission phenotype of Mycobacterium tuberculosis strains is mechanistically linked to induction of distinct pulmonary pathology
As one of the leading causes of visual impairment and blindness , myopia poses a significant public health burden in Asia . The primary determinant of myopia is an elongated ocular axial length ( AL ) . Here we report a meta-analysis of three genome-wide association studies on AL conducted in 1 , 860 Chinese adults , 9...	Myopic individuals exhibit an increase in ocular axial length ( AL ) . As a highly heritable ocular biometry of refractive error , identification of quantitative trait loci influencing AL variation would be valuable in informing the biological etiology of myopia . We have determined that a genetic locus on chromosome 1...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "ophthalmology", "genetics", "biology", "genetics", "of", "disease", "genetics", "and", "genomics" ]	2012	Genetic Variants on Chromosome 1q41 Influence Ocular Axial Length and High Myopia
CTCF is an essential , ubiquitously expressed DNA-binding protein responsible for insulator function , nuclear architecture , and transcriptional control within vertebrates . The gene CTCF was proposed to have duplicated in early mammals , giving rise to a paralogue called “brother of regulator of imprinted sites” ( BO...	Epigenetic mechanisms heritably change gene expression without altering DNA sequence . Currently , little is known about the evolution of epigenetic traits , and the genes that control them . CTCF is an essential epigenetic regulator that is expressed widely in the tissues of vertebrates and modifies the transcription ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "genetics", "and", "genomics/comparative", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics/medical", "genetics" ]	2008	The Evolution of Epigenetic Regulators CTCF and BORIS/CTCFL in Amniotes
Knowledge of infectious disease burden is necessary to appropriately allocate resources for prevention and control . In Latin America , rabies is among the most important zoonoses for human health and agriculture , but the burden of disease attributed to its main reservoir , the common vampire bat ( Desmodus rotundus )...	The number of cases and monetary cost of a disease guides how resources for prevention and control are allocated . In Latin America , rabies transmitted by vampire bats is one of the most recognized zoonoses affecting humans and livestock , but its burden on lives and livelihoods has been difficult to calculate because...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "livestock", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "peru", "preventive", "medicine", "rabies", "farms", "neglected", "tropical", "diseases", "vaccination", "and", "immunization", ...	2017	Quantifying the burden of vampire bat rabies in Peruvian livestock
The oligodendrocyte density is greater and myelin sheaths are thicker in the adult male mouse brain when compared with females . Here , we show that these sex differences emerge during the first 10 postnatal days , precisely at a stage when a late wave of oligodendrocyte progenitor cells arises and starts differentiati...	Sex differences in brain structure are of great scientific and medical interest because the incidence and progress of many neurological and psychiatric disorders differ between males and females . They affect neural networks and also the myelin sheaths that insulate and protect axons and thus allow the rapid conduction...	[ "Abstract", "Introduction", "Results", "Discussion", "Matherials", "and", "methods" ]	[ "plant", "anatomy", "stem", "anatomy", "medicine", "and", "health", "sciences", "internodes", "nervous", "system", "brain", "neuroscience", "macroglial", "cells", "hormones", "plant", "science", "testosterone", "nerve", "fibers", "research", "and", "analysis", "method...	2017	Long-lasting masculinizing effects of postnatal androgens on myelin governed by the brain androgen receptor
Colonization of the human nose by Staphylococcus aureus in one-third of the population represents a major risk factor for invasive infections . The basis for adaptation of S . aureus to this specific habitat and reasons for the human predisposition to become colonized have remained largely unknown . Human nasal secreti...	Many severe bacterial infections are caused by endogenous pathogens colonizing human body surfaces . Eradication of notorious pathogens such as Staphylococcus aureus from risk patients has become an important preventive strategy . However , efficient decolonization agents are rare , and the living conditions of coloniz...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "genome-wide", "association", "studies", "microbial", "metabolism", "enzymes", "host-pathogen", "interaction", "microbiology", "enzyme", "metabolism", "staphylococci", "microbial", "growth", "and", "development", "bacterial", "pathogens", "microbial", "physiol...	2014	Nutrient Limitation Governs Staphylococcus aureus Metabolism and Niche Adaptation in the Human Nose
