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Metformin is used as a first-line therapy for type 2 diabetes ( T2D ) and prescribed for numerous other diseases . However , its mechanism of action in the liver has yet to be characterized in a systematic manner . To comprehensively identify genes and regulatory elements associated with metformin treatment , we carrie...	Metformin is among the most widely prescribed drugs . It is used as a first line therapy for type 2 diabetes ( T2D ) , and for additional diseases including cancer . The variability in response to metformin is substantial and can be caused by genetic factors . However , the molecular mechanisms of metformin action are ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "liver", "evolutionary", "biology", "gene", "regulation", "regulatory", "proteins", "population", "genetics", "dna-binding", "proteins", "regulator", "genes", "genome", "analysis", "transcri...	2016	Genomic Characterization of Metformin Hepatic Response
DNA methylation changes dynamically during development and is essential for embryogenesis in mammals . However , how DNA methylation affects developmental gene expression and cell differentiation remains elusive . During embryogenesis , many key transcription factors are used repeatedly , triggering different outcomes ...	Animal bodies are constructed from many different specialized cell types that are generated during embryogenesis from a single fertilized egg , and acquire their specific characteristics through a series of differentiation steps . After being committed to a specific cell type , it is generally difficult for differentia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "fate", "determination", "cell", "potency", "stem", "cells", "embryonic", "stem", "cells", "gene", "expression", "genetics", "epigenetics", "biology", "dna", "modification", "cell", "differentiation", "dna", "transcription" ]	2013	DNA Methylation Restricts Lineage-specific Functions of Transcription Factor Gata4 during Embryonic Stem Cell Differentiation
Guatemala is presently engaged in the Central America Initiative to interrupt Chagas disease transmission by reducing intradomiciliary prevalence of Triatoma dimidiata , using targeted cross-sectional surveys to direct control measures to villages exceeding the 5% control threshold . The use of targeted surveys to guid...	Chagas disease is a vector-borne parasitic zoonosis endemic throughout South and Central America and Mexico . Guatemala is engaged in the Central America Initiative to interrupt Chagas disease transmission . A major strategy is the reduction of Triatoma dimidiata domiciliary infestations through indoor application of r...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/global", "health", "public", "health", "and", "epidemiology/infectious", "diseases", "ecology/spatial", "and", "landsca...	2011	Triatoma dimidiata Infestation in Chagas Disease Endemic Regions of Guatemala: Comparison of Random and Targeted Cross-Sectional Surveys
Circadian ( daily ) rhythms are a fundamental and ubiquitous property of eukaryotic organisms . However , cyanobacteria are the only prokaryotic group for which bona fide circadian properties have been persuasively documented , even though homologs of the cyanobacterial kaiABC central clock genes are distributed widely...	Circadian ( daily ) rhythms are an adaptation of organisms to the dramatic changes in the environment over day and night , and they are defined by properties that include rhythmic persistence in constant conditions and temperature compensation . These "biological clocks" are practically ubiquitous in eukaryotes , but i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "plant", "physiology", "circadian", "oscillators", "plant", "science", "chronobiology", "evolutionary", "adaptation", "bacteria", "proteins", "prokaryotic", "cells", "cyanobacteria", "circadian", "rhythms", "biochemistry", "nitrogen", "fixation", "cell", ...	2016	Evolution of KaiC-Dependent Timekeepers: A Proto-circadian Timing Mechanism Confers Adaptive Fitness in the Purple Bacterium Rhodopseudomonas palustris
To form functional neuronal connections , axon outgrowth and guidance must be tightly regulated across space as well as time . While a number of genes and pathways have been shown to control spatial features of axon development , very little is known about the in vivo mechanisms that direct the timing of axon initiatio...	During development , nerve cells extend long structures called axons which are required for communication across distant brain regions and/or with other tissues . Many of the signals controlling the direction of axon extension are well understood , but much less is known about the factors that control when this growth ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "function", "developmental", "biology/neurodevelopment" ]	2010	A Developmental Timing Switch Promotes Axon Outgrowth Independent of Known Guidance Receptors
RNA-dependent RNA polymerases ( RdRps ) play a key role in the life cycle of RNA viruses and impact their immunobiology . The arenavirus lymphocytic choriomeningitis virus ( LCMV ) strain Clone 13 provides a benchmark model for studying chronic infection . A major genetic determinant for its ability to persist maps to ...	RNA-dependent RNA-polymerases ( RdRps ) play a key role in the life cycle of RNA viruses . They interact with cellular proteins during replication and transcription processes and impact the immunobiology of viral infections . This study characterized the host protein interactome of the RdRp-containing L protein of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "protein", "interactions", "pathology", "and", "laboratory", "medicine", "microbiology", "viruses", "rna", "viruses", "immunoprecipitation", "co-immunoprecipitation", "molecular", "biology", "techniques", "protein", "interactomes", "...	2017	Characterization of host proteins interacting with the lymphocytic choriomeningitis virus L protein
With new cases of avian influenza H5N1 ( H5N1AV ) arising frequently , the threat of a new influenza pandemic remains a challenge for public health . Several vaccines have been developed specifically targeting H5N1AV , but their production is limited and only a few million doses are readily available . Because there is...	In the past , the emergence of new strains of influenza has been sometimes responsible for large and deadly pandemics . With a very high mortality rate , ( i . e . , about 60% of the reported cases ) , H5N1AV influenza , commonly known as bird flu , is thought to be an important potential threat for a new pandemic . Be...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "computer", "science", "mathematics" ]	2013	Optimal Vaccine Allocation for the Early Mitigation of Pandemic Influenza
Proopiomelanocortin ( POMC ) neurons in the arcuate nucleus of the hypothalamus ( ARC ) respond to numerous hormonal and neural signals , resulting in changes in food intake . Here , we demonstrate that ARC POMC neurons express capsaicin-sensitive transient receptor potential vanilloid 1 receptor ( TRPV1 ) -like recept...	Intense exercise acutely decreases appetite and subsequent food intake . As exercise is accompanied by increased body temperature , we hypothesized that a rise in body temperature during exercise plays a role in reducing food intake . The hypothalamic neurons are major components of the neural circuits that control fee...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "depolarization", "membrane", "potential", "brain", "electrophysiology", "neuroscience", "animal", "models", "arcuate", "nucleus", "receptor", "potentials", "model", "organisms", "physiological", "parameter...	2018	Activation of temperature-sensitive TRPV1-like receptors in ARC POMC neurons reduces food intake
Human breast cancer susceptibility gene , BRCA2 , encodes a 3418-amino acid protein that is essential for maintaining genomic integrity . Among the proteins that physically interact with BRCA2 , Partner and Localizer of BRCA2 ( PALB2 ) , which binds to the N-terminal region of BRCA2 , is vital for its function by facil...	Inheritance of a deleterious mutation in Breast Cancer2 ( BRCA2 ) is a well-established factor associated with increased risk of hereditary breast and ovarian cancers . BRCA2 has numerous roles in maintaining the genome to prevent accumulation of mutations that can lead to cancer formation . Here , we describe the gene...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cancer", "genomics", "medicine", "and", "health", "sciences", "genetic", "networks", "osteosarcoma", "cancers", "and", "neoplasms", "basic", "cancer", "research", "animal", "models", "oncology", "hematologic", "cancers", "and", "related", "disorders", "germ", "cells"...	2016	Interaction with PALB2 Is Essential for Maintenance of Genomic Integrity by BRCA2
Pathogens hide immunogenic epitopes from the host to evade immunity , persist and cause infection . The opportunistic human fungal pathogen Candida albicans , which can cause fatal disease in immunocompromised patient populations , offers a good example as it masks the inflammatory epitope β-glucan in its cell wall fro...	Opportunistic fungal infections , including those caused by C . albicans , have emerged as a significant global health burden and the disseminated form of these infections still have unacceptably high mortality rates despite modern antifungal treatments . The fungal cell wall controls its interaction with the host envi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "cell", "walls", "chitin", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "fungi", "model", "organisms", "microscopy", "materials", "science", "cell...	2016	Neutrophil Attack Triggers Extracellular Trap-Dependent Candida Cell Wall Remodeling and Altered Immune Recognition