As a result of poor economic opportunities and an increasing shortage of affordable housing , much of the spatial growth in many of the world's fastest-growing cities is a result of the expansion of informal settlements where residents live without security of tenure and with limited access to basic infrastructure . Al...	In 2008 , for the first time in human history , more than half of the world's population was living in urban areas , and this proportion is expected to increase . As a result of poor economic opportunities and an increasing shortage of affordable housing , much of the spatial growth in many of the world's fastest growi...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/social", "and", "behavioral", "determinants", "of", "health", "infectious", "diseases/gastrointestinal", "infections", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Informal Urban Settlements and Cholera Risk in Dar es Salaam, Tanzania
Despite environmental , social and ecological dependencies , emergence of zoonotic viruses in human populations is clearly also affected by genetic factors which determine cross-species transmission potential . RNA viruses pose an interesting case study given their mutation rates are orders of magnitude higher than any...	Moving away from genome scan methods used for human GWAS ( ultimately inappropriate for the short highly polymorphic genomes of RNA viruses ) , our work shows the power and potential of multi-class machine learning algorithms in inferring the functional genetic changes associated with phenotypic change ( e . g . crossi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Feature Selection Methods for Identifying Genetic Determinants of Host Species in RNA Viruses
Epithelial cells are a major port of entry for many viruses , but the molecular networks which protect barrier surfaces against viral infections are incompletely understood . Viral infections induce simultaneous production of type I ( IFN-α/β ) and type III ( IFN-λ ) interferons . All nucleated cells are believed to re...	Virus-induced interferon consists of two distinct families of molecules , IFN-α/β and IFN-λ . IFN-α/β family members are key antiviral molecules that confer protection against a large number of viruses infecting a wide variety of cell types . By contrast , IFN-λ responses are largely confined to epithelial cells due to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Leukocyte-Derived IFN-α/β and Epithelial IFN-λ Constitute a Compartmentalized Mucosal Defense System that Restricts Enteric Virus Infections
The objective of this paper is to report evaluated observations from survey records captured through a cross-sectional observational study regarding canine populations and dog owners in rabies enzootic KwaZulu-Natal province , South Africa . Our aim was to evaluate respondent knowledge of canine rabies and response to ...	Canine rabies has been enzootic to KwaZulu-Natal province , South Africa since the mid-1970's . Vaccination requirements for domestic species and animal control laws enforced in industrialized countries frequently eliminate the need for rabies post exposure prophylaxis ( PEP ) when an animal bite occurs . Rabies deaths...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "preventive", "medicine", "infectious", "diseases", "rabies", "veterinary", "diseases", "public", "health", "and", "epidemiology", "veterinary", "epidemiology", "global", "health", "zoonotic", "diseases", "public", "health", "veterinary", "science" ]	2013	Dog Bite Histories and Response to Incidents in Canine Rabies-Enzootic KwaZulu-Natal, South Africa
Antimicrobial peptides play an important role in host defense against microbial pathogens . Their high cationic charge and strong amphipathic structure allow them to bind to the anionic microbial cell membrane and disrupt the membrane bilayer by forming pores or channels . In contrast to the classical pore-forming pept...	In most healthy individuals , the yeast Candida albicans is found within the oral cavity as part of the normal microflora . Though under immunocompromising conditions , this benign microbe can become an opportunistic pathogen causing oral candidiasis ( i . e . thrush ) . Although antifungal drugs are typically efficaci...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/medical", "microbiology", "microbiology/innate", "immunity" ]	2008	The Antimicrobial Peptide Histatin-5 Causes a Spatially Restricted Disruption on the Candida albicans Surface, Allowing Rapid Entry of the Peptide into the Cytoplasm
Successful reproduction is critical to pass genes to the next generation . Seminal proteins contribute to important reproductive processes that lead to fertilization in species ranging from insects to mammals . In Drosophila , the male's accessory gland is a source of seminal fluid proteins that affect the reproductive...	In sexually reproducing organisms , sperm enter the female in combination with seminal proteins that are critical for fertility . These proteins can activate sperm or enhance sperm storage within the female , and can improve the chance that sperm will fertilize eggs . Understanding the action of seminal proteins has po...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "drosophila", "genetics", "and", "genomics", "developmental", "biology" ]	2007	Sustained Post-Mating Response in Drosophila melanogaster Requires Multiple Seminal Fluid Proteins
Categorization is an important cognitive process . However , the correct categorization of a stimulus is often challenging because categories can have overlapping boundaries . Whereas perceptual categorization has been extensively studied in vision , the analogous phenomenon in audition has yet to be systematically exp...	Categorization is an important cognitive process that allows us to simplify , extract meaning from , and respond to objects in the sensory environment . However , categorization is complicated because an object can belong to multiple categories . Thus , to inform our categorical judgments , we must make use of prior in...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "auditory", "system", "cognitive", "neuroscience", "computational", "neuroscience", "psychophysics", "biology", "and", "life", "sciences", "psychoacoustics", "sensory", "perception", "computational", "biology", "sensory", "systems", "neuroscience" ]	2014	Characterizing the Impact of Category Uncertainty on Human Auditory Categorization Behavior
Ribosomal protein L3 is an evolutionarily conserved protein that participates in the assembly of early pre-60S particles . We report that the rpl3[W255C] allele , which affects the affinity and function of translation elongation factors , impairs cytoplasmic maturation of 20S pre-rRNA . This was not seen for other muta...	Recent progress has provided us with detailed knowledge of the structure and function of eukaryotic ribosomes . However , our understanding of the intricate processes of pre-ribosome assembly and the transition to translation-competent ribosomal subunits remains incomplete . The early and intermediate steps of ribosome...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "model", "organisms", "genetics", "biology", "microbiology", "molecular", "cell", "biology" ]	2014	Final Pre-40S Maturation Depends on the Functional Integrity of the 60S Subunit Ribosomal Protein L3
Chronic lung infections in cystic fibrosis ( CF ) patients are composed of complex microbial communities that incite persistent inflammation and airway damage . Despite the high density of bacteria that colonize the lower airways , nutrient sources that sustain bacterial growth in vivo , and how those nutrients are der...	Persistent CF lung infections are composed of hundreds of microbial taxa whose interactions contribute to respiratory failure . Despite their importance , the complex interplay between the lung microbiota and host environment is poorly understood . For example , the nutrients that sustain bacterial growth in vivo , and...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "pathogens", "metabolic", "processes", "microbiology", "pseudomonas", "aeruginosa", "fermentation", "opportunistic", "pathogens", "bacteria", ...	2016	Evidence and Role for Bacterial Mucin Degradation in Cystic Fibrosis Airway Disease
The diversity of life is one of the most striking aspects of our planet; hence knowing how many species inhabit Earth is among the most fundamental questions in science . Yet the answer to this question remains enigmatic , as efforts to sample the world's biodiversity to date have been limited and thus have precluded d...	Knowing the number of species on Earth is one of the most basic yet elusive questions in science . Unfortunately , obtaining an accurate number is constrained by the fact that most species remain to be described and because indirect attempts to answer this question have been highly controversial . Here , we document th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "plant", "science", "ecology", "plant", "biology", "molecular", "biology", "marine", "and", "aquatic", "sciences", "synthetic", "biology", "biology", "marine", "biology", "genetics", "and", "genomics" ]	2011	How Many Species Are There on Earth and in the Ocean?