The chromosomes of eukaryotes are organized into structurally and functionally discrete domains . This implies the presence of insulator elements that separate adjacent domains , allowing them to maintain different chromatin structures . We show that the Fun30 chromatin remodeler , Fft3 , is essential for maintaining a...	Active and inactive chromatin domains are often juxtaposed along the chromosome arms , and this demands mechanisms that separate them apart . This is performed by insulators that block the spreading of chromatin domains beyond their natural borders . Here , we show that an ATP-dependent chromatin remodeler , Fission ye...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/chromosome", "biology", "genetics", "and", "genomics/epigenetics", "genetics", "and", "genomics", "cell", "biology/gene", "expression" ]	2011	The FUN30 Chromatin Remodeler, Fft3, Protects Centromeric and Subtelomeric Domains from Euchromatin Formation
Whether mutations in bacteria exhibit a noticeable delay before expressing their corresponding mutant phenotype was discussed intensively in the 1940s to 1950s , but the discussion eventually waned for lack of supportive evidence and perceived incompatibility with observed mutant distributions in fluctuation tests . Ph...	What is the time delay between the occurrence of a genetic mutation in a bacterial cell and manifestation of its phenotypic effect ? We show that antibiotic resistance mutations in Escherichia coli show a remarkably long phenotypic delay of three to four bacterial generations . The primary underlying mechanism of this ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "microbial", "mutation", "cell", "cycle", "and", "cell", "division", "drugs", "population", "genetics", "ploidy", "microbiology", "cell", "processes", "departures", "from", "diploidy", "antibiotic", "resistance"...	2018	Effective polyploidy causes phenotypic delay and influences bacterial evolvability
Allele frequency differences across populations can provide valuable information both for studying population structure and for identifying loci that have been targets of natural selection . Here , we examine the relationship between recombination rate and population differentiation in humans by analyzing two uniformly...	A common assumption when analyzing patterns of human genetic variation is that most of the genome can be treated as “nearly neutral , ” in the sense that the effects of natural selection on allele frequencies are very small compared with the influence of population demographic history . To test the validity of this ass...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "computational", "biology/population", "genetics", "genetics", "and", "genomics/population", "genetics" ]	2010	Human Population Differentiation Is Strongly Correlated with Local Recombination Rate
Recent studies have shown significant decline in the final cure rate after miltefosine treatment in visceral leishmaniasis . This study evaluates the efficacy of miltefosine in the treatment of post kala-azar dermal leishmaniasis ( PKDL ) patients recruited over a period of 5 years with 18 months of follow-up . In this...	Increasing resistance to antimonials has paved the way for the oral drug miltefosine for PKDL treatment . Recent studies show a significant decline in the final cure rate of VL after miltefosine treatment in the Indian subcontinent . This is the first study to evaluate the efficacy of miltefosine treatment in a large n...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Decline in Clinical Efficacy of Oral Miltefosine in Treatment of Post Kala-azar Dermal Leishmaniasis (PKDL) in India
Microarray comparative genomic hybridisation ( aCGH ) provides an estimate of the relative abundance of genomic DNA ( gDNA ) taken from comparator and reference organisms by hybridisation to a microarray containing probes that represent sequences from the reference organism . The experimental method is used in a number...	We describe the first use of a method for the analysis of bacterial microarray comparative genomic hybridisation ( aCGH ) that includes information about the spatial organisation of genes in the reference bacterium . We demonstrate that using this information improves predictive performance over standard bacterial aCGH...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/genomics", "plant", "biology/plant-biotic", "interactions", "computational", "biology/comparative", "sequence", "analysis", "microbiology/microbial", "evolution", "and", "genomics", "computational", "biology/genomics" ]	2009	Microarray Comparative Genomic Hybridisation Analysis Incorporating Genomic Organisation, and Application to Enterobacterial Plant Pathogens
The consolidation of scientific knowledge proceeds through the interpretation and then distillation of data presented in research reports , first in review articles and then in textbooks and undergraduate courses , until truths become accepted as such both amongst “experts” and in the public understanding . Where data ...	Publication bias is known to be a major problem in the reporting of clinical trials , but its impact in basic research has not previously been quantified . Here we show that publication bias is prevalent in reports of laboratory-based research in animal models of stroke , such that data from as many as one in seven exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "neurological", "disorders" ]	2010	Publication Bias in Reports of Animal Stroke Studies Leads to Major Overstatement of Efficacy
The existence of the ocular microbiota has been reported but functional analyses to evaluate its significance in regulating ocular immunity are currently lacking . We compared the relative contribution of eye and gut commensals in regulating the ocular susceptibility to Pseudomonas aeruginosa–induced keratitis . We fin...	Contact lens wear is associated with frequent Pseudomonas aeruginosa–induced keratitis , however the reasons for this association remain unclear . Recent genomics–based approaches revealed that contact lens wearers harbor altered ocular commensal communities when compared to non-lens wearers raising important questions...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "antimicrobials", "medicine", "and", "health", "sciences", "immune", "cells", "microbiome", "pathology", "and", "laboratory", "medicine", "keratitis", "pathogens", "drugs", "immunology", "ocular", "anatomy", "microbiology", "pseudomonas", "aeruginosa", ...	2016	Impact of Microbiota on Resistance to Ocular Pseudomonas aeruginosa-Induced Keratitis
Cancer is an evolutionary process in which cells acquire new transformative , proliferative and metastatic capabilities . A full understanding of cancer requires learning the dynamics of the cancer evolutionary process . We present here a large-scale analysis of the dynamics of this evolutionary process within tumors ,...	Cancer is a short-term evolutionary process that occurs within our bodies . Here , we demonstrate that the cancer evolutionary process differs greatly from other evolutionary processes . Most evolutionary processes are dominated by purifying selection ( that removes harmful mutations ) . In contrast , in cancer evoluti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "organismal", "evolution", "cancer", "genetics", "breast", "tumors", "genome", "evolution", "human", "evolution", "population", "genetics", "evolutionary", "selection", "computational", "biology", "cancers", "and", "neoplasms", "basic", "cancer", "research", ...	2014	Cancer Evolution Is Associated with Pervasive Positive Selection on Globally Expressed Genes
Scientific analysis often relies on the ability to make accurate predictions of a system’s dynamics . Mechanistic models , parameterized by a number of unknown parameters , are often used for this purpose . Accurate estimation of the model state and parameters prior to prediction is necessary , but may be complicated b...	The question of how best to predict the evolution of a dynamical system has received substantial interest in the scientific community . While traditional mechanistic modeling approaches have dominated , data-driven approaches which rely on data to build predictive models have gained increasing popularity . The reality ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results" ]	[ "invertebrates", "neural", "networks", "random", "variables", "neuroscience", "animals", "covariance", "developmental", "biology", "systems", "science", "mathematics", "forecasting", "statistics", "(mathematics)", "pupae", "research", "and", "analysis", "methods", "computer...	2017	Hybrid modeling and prediction of dynamical systems
The treatment of schistosomiasis , a disease caused by blood flukes parasites of the Schistosoma genus , depends on the intensive use of a single drug , praziquantel , which increases the likelihood of the development of drug-resistant parasite strains and renders the search for new drugs a strategic priority . Current...	Schistosomiasis , a neglected parasitic disease caused by flatworms of the genus Schistosoma , is responsible for hundreds of thousands of deaths yearly . Its treatment currently depends on a single drug , praziquantel , with reports of drug-resistant parasites . Human epigenetic enzymes , in particular histone deacety...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Structural Basis for the Inhibition of Histone Deacetylase 8 (HDAC8), a Key Epigenetic Player in the Blood Fluke Schistosoma mansoni