The chromosome 9p21 ( Chr9p21 ) locus of coronary artery disease has been identified in the first surge of genome-wide association and is the strongest genetic factor of atherosclerosis known today . Chr9p21 encodes the long non-coding RNA ( ncRNA ) antisense non-coding RNA in the INK4 locus ( ANRIL ) . ANRIL expressio...	Chromosome 9p21 is the strongest genetic factor for coronary artery disease and encodes the long non-coding RNA ( ncRNA ) ANRIL . Here , we show that increased ANRIL expression mediates atherosclerosis risk through trans-regulation of gene networks leading to pro-atherogenic cellular properties , such as increased prol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "coronary", "artery", "disease", "medicine", "genome", "expression", "analysis", "cell", "adhesion", "cell", "growth", "gene", "expression", "genetics", "atherosclerosis", "epigenetics", "cardiovascular", "biology", "genomics", "molecular", "cell", "biology", "gene", "n...	2013	Alu Elements in ANRIL Non-Coding RNA at Chromosome 9p21 Modulate Atherogenic Cell Functions through Trans-Regulation of Gene Networks
In principle it appears advantageous for single neurons to perform non-linear operations . Indeed it has been reported that some neurons show signatures of such operations in their electrophysiological response . A particular case in point is the Lobula Giant Movement Detector ( LGMD ) neuron of the locust , which is r...	The tiny brains of insects of about 1mm3 smoothly control a flying platform while avoiding obstacles , regulating its distance to objects and search for objects of interest . This is largely achieved through a complex hierarchical processing of signals from the multitude of ommatidia in their eye to a set of highly spe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "science/natural", "and", "synthetic", "vision", "computational", "biology/synthetic", "biology", "computer", "science/applications", "neuroscience/motor", "systems", "biophysics/theory", "and", "simulation", "computer", "science/systems", "and", "control", "theory"...	2010	Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector
Leprosy is a chronic infectious disease that is caused by the obligate intracellular pathogen Mycobacterium leprae ( M . leprae ) , which is the leading cause of all non-traumatic peripheral neuropathies worldwide . Although both myelinating and non-myelinating Schwann cells are infected by M . leprae in patients with ...	Leprosy is a chronic infectious disease that is caused by the obligate intracellular pathogen Mycobacterium leprae ( M . leprae ) . Leprosy is the leading cause of all non-traumatic peripheral neuropathies worldwide . Both myelinating and non-myelinating Schwann cells are infected by M . leprae in lepromatous leprosy ,...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "cell", "death", "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "pathogens", "cell", "processes", "tropical", "diseases", "macroglial", "cells", "bacterial", "di...	2017	The formation of lipid droplets favors intracellular Mycobacterium leprae survival in SW-10, non-myelinating Schwann cells
X chromosome inactivation ( XCI ) is the mammalian mechanism of dosage compensation that balances X-linked gene expression between the sexes . Early during female development , each cell of the embryo proper independently inactivates one of its two parental X-chromosomes . In mice , the choice of which X chromosome is ...	Although mammalian females have two X chromosomes in each cell , only one is functional , while gene expression from the other is silenced through a process called X chromosome inactivation . Little is known about the early stages of this process including how one parental X chromosome is inactivated over the other on ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Genetic Architecture of Skewed X Inactivation in the Laboratory Mouse
Antibodies against the prion protein PrPC can antagonize prion replication and neuroinvasion , and therefore hold promise as possible therapeutics against prion diseases . However , the safety profile of such antibodies is controversial . It was originally reported that the monoclonal antibody D13 exhibits strong targe...	The human prion disease , Creutzfeldt-Jakob disease ( CJD ) , is a progressive neurodegenerative syndrome . Although far less prevalent , CJD shows many molecular and clinical similarities to Alzheimer's disease , such as the buildup of protein aggregates in the brain and the absence of effective treatments . Many atte...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "animal", "diseases", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "diagnostic", "radiology", "brain", "damage", "immunology", "brain", "neuroscience", "toxicology", "magnet...	2016	Differential Toxicity of Antibodies to the Prion Protein