Diversification of antiretroviral factors during host evolution has erected formidable barriers to cross-species retrovirus transmission . This phenomenon likely protects humans from infection by many modern retroviruses , but it has also impaired the development of primate models of HIV-1 infection . Indeed , rhesus m...	Retroviruses such as HIV-1 often exhibit limited capacity to infect species other than their natural hosts . This phenomenon is partly due to the existence of antiviral proteins that protect against infection by viruses that have not adapted to a particular species . For example , the resistance of rhesus macaques , th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Assisted Evolution Enables HIV-1 to Overcome a High TRIM5α-Imposed Genetic Barrier to Rhesus Macaque Tropism
UBC9 , the sole E2-conjugating enzyme required for SUMOylation , is a key regulator of essential cellular functions and , as such , is frequently altered in cancers . Along these lines , we recently reported that its expression gradually increases during early stages of human papillomavirus ( HPV ) -mediated cervical l...	High risk HPV is the primary cause of cervical cancer and in recent years a clear role for the virus in other anogenital malignancies , in head and neck and in nonmelanoma skin cancers is emerging . Cellular transformation is mediated by the viral oncoproteins E6 and E7 that have the ability to target several pathways ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "death", "medicine", "and", "health", "sciences", "autophagic", "cell", "death", "lysosomes", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "pathogens", "cell", "processes", "microbiology", "viruses", "oncology", "sumoylation", "dna", "vi...	2017	Autophagy regulates UBC9 levels during viral-mediated tumorigenesis
Cognitive self-regulation can strongly modulate pain and emotion . However , it is unclear whether self-regulation primarily influences primary nociceptive and affective processes or evaluative ones . In this study , participants engaged in self-regulation to increase or decrease pain while experiencing multiple levels...	Does cognitive self-regulation influence pain experience by affecting the primary representations of painful ( nociceptive ) stimuli in the brain ? Or does it regulate reported pain via a neural pathway that is distinct from the one that mediates nociceptive pain ? The present study demonstrates that nociceptive and co...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "pain", "psychology", "cognitive", "neuroscience", "psychology", "medicine", "and", "health", "sciences", "pain", "management", "biology", "and", "life", "sciences", "neuroscience" ]	2015	Distinct Brain Systems Mediate the Effects of Nociceptive Input and Self-Regulation on Pain
Gene therapy represents an alternative and promising anti-HIV modality to highly active antiretroviral therapy . It involves the introduction of a protective gene into a cell , thereby conferring protection against HIV . While clinical trials to date have delivered gene therapy to CD4+T cells or to CD34+ hematopoietic ...	HIV infects and depletes the body's immune cells ( CD4+T cells ) , and if untreated results in Acquired Immunodeficiency Syndrome ( AIDS ) and mortality approximately 10 years after initial infection . To protect the host against HIV induced immune depletion , either the main target cells ( CD4+T cells ) or the stem ce...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "immune", "cells", "applied", "mathematics", "immunology", "microbiology", "immunodeficiency", "viruses", "mathematics", "infectious", "diseases", "theoretical", "biology", "animal", "cells", "medical", "microbiology...	2014	A Quantitative Comparison of Anti-HIV Gene Therapy Delivered to Hematopoietic Stem Cells versus CD4+ T Cells
Striatal projection neurons form a sparsely-connected inhibitory network , and this arrangement may be essential for the appropriate temporal organization of behavior . Here we show that a simplified , sparse inhibitory network of Leaky-Integrate-and-Fire neurons can reproduce some key features of striatal population a...	Neuronal networks that are loosely coupled by inhibitory connections can exhibit potentially useful properties . These include the ability to produce slowly-changing activity patterns , that could be important for organizing actions and thoughts over time . The striatum is a major brain structure that is critical for a...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "action", "potentials", "medicine", "and", "health", "sciences", "neural", "networks", "neurodegenerative", "diseases", "membrane", "potential", "genetic", "diseases", "electrophysiology", "neuroscience", "animal", "models", "model", "organisms", "computational", "neuroscie...	2016	Cell Assembly Dynamics of Sparsely-Connected Inhibitory Networks: A Simple Model for the Collective Activity of Striatal Projection Neurons
Cellular junctions are crucial for the formation of multicellular organisms , where they anchor cells to each other and/or supportive tissue and enable cell-to-cell communication . Some unicellular organisms , such as the parasitic protist Trypanosoma brucei , also have complex cellular junctions . The flagella connect...	Trypanosoma brucei is an uni-cellular parasite transmitted to humans and cattle by the bloodsucking tsetse fly . Once swimming in the mammalian bloodstream , it causes the devastating African sleeping sickness in humans and nagana in cattle . During its complex life cycle , it undergoes many cell shape changes , which ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "classical", "mechanics", "pathology", "and", "laboratory", "medicine", "microtubules", "diagnostic", "radiology", "engineering", "and", "technology", "built", "structures", "pathogens", "cell", "cycle", "and", "cell", "division"...	2016	3D Architecture of the Trypanosoma brucei Flagella Connector, a Mobile Transmembrane Junction
Understanding the core set of genes that are necessary for basic developmental functions is one of the central goals in biology . Studies in model organisms identified a significant fraction of essential genes through the analysis of null-mutations that lead to lethality . Recent large-scale next-generation sequencing ...	Essential genes are necessary for fundamental processes in an organism and lead to pre- or neonatal lethality when disrupted . In this work , we characterize 2 , 472 human orthologs of mouse essential genes in terms of their evolutionary and population genetics properties using data from recent deep sequencing initiati...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "mutation", "genome", "evolution", "population", "genetics", "computational", "biology", "gene", "function", "genome", "sequencing", "mutation", "mutation", "types", "genetic", "polymorphism", "biology", "evolutionary", "genetics", "mutagenesis", "natural", "se...	2013	From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes
Comparing the gene-expression profiles of sick and healthy individuals can help in understanding disease . Such differential expression analysis is a well-established way to find gene sets whose expression is altered in the disease . Recent approaches to gene-expression analysis go a step further and seek differential ...	The most fundamental and popular gene-expression experiments measure genome-wide transcription levels in two populations: perturbed and wild type , or cases and controls . The genes that show significantly different expression between the two populations ( the differentially expressed genes ) are useful for understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology" ]	2013	Dissection of Regulatory Networks that Are Altered in Disease via Differential Co-expression
Respiratory syncytial virus ( RSV ) infection is the leading viral cause of severe lower respiratory tract illness in young infants . Clinical studies have documented that certain polymorphisms in the gene encoding the regulatory cytokine IL-10 are associated with the development of severe bronchiolitis in RSV infected...	IL-10 is a major anti-inflammatory protein that plays an essential role in regulating the balance between pathogen clearance by the immune response and immune mediated injury resulting from the immune response to pathogen infection . In this report , we demonstrate that anti-viral effector T cells , a critical cell typ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "medicine", "infectious", "diseases", "virology", "immunology", "biology", "microbiology", "viral", "diseases", "immunomodulation", "immune", "response" ]	2011	Autocrine Regulation of Pulmonary Inflammation by Effector T-Cell Derived IL-10 during Infection with Respiratory Syncytial Virus
The largest gaps in the human genome assembly correspond to multi-megabase heterochromatic regions composed primarily of two related families of tandem repeats , Human Satellites 2 and 3 ( HSat2 , 3 ) . The abundance of repetitive DNA in these regions challenges standard mapping and assembly algorithms , and as a resul...	At least 5–10% of the human genome remains unassembled , unmapped , and poorly characterized . The reference assembly annotates these missing regions as multi-megabase heterochromatic gaps , found primarily near centromeres and on the short arms of the acrocentric chromosomes . This missing fraction of the genome consi...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "algorithms", "computer", "and", "information", "sciences", "mathematics", "genetics", "applied", "mathematics", "biology", "and", "life", "sciences", "population", "biology", "computing", "methods", "genomics", "computerized", "simulations", "physical", "sciences", "comp...	2014	Genomic Characterization of Large Heterochromatic Gaps in the Human Genome Assembly
Schistosoma japonicum is a parasitic flatworm that causes human schistosomiasis , which is a significant cause of morbidity in China and the Philippines . A single draft genome was available for S . japonicum , yet this assembly is very fragmented and only covers 90% of the genome , which make it difficult to be applie...	Schistosomiasis is an acute and chronic disease that remains one of the most prevalent and serious of the parasitic diseases in the world . Three major Schistosoma species cause human schistosomiasis , including Schistosoma japonicum , S . mansoni and S . haematobium . However , the three schistosome references or draf...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "helminths", "invertebrate", "genomics", "animals", "genomic", "databases", "genome", "analysis", "mammalian", "genomics", "research", "and", "analysis", "methods", "schistosoma", "japonicum", "genomic", "libraries",...	2019	An improved genome assembly of the fluke Schistosoma japonicum
The main consequence of chronic Trypanosoma cruzi infection is the development of myocarditis in approximately 20–30% of infected individuals but not until 10–20 years after the initial infection . We have previously shown that circulating interferon-γ-secreting T cells responsive to Trypanosoma cruzi antigens in chron...	Chagas disease is a neglected tropical disease affecting approximately 10 million people in the world . It is caused by infection with the protozoan Trypanosoma cruzi . As a consequence of migration flows , the disease has been also become established in non-endemic countries . In this study , the functional and phenot...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "cardiology" ]	2014	Presence of Antigen-Experienced T Cells with Low Grade of Differentiation and Proliferative Potential in Chronic Chagas Disease Myocarditis
Cystic Fibrosis ( CF ) exhibits morbidity in several organs , including progressive lung disease in all patients and intestinal obstruction at birth ( meconium ileus ) in ~15% . Individuals with the same causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes . With >6 , 50...	Cystic Fibrosis ( CF ) impacts the normal functioning of several organs including the pancreas , intestines and lungs . CF is caused by mutations in the CF transmembrane conductance regulator , but individuals with the same mutations have different disease severity . For example , only ~15% of individuals with CF are b...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "sociology", "genetic", "diseases", "fibrosis", "social", "sciences", "pulmonology", "simulation", "and", "modeling", "developmental", "biology", "cystic", "fibrosis", "genome", "analysis", ...	2019	Genetic association and transcriptome integration identify contributing genes and tissues at cystic fibrosis modifier loci
Namibia is now ready to begin mass drug administration of praziquantel and albendazole against schistosomiasis and soil-transmitted helminths , respectively . Although historical data identifies areas of transmission of these neglected tropical diseases ( NTDs ) , there is a need to update epidemiological data . For th...	Historical data indicates Namibia , particularly northern Namibia , as endemic for geohelminths and schistosomiasis , albeit to a lower extent than other areas in Sub-Saharan Africa . The National Ministry of Health and Social Services , with extensive backing from other governmental and non-governmental organizations ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Mapping of Schistosomiasis and Soil-Transmitted Helminths in Namibia: The First Large-Scale Protocol to Formally Include Rapid Diagnostic Tests
Body shapes are much more variable than body plans . One way to alter body shapes independently of body plans would be to mechanically deform bodies . To what extent body shapes are regulated physically , or molecules involved in physical control of morphogenesis , remain elusive . During fly metamorphosis , the cuticl...	Shapes of objects , living or not , should depend on their material properties and forces acting on them . Mechanical processes that create whole body shapes of multicellular organisms , or genes that regulate such processes , are largely unknown . Insect bodies are coated by cuticle , a matrix composed of proteins and...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "skin", "dehydration", "(medicine)", "chitin", "invertebrates", "medicine", "and", "health", "sciences", "integumentary", "system", "pathology", "and", "laboratory", "medicine", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "mode...	2017	Mechanical Control of Whole Body Shape by a Single Cuticular Protein Obstructor-E in Drosophila melanogaster
Toxocariasis is an important neglected tropical disease that can manifest as visceral or ocular larva migrans , or covert toxocariasis . All three forms pose a public health problem and cause significant morbidity in areas of high prevalence . To determine the burden of toxocariasis in North America , we conducted a sy...	Toxocariasis is a parasitic worm infection that is transmitted by the ingestion of parasite eggs present in the feces of dogs and cats . After ingestion of the Toxocara eggs , the released larvae migrate through human organs , including the lungs , liver , brain , and eyes , where they cause inflammation and organ dama...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "helminth", "infections", "infectious", "diseases", "medicine", "and", "health", "sciences", "toxocariasis", "larva", "migrans", "parasitic", "intestinal", "diseases", "infectious", "disease", "control", "parasitic", "diseases", "nematode", "infections" ]	2014	Toxocariasis in North America: A Systematic Review
Dengue is the most important arboviral infection of humans . Thrombocytopenia is frequently observed in the course of infection and haemorrhage may occur in severe disease . The degree of thrombocytopenia correlates with the severity of infection , and may contribute to the risk of haemorrhage . As a result of this pro...	A low platelet count is a common feature of dengue infection . It is thought that the platelet count correlates with the severity of the infection and may contribute to the risk of developing haemorrhage , a well-recognised complication of dengue . As a result of this platelet transfusions are used in some settings to ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "global", "health", "neglected", "tropical", "diseases", "viral", "diseases" ]	2012	Prophylactic Platelets in Dengue: Survey Responses Highlight Lack of an Evidence Base
Sporothrix schenckii , previously assumed to be the sole agent of human and animal sporotrichosis , is in fact a species complex . Recently recognized taxa include S . brasiliensis , S . globosa , S . mexicana , and S . luriei , in addition to S . schenckii sensu stricto . Over the last decades , large epidemics of spo...	Sporotrichosis is a subcutaneous mycosis acquired by traumatic inoculation of soil and plant material contaminated with infectious propagules of the pathogen . The transmission of the disease by cats to other animals and humans occurs by biting or scratching , promoting direct inoculation of yeast cells into host tissu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "fungi", "mycology", "veterinary", "epidemiology", "emerging", "infectious", "diseases", "veterinary", "microbiology", "biology", "microbiology", "veterinary", "science" ]	2013	Phylogenetic Analysis Reveals a High Prevalence of Sporothrix brasiliensis in Feline Sporotrichosis Outbreaks
In French Guiana , from 1984 to 2011 , 14 animal rabies cases and 1 human rabies case ( 2008 ) were diagnosed . In January 2011 , vampire-bat attacks occurred in 2 isolated villages . In mid-January , a medical team from the Cayenne Centre for Anti-Rabies Treatment visited the sites to manage individuals potentially ex...	Rabies is a disease almost invariably fatal in humans once the first clinical signs appear . In French Guiana bats represent the virus reservoir , especially vampire bats . From 1984 to 2011 , 14 animal rabies cases and 1 human rabies case ( 2008 ) were diagnosed . In case of bat bite , anti-rabies immunoglobulins ( RI...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "survey", "methods", "infectious", "disease", "epidemiology", "epidemiology", "spatial", "epidemiology", "epidemiological", "methods" ]	2013	Rabies Risk: Difficulties Encountered during Management of Grouped Cases of Bat Bites in 2 Isolated Villages in French Guiana
Protection and recovery from visceral leishmaniasis ( VL ) have been associated with cell-mediated immune ( CMI ) responses , whereas no protective role has been attributed to humoral responses against specific parasitic antigens . In this report , we compared carefully selected groups of individuals with distinct resp...	One of the most striking features of infection by Leishmania chagasi is that infection leads to a spectrum of clinical outcomes ranging from asymptomatic infection to active disease . The existence of asymptomatic infected people has served as an incentive to believe that an effective vaccine is possible , but unfortun...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "leishmaniasis", "parasitic", "diseases" ]	2012	Immunodominant Antigens of Leishmania chagasi Associated with Protection against Human Visceral Leishmaniasis