Proneural genes are among the most early-acting genes in nervous system development , instructing blast cells to commit to a neuronal fate . Drosophila Atonal and Achaete-Scute complex ( AS-C ) genes , as well as their vertebrate orthologs , are basic helix-loop-helix ( bHLH ) transcription factors with such proneural ...	Across the animal kingdom , transcription factors of the basic helix-loop-helix ( bHLH ) family act during embryonic nervous system patterning as proneural genes to promote neuroblast identity . We describe here a distinct function for a specific member of this family , hlh-4 , in the nematode Caenorhabditis elegans . ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "caenorhabditis", "neuronal", "differentiation", "neuroscience", "animals", "cell", "differentiation", "motor", "neurons", "animal", "models", "developmental", "biology", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems"...	2018	Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity
The actin cytoskeleton is a dynamic structure that coordinates numerous fundamental processes in eukaryotic cells . Dozens of actin-binding proteins are known to be involved in the regulation of actin filament organization or turnover and many of these are stimulus-response regulators of phospholipid signaling . One of...	The actin cytoskeleton is a prominent feature of eukaryotes and plays a central role in many essential aspects of their lives . This highly malleable structure responds to a wide range of stimuli with rapid changes in organization or dynamics . These responses are thought to be mediated by dozens of actin-binding prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "signal", "transduction", "molecular", "cell", "biology", "biophysic", "al", "simulations", "biology", "computational", "biology" ]	2012	Structural Insights into the Inhibition of Actin-Capping Protein by Interactions with Phosphatidic Acid and Phosphatidylinositol (4,5)-Bisphosphate
Many existing cohorts contain a range of relatedness between genotyped individuals , either by design or by chance . Haplotype estimation in such cohorts is a central step in many downstream analyses . Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations , we have inv...	Every individual carries two copies of each chromosome ( haplotypes ) , one from each of their parents , that consist of a long sequence of alleles . Modern genotyping technologies do not measure haplotypes directly , but the combined sum ( or genotype ) of alleles at each site . Statistical methods are needed to infer...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "haplotypes", "animal", "genetics", "mathematics", "statistics", "(mathematics)", "genetic", "screens", "genome", "analysis", "gene", "identification", "and", "analysis", "genetic", "association", "studies", "genetics", "biology", ...	2014	A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness
Venereal syphilis is a multi-stage , sexually transmitted disease caused by the spirochetal bacterium Treponema pallidum ( Tp ) . Herein we describe a cohort of 57 patients ( age 18–68 years ) with secondary syphilis ( SS ) identified through a network of public sector primary health care providers in Cali , Colombia ....	Venereal syphilis is a sexually transmitted disease caused by the bacterium Treponema pallidum ( Tp ) . We describe 57 patients ( age 18–68 years ) from Cali , Colombia diagnosed with secondary syphilis ( SS ) . Most were women ( 64 . 9% ) ; predominantly Afro-Colombian ( 38 . 6% ) or mestizo ( 56 . 1% ) , and all of l...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/sexually", "transmitted", "diseases" ]	2010	Secondary Syphilis in Cali, Colombia: New Concepts in Disease Pathogenesis
Small interfering RNAs regulate gene expression in diverse biological processes , including heterochromatin formation and DNA elimination , developmental regulation , and cell differentiation . In the single-celled eukaryote Entamoeba histolytica , we have identified a population of small RNAs of 27 nt size that ( i ) ...	Regulation of gene expression can occur via multiple conserved pathways . One such mechanism is mediated by RNA molecules of about 21–24 nucleotides ( called small RNAs ) , which can affect rates of RNA degradation or protein production . These small RNA molecules regulate diverse biological processes in a broad range ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "infectious", "diseases/neglected", "tropical", "diseases", "molecular", "biology/mrna", "stability", "molecular", "biology", "microbiology", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "infectio...	2008	Small RNAs with 5′-Polyphosphate Termini Associate with a Piwi-Related Protein and Regulate Gene Expression in the Single-Celled Eukaryote Entamoeba histolytica
Metazoan genomes encode hundreds of RNA-binding proteins ( RBPs ) . These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing , export , stability and translation . Despite their ubiquity and importance , the binding preferences for most ...	Many disease-associated mutations do not change the protein sequence of genes; instead they change the instructions on how a gene's mRNA transcript should be processed . Translating these instructions allows us to better understand the connection between these mutations and disease . RNA-binding proteins ( RBP ) perfor...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "molecular", "biology/rna-protein", "interactions", "computational", "biology/sequence", "motif", "analysis" ]	2010	RNAcontext: A New Method for Learning the Sequence and Structure Binding Preferences of RNA-Binding Proteins