Chromosomal deletions or reciprocal duplications of the 16p13 . 1 region have been implicated in a variety of neuropsychiatric disorders such as autism , schizophrenia , epilepsies , and attention-deficit hyperactivity disorder ( ADHD ) . In this study , we investigated the association of recurrent genomic copy number ...	Thoracic aortic aneurysms and acute aortic dissections ( TAAD ) have ranked as high as the fifteenth leading cause of death in the United States . TAAD can be inherited in families in an autosomal dominant manner , and mutations in ACTA2 and MYH11 , genes encoding two major components of the smooth muscle contractile u...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "medicine", "genetics", "vascular", "biology", "biology", "human", "genetics", "genetics", "of", "disease", "genetics", "and", "genomics", "cardiovascular" ]	2011	Recurrent Chromosome 16p13.1 Duplications Are a Risk Factor for Aortic Dissections
Laboratory strains of the mouse polyoma virus differ markedly in their abilities to replicate and induce tumors in newborn mice . Major determinants of pathogenicity lie in the sialic binding pocket of the major capsid protein Vp1 and dictate receptor-binding properties of the virus . Substitutions at two sites in Vp1 ...	Strains of the mouse polyoma virus adapted to growth in cell culture vary greatly in their abilities to cause disease . Pathogenicities of these laboratory strains range from “attenuated” to “highly virulent” when tested in animals . The biological differences are based in large part on variations in the outer capsid p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "polyoma", "virus", "natural", "transmission", "receptor", "binding", "virology", "microbiology", "tumor", "induction" ]	2007	Receptor-Binding and Oncogenic Properties of Polyoma Viruses Isolated from Feral Mice
Deacetylases of the Sir2 or sirtuin family are thought to regulate life cycle progression and life span in response to nutrient availability . This family has undergone successive rounds of duplication and diversification , enabling the enzymes to perform a wide variety of biological functions . Two evolutionarily cons...	The Sir2 deacetylases or sirtuins are an important family of proteins thought to regulate life cycle progression and life span according to nutrient availability . These proteins have diversified over the course of evolution such that humans possess seven family members and the laboratory yeast S . cerevisiae possesses...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Deacetylase Sir2 from the Yeast Clavispora lusitaniae Lacks the Evolutionarily Conserved Capacity to Generate Subtelomeric Heterochromatin
The S-phase checkpoint plays an essential role in regulation of the ribonucleotide reductase ( RNR ) activity to maintain the dNTP pools . How eukaryotic cells respond appropriately to different levels of replication threats remains elusive . Here , we have identified that a conserved GSK-3 kinase Mck1 cooperates with ...	The appropriate amount and balance of four dNTPs are crucial for all cells correctly copying and passing on their genetic material generation by generation . Eukaryotes have developed an alert and response system to deal with the disturbance . Here , we uncovered a second-level effector branch . It is activated by the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "cell", "processes", "messenger", "rna", "biochemical", "analysis", "fungi", "in", "vitro", "kinase", "assay", "model", "organisms", "enzyme", "assays", "experimental", "organism", ...	2019	Mck1 defines a key S-phase checkpoint effector in response to various degrees of replication threats
CD4 T cell-mediated help to CD8 T cells and B cells is a critical arm of the adaptive immune system required for control of pathogen infection . CD4 T cells express cytokines and co-stimulatory molecules that support a sustained CD8 T cell response and also enhance generation of protective antibody by germinal center B...	Enhancing the production of protective antibodies in response to infection or vaccine is critically important for host protection . However , we have only limited knowledge about molecular targets to enhance functions of CD4 helper T cells that are essential for antibody affinity maturation and class switching . In thi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "t", "helper", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "immunology", "cell", "differentiation", "developmental", "biology", "tcr", "signaling", "cascade", "cytotoxic", "t", "cells", "antibodies", ...	2018	The adaptor molecule CD2AP in CD4 T cells modulates differentiation of follicular helper T cells during chronic LCMV infection
Protein motions are a key feature to understand biological function . Recently , a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0 . 5 Å C-alpha root-mean-square-deviation ( RMSD ) . To understand this distribution in terms of structure-function relation...	Protein motions are commonly quantified measuring structural differences between conformers . The extension of these differences are called conformational diversity . These motions are essential to understand protein biology . We have found that the distribution of conformational diversity in a large dataset of protein...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "crystal", "structure", "condensed", "matter", "physics", "protein", "structure", "protein", "structure", "databases", "crystallography", "intrinsically", "disordered", "proteins", "crystallization", "research", "and", "analysis", "methods", "solid", "state", "physics", "...	2017	Conformational diversity analysis reveals three functional mechanisms in proteins
Human blood Vγ9/Vδ2 T cells , monocytes and neutrophils share a responsiveness toward inflammatory chemokines and are rapidly recruited to sites of infection . Studying their interaction in vitro and relating these findings to in vivo observations in patients may therefore provide crucial insight into inflammatory even...	The immune system of all jawed vertebrates harbors three distinct lymphocyte populations – αβ T cells , γδ T cells and B cells – yet only higher primates including humans possess so-called Vγ9/Vδ2 T cells , an enigmatic γδ T cell subset that uniformly responds to the majority of bacterial pathogens . For reasons that a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology", "immunology", "biology", "microbiology", "bacterial", "pathogens" ]	2011	Human Neutrophil Clearance of Bacterial Pathogens Triggers Anti-Microbial γδ T Cell Responses in Early Infection
Dengue vaccines are now in late-stage development , and evaluation and robust estimates of dengue disease burden are needed to facilitate further development and introduction . In Cambodia , the national dengue case-definition only allows reporting of children less than 16 years of age , and little is known about dengu...	Dengue is a major public health problem in South-East Asia . Several dengue vaccine candidates are now in late-stage development and are being evaluated in clinical trials . Accurate estimates of true dengue disease burden will become an important factor in the public-health decision-making process for endemic countrie...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/infectious", "diseases", "public", "health", "and", "epidemiology" ]	2010	Dengue Incidence in Urban and Rural Cambodia: Results from Population-Based Active Fever Surveillance, 2006–2008
In recent years , the neglected diseases drug discovery community has elected phenotypic screening as the key approach for the identification of novel hit compounds . However , when this approach is applied , important questions related to the mode of action for these compounds remain unanswered . One of such questions...	Visceral leishmaniasis is a parasitic disease , caused by Leishmania donovani and Leishmania infantum species , found in Asia , South America , East Africa and Southern Europe . Currently available treatments present either serious side effects or high prices and , therefore , the identification of a new generation of ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "chemical", "compounds", "drugs", "microbiology", "antifungals", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "developmental", "biology", "protozoans", "leishmania", "pharmaceut...	2017	Unravelling the rate of action of hits in the Leishmania donovani box using standard drugs amphotericin B and miltefosine
The genomes of plus-strand RNA viruses contain many regulatory sequences and structures that direct different viral processes . The traditional view of these RNA elements are as local structures present in non-coding regions . However , this view is changing due to the discovery of regulatory elements in coding regions...	The genomes of many important pathogenic viruses are made of RNA . These genomes encode viral proteins and contain regulatory sequences and structures . In some viruses , distant regions of the RNA genome can interact with each other via base pairing , which suggests that certain genomes may take on well-defined confor...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Global Organization of a Positive-strand RNA Virus Genome
Tec family kinases are intracellular non-receptor tyrosine kinases implicated in numerous functions , including T cell and B cell regulation . However , a role in microbial pathogenesis has not been described . Here , we identified Tec kinase as a novel key mediator of the inflammatory immune response in macrophages in...	Inflammasomes represent multi-protein complexes and their activation during microbial infections is key in driving hyperinflammation through the maturation and release of IL-1β , as well as by directly inducing several pro-inflammatory cytokines during the host pathogen interaction . Thus , inflammasomes are involved i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "innate", "immune", "system", "immune", "cells", "cytokines", "immunology", "microbiology", "developmental", "biology", "interleukins", "molecular", "development", "fungal", "pathogens", "mycology", "inflammation", "animal", "cells", "medical", "microbiology", "microbial", ...	2014	The Non-receptor Tyrosine Kinase Tec Controls Assembly and Activity of the Noncanonical Caspase-8 Inflammasome
Echolocating bats can identify three-dimensional objects exclusively through the analysis of acoustic echoes of their ultrasonic emissions . However , objects of the same structure can differ in size , and the auditory system must achieve a size-invariant , normalized object representation for reliable object recogniti...	Bats can orientate and hunt for prey in complete darkness using echolocation . Bats use this extraordinary ability , not only to localize objects in space , but also to identify them . The same object , however , can come in different sizes . Here , we use a combination of psychophysical phantom-target experiments and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "neuroscience", "mammals" ]	2007	Object-Oriented Echo Perception and Cortical Representation in Echolocating Bats
RNA hairpins are a common type of secondary structures that play a role in every aspect of RNA biochemistry including RNA editing , mRNA stability , localization and translation of transcripts , and in the activation of the RNA interference ( RNAi ) and microRNA ( miRNA ) pathways . Participation in these functions oft...	In virtually all RNA molecules , single stranded regions undergo complementary base-pairing with neighboring regions to form double-stranded structures called stem-loops or hairpins . During the fundamental processes of transcription and translation , these RNA structures are reshaped by helicases—enzymes that separate...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2016	The Drosophila Helicase MLE Targets Hairpin Structures in Genomic Transcripts
In nearly all eukaryotes , cellular differentiation is governed by changes in transcription , and stabilized by chromatin and DNA modification . Gene expression control in the pathogen Trypanosoma brucei , in contrast , relies almost exclusively on post-transcriptional mechanisms , so RNA binding proteins must assume t...	African trypanosomes cause major economic losses in Africa and other tropical countries through infection of cattle and other domestic animals . In addition , infection of humans results in sleeping sickness , which is usually lethal . Within mammals , the parasites multiply as "bloodstream forms" in the blood and tiss...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "rna-binding", "proteins", "rna", "interference", "messenger", "rna", "microbiology", "protozoan", "life", "cycles", "cell", "differentiation", "developmental", "biology", "sequence", "motif", "analysis", "epigenetics", "epimastigotes", "research", "a...	2017	Expression of the RNA-binding protein RBP10 promotes the bloodstream-form differentiation state in Trypanosoma brucei
Burkholderia pseudomallei ( Bp ) , the causative agent of the often-deadly infectious disease melioidosis , contains one of the largest prokaryotic genomes sequenced to date , at 7 . 2 Mb with two large circular chromosomes ( 1 and 2 ) . To comprehensively delineate the Bp transcriptome , we integrated whole-genome til...	Bacterial transcriptomes are dynamic , context-specific and condition-dependent . Infection by the soil bacterium , Burkholderia pseudomallei , causes melioidosis , an often fatal infectious disease of humans and animals . Possessing a large multi-chromosomal genome , B . pseudomallei is able to persist and survive in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Condition-Dependent Transcriptional Landscape of Burkholderia pseudomallei
Mechanosensory hair cell death is a leading cause of hearing and balance disorders in the human population . Hair cells are remarkably sensitive to environmental insults such as excessive noise and exposure to some otherwise therapeutic drugs . However , individual responses to damaging agents can vary , in part due to...	The majority of hearing loss in humans is caused by death of inner ear mechanosensory hair cells . The aminoglycosides , a family of antibiotics , cause permanent hearing loss and transient vestibular disorders in this fashion . If we can find ways to reduce the hair cell toxicity of these antibiotics , we will be bett...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "models", "cell", "death", "zebrafish", "auditory", "system", "model", "organisms", "molecular", "cell", "biology", "cell", "biology", "biology", "sensory", "systems", "neuroscience" ]	2012	Loss of Slc4a1b Chloride/Bicarbonate Exchanger Function Protects Mechanosensory Hair Cells from Aminoglycoside Damage in the Zebrafish Mutant persephone
The experimental infection of dogs with TriGAS induced high levels of VNA in the serum , whereas wt RABV infection did not . Dogs infected with TriGAS developed antibodies against the virus including its glycoprotein , whereas dogs infected with DRV-NG11 only developed rabies antibodies that are presumably specific for...	Remarkable advances have been made in elucidating the pathogenesis of rabies . One of the hallmarks of rabies infection is that human patients do not develop VNA . In this present study , immune responses were investigated in dogs after infection with a highly attenuated RABV ( TriGAS ) or a highly pathogenic , truly w...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Differential Host Immune Responses after Infection with Wild-Type or Lab-Attenuated Rabies Viruses in Dogs
Segregation Distorter ( SD ) is a selfish , coadapted gene complex on chromosome 2 of Drosophila melanogaster that strongly distorts Mendelian transmission; heterozygous SD/SD+ males sire almost exclusively SD-bearing progeny . Fifty years of genetic , molecular , and theory work have made SD one of the best-characteri...	Mendel's first law of segregation holds that a heterozygous parent will transmit alternative alleles to offspring equally . Segregation Distorter ( SD ) is a naturally occurring selfish gene complex in D . melanogaster that subverts Mendel's first law . During spermatogenesis in heterozygous SD/SD+ males , SD effective...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "evolutionary", "biology", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2009	Large-Scale Selective Sweep among Segregation Distorter Chromosomes in African Populations of Drosophila melanogaster
Chromosomes that fail to synapse during meiosis become enriched for chromatin marks associated with heterochromatin assembly . This response , called meiotic silencing of unsynapsed or unpaired chromatin ( MSUC ) , is conserved from fungi to mammals . In Caenorhabditis elegans , unsynapsed chromosomes also activate a m...	Sexual reproduction relies on meiosis . This specialized cell division generates gametes , such as sperm and eggs , with a single copy of the genome so that fertilization restores diploidy . During meiosis , homologous chromosomes undergo synapsis , in which they assemble a proteinaceous structure called the synaptonem...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2012	Histone Methyltransferases MES-4 and MET-1 Promote Meiotic Checkpoint Activation in Caenorhabditis elegans
The knowledge that many pathogens rely on cell-to-cell communication mechanisms known as quorum sensing , opens a new disease control strategy: quorum quenching . Here we report on one of the rare examples where Gram-positive bacteria , the ‘Staphylococcus intermedius group’ of zoonotic pathogens , excrete two compound...	While studying the potential interaction of staphylococci with Gram-negative bacteria , we came across another communication system in a Staphylococcus species group , which consists of closely related coagulase-positive bacterial species that play a role as zoonotic pathogens . We found that these species excrete two ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	A New Class of Quorum Quenching Molecules from Staphylococcus Species Affects Communication and Growth of Gram-Negative Bacteria
Influenza A viruses ( IAV ) bind to sialic-acids at cellular surfaces and enter cells by using endocytotic routes . There is evidence that this process does not occur constitutively but requires induction of specific cellular signals , including activation of PI3K that promotes virus internalization . This implies enga...	Obligate intracellular pathogens such as influenza viruses have to enter the host cell to ensure replication and propagation . This process implies the penetration of the plasma membrane . To overcome this membrane barrier viruses have evolved several strategies to abuse the cellular signal-transduction machinery upon ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry" ]	2010	The Epidermal Growth Factor Receptor (EGFR) Promotes Uptake of Influenza A Viruses (IAV) into Host Cells