Hepatitis D virus ( HDV ) is the smallest virus known to infect human . About 15 million people worldwide are infected by HDV among those 240 million infected by its helper hepatitis B virus ( HBV ) . Viral hepatitis D is considered as one of the most severe forms of human viral hepatitis . No specific antivirals are c...	Currently 15 million people worldwide are infected by hepatitis D virus ( HDV ) . HDV is the smallest virus known to infect human . With co-infection of its helper hepatitis B virus ( HBV ) , viral hepatitis D is considered as the most severe form of viral hepatitis . No specific anti-HDV drugs are available; antiviral...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Hepatitis D Virus Infection of Mice Expressing Human Sodium Taurocholate Co-transporting Polypeptide
Notch ( N ) signaling is central to the self-renewal of neural stem cells ( NSCs ) and other tissue stem cells . Its deregulation compromises tissue homeostasis and contributes to tumorigenesis and other diseases . How N regulates stem cell behavior in health and disease is not well understood . Here we show that N reg...	Stem cells are functional units in the development , maintenance , and regeneration of tissues in multicellular organisms . Defects in stem cell regulation can compromise tissue homeostasis and result in proliferative or degenerative diseases . Our understanding of the molecular and cellular mechanisms regulating the i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "rna", "interference", "mechanisms", "of", "signal", "transduction", "gene", "regulation", "cloning", "animals", "animal", "models", "physiological", "processes", "micrornas", "model", "organisms", "drosophila", ...	2017	The bantam microRNA acts through Numb to exert cell growth control and feedback regulation of Notch in tumor-forming stem cells in the Drosophila brain
The evolution of heteromorphic sex chromosomes has repeatedly resulted in the evolution of sex chromosome-specific forms of regulation , including sex chromosome dosage compensation in the soma and meiotic sex chromosome inactivation in the germline . In the male germline of Drosophila melanogaster , a novel but poorly...	The evolution of different sex chromosomes ( e . g . , X and Y ) has occurred many times in animals and plants . One consequence of having different chromosome copy numbers between the sexes ( XY males and XX females ) is the evolution of sex chromosome-specific regulation , both in the soma ( i . e . , X chromosome do...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequencing", "techniques", "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "animals", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "x-linked", "traits", "sequence", "motif", "analysis", "molecular", "biology"...	2016	Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline
Mutations in the gene encoding transcription factor TFAP2A result in pigmentation anomalies in model organisms and premature hair graying in humans . However , the pleiotropic functions of TFAP2A and its redundantly-acting paralogs have made the precise contribution of TFAP2-type activity to melanocyte differentiation ...	Identifying the elements and structure of the gene regulatory network governing melanocyte differentiation may yield insight into the mechanisms of pigmentation diseases and melanoma progression . Pigmentation is abnormal in Tfap2a mutants , but deciphering the exact role of TFAP2A in the network has been complicated b...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "cancers", "and", "neoplasms", "vertebrates", "neuroscience", "animals", "epithelial", "cells", "animal", "models", "osteichthyes", "oncology", "developmental", "biology", "model", "organisms", "stem", "cell...	2017	TFAP2 paralogs regulate melanocyte differentiation in parallel with MITF
Resistance-nodulation-division ( RND ) efflux systems are ubiquitous transporters in Gram-negative bacteria that are essential for antibiotic resistance . The RND efflux systems also contribute to diverse phenotypes independent of antimicrobial resistance , but the mechanism by which they affect most of these phenotype...	Multidrug efflux systems belonging to the RND superfamily contribute to the expression of diverse phenotypes in Gram-negative bacteria , but the mechanisms linking RND efflux to these phenotypes is unclear . Herein , we provide evidence suggesting that the V . cholerae RND systems influence global transcription pattern...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "gene", "regulation", "pathogens", "vibrio", "microbiology", "carbohydrates", "cell", "metabolism", "organic",...	2018	The Vibrio cholerae RND efflux systems impact virulence factor production and adaptive responses via periplasmic sensor proteins
During blood feeding , sand flies inject Leishmania parasites in the presence of saliva . The types and functions of cells present at the first host-parasite contact are critical to the outcome on infection and sand fly saliva has been shown to play an important role in this setting . Herein , we investigated the in vi...	Transmission of Leishmania parasites occurs during blood feeding , when infected female sand flies inject humans with parasites and saliva . Chemokines and cytokines are secreted proteins that regulate the initial immune responses and have the potential of attracting and activating cells . Herein , we studied the expre...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "immunology/immunomodulation", "immunology/immune", "response", "immunology/immunity", "to", "infections" ]	2010	Immunity to Lutzomyia intermedia Saliva Modulates the Inflammatory Environment Induced by Leishmania braziliensis