To evaluate the effect of ivermectin mass drug administration on strongyloidiasis and other soil transmitted helminthiases . We conducted a retrospective analysis of data collected in Esmeraldas ( Ecuador ) during surveys conducted in areas where ivermectin was annually administered to the entire population for the con...	Strongyloides stercoralis ( Ss ) is a soil-transmitted helminth ( STH ) that is not yet targeted by control programs , although it is highly prevalent in many areas of the world and may cause severe consequences , in particular to immunosuppressed patients , with a high fatality rate . Unfortunately , albendazole , the...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	Mass Administration of Ivermectin for the Elimination of Onchocerciasis Significantly Reduced and Maintained Low the Prevalence of Strongyloides stercoralis in Esmeraldas, Ecuador
Distal regulatory elements , including enhancers , play a critical role in regulating gene activity . Transcription factor binding to these elements correlates with Low Methylated Regions ( LMRs ) in a process that is poorly understood . Here we ask whether and how actual occupancy of DNA-binding factors is linked to D...	Cell identity is determined by differential gene expression , which in turn is controlled by the combined activity of proximal and distal regulatory elements such as enhancers . DNA within active enhancer elements is marked by a hypomethylated state as a result of transcription factor ( TF ) binding . Here , using CTCF...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions
Malaria is still one of the most devastating infectious diseases , affecting hundreds of millions of patients worldwide . Even though there are several established drugs in clinical use for malaria treatment , there is an urgent need for new drugs acting through novel mechanisms of action due to the rapid development o...	There is an urgent need for new antimalarials acting through novel mechanisms of action that can overcome the increasing incidence of resistance observed for currently used drugs . In this respect , drug polypharmacology is emerging as an attractive strategy to reduce the chances of the parasite evolving drug resistanc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Prediction of the P. falciparum Target Space Relevant to Malaria Drug Discovery
The new epidemiological scenario of orally transmitted Chagas disease that has emerged in Brazil , and mainly in the Amazon region , needs to be addressed with a new and systematic focus . Belém , the capital of Pará state , reports the highest number of acute Chagas disease ( ACD ) cases associated with the consumptio...	After the interruption of Trypanosoma cruzi transmission by Triatoma infestans , a new epidemiological scenario emerged in Brazil: the oral route . In the Amazon region , considered as a non-endemic Chagas disease region , T . cruzi is thought to exist as an enzootic parasite of wild animals . Currently , this region c...	[ "Abstract", "Introduction", "Methods", "Discussion" ]	[ "trypanosoma", "protozoans", "biology", "and", "life", "sciences", "protozoology", "microbiology", "parasitic", "protozoans", "organisms" ]	2014	Distantiae Transmission of Trypanosoma cruzi: A New Epidemiological Feature of Acute Chagas Disease in Brazil
The genome sequencing of Buchnera aphidicola BCc from the aphid Cinara cedri , which is the smallest known Buchnera genome , revealed that this bacterium had lost its symbiotic role , as it was not able to synthesize tryptophan and riboflavin . Moreover , the biosynthesis of tryptophan is shared with the endosymbiont S...	A critical issue in evolutionary biology is to find traits or organisms that provide evidence of the transition from one lifestyle to another , no matter how gradual the process may be . The evolutionary history of intracellular symbiosis , involving the transition of bacteria from free-living to obligate lifestyle , c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "systems", "biology", "biology", "genomics", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics" ]	2011	Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont
Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes . However , the way in which sequence dictates alternative folding pathways of gene regulation remains unclear . In this study , we compute energy landscapes , which describe the accessible secondary structures for a range of s...	Riboswitches are RNAs that modulate gene expression by ligand-induced conformational changes . However , the way that sequence dictates alternative folding pathways of gene regulation remains unclear . In this study , we mimic transcription by computing energy landscapes which describe accessible secondary structures f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "computational", "biology" ]	2012	Dynamic Energy Landscapes of Riboswitches Help Interpret Conformational Rearrangements and Function
We present molecular dynamics simulations of unliganded human hemoglobin ( Hb ) A under physiological conditions , starting from the R , R2 , and T state . The simulations were carried out with protonated and deprotonated HC3 histidines His ( β ) 146 , and they sum up to a total length of 5 . 6µs . We observe spontaneo...	As the prototypic allosteric protein , human hemoglobin ( Hb ) has drawn extensive scientific efforts for many decades . Human Hb exists in two quaternary conformations , the low-affinity ( or deoxy ) T state , and the high-affinity ( or oxy ) R state , and the transition between the T and the R state is mainly charact...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics", "biophysics/theory", "and", "simulation" ]	2010	Spontaneous Quaternary and Tertiary T-R Transitions of Human Hemoglobin in Molecular Dynamics Simulation
Seed development in flowering plants is initiated after a double fertilization event with two sperm cells fertilizing two female gametes , the egg cell and the central cell , leading to the formation of embryo and endosperm , respectively . In most species the endosperm is a polyploid tissue inheriting two maternal gen...	Flowering plants reproduce by forming seeds that contain an embryo surrounded by a nourishing endosperm tissue that , similar to the mammalian placenta , supports embryo growth . Normal endosperm development requires the FERTILIZATION INDEPENDENT SEED ( FIS ) Polycomb Repressive Complex2 ( PRC2 ) . In most flowering pl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "plant", "science", "evolutionary", "biology", "plant", "growth", "and", "development", "plant", "biology", "genetics", "plant", "genetics", "epigenetics", "biology", "genetics", "and", "genomics", "evolutionary", "developmental", "biology" ]	2013	Increased Maternal Genome Dosage Bypasses the Requirement of the FIS Polycomb Repressive Complex 2 in Arabidopsis Seed Development
Hookworm infections are one of the most important parasitic infections of humans worldwide , considered by some second only to malaria in associated disease burden . Single-dose mass drug administration for soil-transmitted helminths , including hookworms , relies primarily on albendazole , which has variable efficacy ...	Hookworm infections are one of the great parasitic diseases of our time , infecting more than half a billion people worldwide and are a significant source of iron-deficient anemia . Although mass drug administrations to eliminate hookworms from children and pregnant women are being deployed , all the drugs for treatmen...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "drugs", "and", "devices", "microbiology", "parasitic", "diseases", "toxicology", "hookworm", "infection", "global", "health", "neglected", "tropical", "diseases", "pharmacology", "applied", "microbiology", "infectious", "diseases", "soil-transmitted", "helminth...	2012	Mechanistic and Single-Dose In Vivo Therapeutic Studies of Cry5B Anthelmintic Action against Hookworms
Currently dengue viruses ( DENV ) pose an increasing threat to over 2 . 5 billion people in over 100 tropical and sub-tropical countries worldwide . International air travel is facilitating rapid global movement of DENV , increasing the risk of severe dengue epidemics by introducing different serotypes . Accurate diagn...	Dengue viruses ( DENV ) are the most widespread arthropod-borne viruses which have shown an unexpected geographic expansion , as well as an increase in the number and severity of outbreaks in the last decades . In this context , the accurate diagnosis and reliable surveillance of dengue infections are essential . The l...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/diagnosis", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "virology/emerging", "viral", "diseases" ]	2010	2nd International External Quality Control Assessment for the Molecular Diagnosis of Dengue Infections
Cerebral malaria ( CM ) is the most severe manifestation of Plasmodium falciparum infection in children and non-immune adults . Previous work has documented a persistent cognitive impairment in children who survive an episode of CM that is mimicked in animal models of the disease . Potential therapeutic interventions f...	Cerebral malaria ( CM ) is the direst consequence of Plasmodium falciparum infection . Cognitive impairment is a common sequela in children surviving CM . Identification of adjunctive therapies that reduce the complications of CM in survivors is a priority . Statins have been suggested for the treatment of neuroinflamm...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "neuroscience" ]	2012	Statins Decrease Neuroinflammation and Prevent Cognitive Impairment after Cerebral Malaria