Hookworm disease is one of the most common infections and cause of a high disease burden in the tropics and subtropics . Remotely sensed ecological data and model-based geostatistics have been used recently to identify areas in need for hookworm control . Cross-sectional interview data and stool samples from 6 , 375 pa...	Hookworm disease , caused by the nematodes Ancylostoma duodenale and Necator americanus , is an important cause of maternal and child morbidity in the developing countries of the tropics and subtropics . In children , hookworm disease has been shown to potentially result in growth retardation as well as intellectual an...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "global", "health", "infectious", "disease", "epidemiology", "epidemiology" ]	2013	Hookworm Infection and Environmental Factors in Mbeya Region, Tanzania: A Cross-Sectional, Population-Based Study
Virus satellites are widespread subcellular entities , present both in eukaryotic and in prokaryotic cells . Their modus vivendi involves parasitism of the life cycle of their inducing helper viruses , which assures their transmission to a new host . However , the evolutionary and ecological implications of satellites ...	Satellites are defined as viruses that have a life cycle dependent on a helper virus . Thus , they can be considered as parasites of parasites . In addition to their fascinating life cycle , these widespread infectious elements , present both in eukaryotic and prokaryotic cells , have a dramatic role in virulence by co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Virus Satellites Drive Viral Evolution and Ecology
Proteolytic processing is an irreversible posttranslational modification affecting a large portion of the proteome . Protease-cleaved mediators frequently exhibit altered activity , and biological pathways are often regulated by proteolytic processing . Many of these mechanisms have not been appreciated as being protea...	Proteases modify the structure and activity of all proteins by peptide bond hydrolysis and are increasingly recognized as integral regulatory components of numerous biological mechanisms . Deregulated protease activity is a common characteristic of many diseases . However , protease drug development is complicated by a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "metabolism", "protein", "interactions", "regulatory", "proteins", "signaling", "networks", "animal", "models", "model", "organisms", "network", "analysis", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "proteins", "r...	2014	Network Analyses Reveal Pervasive Functional Regulation Between Proteases in the Human Protease Web
The down-regulation of the tumor-suppressor gene RASSF1A has been shown to increase cell proliferation in several tumors . RASSF1A expression is regulated through epigenetic events involving the polycomb repressive complex 2 ( PRC2 ) ; however , the molecular mechanisms modulating the recruitment of this epigenetic mod...	RASSF1A is a tumor suppressor gene whose expression is repressed through epigenetic events in a wide range of different cancers . Repression is effected by DNA hypermethylation of the RASSF1A promoter , which in turn is triggered through histone H3K9/H3K27 trimethylation repressive marks . The addition of the H3K27me3 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "nucleic", "acids", "gene", "expression", "genetics", "gene", "regulation", "epigenetics", "molecular", "genetics", "biology", "dna", "modification", "chromatin", "dna", "transcription", "histone", "modification" ]	2013	The Intronic Long Noncoding RNA ANRASSF1 Recruits PRC2 to the RASSF1A Promoter, Reducing the Expression of RASSF1A and Increasing Cell Proliferation
The sex chromosomes are enriched with germline genes that are activated during the late stages of spermatogenesis . Due to meiotic sex chromosome inactivation ( MSCI ) , these sex chromosome-linked genes must escape silencing for activation in spermatids , thereby ensuring their functions for male reproduction . RNF8 ,...	To produce unimpaired sperm , precise activation of germline-specific genes is an essential step during the late stages of spermatogenesis . However , sex chromosomes carrying these genes become silenced in a chromosome-wide manner during meiosis in a process called meiotic sex chromosome inactivation . Sex chromosome ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "meiosis", "spermatocytes", "cell", "cycle", "and", "cell", "division", "cell", "processes", "germ", "cells", "animal", "models", "model", "organisms", "experimental", "organism", "systems", "sperm", "research", "and", "analysis", "methods", "specimen", "preparation",...	2018	RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes

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