We have previously demonstrated that acquisition of intricate patterns of activating ( H3K4me3 , H3K9/K14ac ) and repressive ( H3K27me3 ) histone modifications is a hallmark of KSHV latency establishment . The precise molecular mechanisms that shape the latent histone modification landscape , however , remain unknown ....	KSHV is the etiological agent of several cancers including Kaposi's sarcoma , one of the most frequent tumors in Sub-Saharan Africa . Since the proliferating cells in these cancers are latently infected with KSHV , there is an urgent need to elucidate the molecular basis underlying latency establishment . While it is w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "viral", "persistence", "and", "latency", "virology", "viruses", "and", "cancer", "genetics", "epigenetics", "biology", "and", "life", "sciences", "immunology", "microbiology", "immune", "system" ]	2014	Influence of ND10 Components on Epigenetic Determinants of Early KSHV Latency Establishment
Local mRNA translation in neurons has been mostly studied during axon guidance and synapse formation but not during initial neurite outgrowth . We performed a genome-wide screen for neurite-enriched mRNAs and identified an mRNA that encodes mitogen-activated protein kinase kinase 7 ( MKK7 ) , a MAP kinase kinase ( MAPK...	MRNA transcripts are usually translated into proteins in the cytosol . Some mRNAs , however , are first transported to specific subcellular regions where they are translated to perform localized functions . This is especially important in highly polarized cells such as neurons . Here , we find that a transcript encodin...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "cell", "physiology", "physiology", "biology", "anatomy", "and", "physiology" ]	2012	Growth Cone MKK7 mRNA Targeting Regulates MAP1b-Dependent Microtubule Bundling to Control Neurite Elongation
To date , no universally effective and safe vaccine has been developed for general human use . Leishmania donovani Peroxidoxin-1 ( LdPxn-1 ) is a member of the antioxidant family of proteins and is predominantly expressed in the amastigote stage of the parasite . The aim of this study was to evaluate the immunogenicity...	Leishmaniasis , a disease caused by protozoan parasites under the genus Leishmania , claims the lives of thousands of people annually . It mainly affects people in poor communities in Africa , Asia and South America . Although several drugs are available for the treatment of leishmaniasis , their efficacy is limited by...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	DNA-Protein Immunization Using Leishmania Peroxidoxin-1 Induces a Strong CD4+ T Cell Response and Partially Protects Mice from Cutaneous Leishmaniasis: Role of Fusion Murine Granulocyte-Macrophage Colony-Stimulating Factor DNA Adjuvant
Natural killer ( NK ) cells are an important element in the immune defense against the orthopox family members vaccinia virus ( VV ) and ectromelia virus ( ECTV ) . NK cells are regulated through inhibitory and activating signaling receptors , the latter involving NKG2D and the natural cytotoxicity receptors ( NCR ) , ...	Natural killer ( NK ) cells , which belong to the innate immune system , play a critical role in the defence against viruses . The orthopoxvirus family member vaccinia virus is not only used for vaccinations of humans , but is also presently considered as a promising agent for oncolytic virotherapy of tumors . It is , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2011	Modulation of NKp30- and NKp46-Mediated Natural Killer Cell Responses by Poxviral Hemagglutinin
To cause a systemic infection , Salmonella must respond to many environmental cues during mouse infection and express specific subsets of genes in a temporal and spatial manner , but the regulatory pathways are poorly established . To unravel how micro-environmental signals are processed and integrated into coordinated...	We have used the intracellular pathogen Salmonella to investigate how pathogenic bacterium correctly expresses virulence factors during infection . After ingestion by its host , Salmonella confronts multiple challenging microenvironments such as acidic pH in the stomach , nutrient starvation , and host innate immune re...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/transcriptional", "regulation", "microbiology/cellular", "microbiology", "and", "pathogenesis", "computational", "biology/systems", "biology", "computational", "biology/signaling", "networks" ]	2009	Coordinated Regulation of Virulence during Systemic Infection of Salmonella enterica Serovar Typhimurium
Meiotic recombination of sex chromosomes is thought to be repressed in organisms with heterogametic sex determination ( e . g . mammalian X/Y chromosomes ) , due to extensive divergence and chromosomal rearrangements between the two chromosomes . However , proper segregation of sex chromosomes during meiosis requires c...	Recombination has been thought to be repressed within sex chromosomes , as well as within the mating-type ( MAT ) loci in many fungi , due to the highly diverged and rearranged nature between alleles defining opposite sexes or mating-types . However , it has long been appreciated that recombination can occur within the...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "mycology", "fungal", "evolution", "microbial", "evolution", "genetics", "microbial", "pathogens", "population", "genetics", "biology", "evolutionary", "biology", "genomic", "evolution", "molecular", "genetics", "evolutionary", "genetics", "microbiology", "genetics", "and",...	2012	Gene Conversion Occurs within the Mating-Type Locus of Cryptococcus neoformans during Sexual Reproduction
Dengue virus ( DENV ) is thought to have emerged from a sylvatic cycle in Africa but has since become adapted to an urban-centric transmission cycle . These urban areas include villages in West Africa where DENV is not often routinely considered for patients presenting with febrile illnesses , as other endemic diseases...	Identifying the infectious diseases in developing nations could assist in clinical response , disaster response , and in assessing the need for specific public health infrastructure and therapeutics . Here we tested serum from patients in Sierra Leone who sought treatment for fever ( and which remained undiagnosed ) fo...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "geographical", "locations", "microbiology", "tropical", "diseases", "parasitic", "diseases", "viruses", "rna", "...	2016	Short Report: Serological Evidence of Under-Reported Dengue Circulation in Sierra Leone
Current climate change may be a major threat to global biodiversity , but the extent of species loss will depend on the details of how species respond to changing climates . For example , if most species can undergo rapid change in their climatic niches , then extinctions may be limited . Numerous studies have now docu...	Climate change is an important threat to the world’s plant and animal species , including species on which humans depend . However , predicting how species will respond to future climate change is very difficult . In this study , I analyze the extinctions caused by the climate change that has already occurred . Numerou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "taxonomy", "invertebrates", "ecology", "and", "environmental", "sciences", "ecological", "niches", "atmospheric", "science", "plant", "taxonomy", "animals", "animal", "taxonomy", "data", "management", "plant", "science", "fresh", "water", "habitats", "zoology", "climat...	2016	Climate-Related Local Extinctions Are Already Widespread among Plant and Animal Species
The Zanzibar Elimination of Schistosomiasis Transmission ( ZEST ) project aimed to eliminate urogenital schistosomiasis as a public health problem from Pemba and to interrupt Schistosoma haematobium transmission from Unguja in 5 years . A repeated cross-sectional cluster-randomized trial was implemented from 2011/12 ti...	Schistosomiasis is a disease caused by parasitic blood flukes of the genus Schistosoma . The highest burden is concentrated in sub-Saharan Africa . On the Zanzibar islands , urogenital schistosomiasis has been successfully controlled over the past decades . The Zanzibar Elimination of Schistosomiasis Transmission ( ZES...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "education", "helminths", "sociology", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "animals", "urine", "gastropods", "tanzani...	2019	A 5-Year intervention study on elimination of urogenital schistosomiasis in Zanzibar: Parasitological results of annual cross-sectional surveys
The hydrolysis of ATP associated with actin and profilin-actin polymerization is pivotal in cell motility . It is at the origin of treadmilling of actin filaments and controls their dynamics and mechanical properties , as well as their interactions with regulatory proteins . The slow release of inorganic phosphate ( Pi...	Actin proteins assemble into microfilaments that control cell shape and movement by polymerizing or depolymerizing . These actin monomers can bind ATP or ADP molecules . The incorporation of an ATP-actin monomer into a growing filament results in rapid cleavage of ATP into ADP and inorganic phosphate ( Pi ) , followed ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "cell", "motility", "actin", "filaments", "fluid", "mechanics", "macromolecular", "assemblies", "regulatory", "proteins", "chemical", "biology", "biomimetics", "bioengineering", "proteins", "chemistry", "biology", "biophysics", "polymerization", "physics", ...	2011	Individual Actin Filaments in a Microfluidic Flow Reveal the Mechanism of ATP Hydrolysis and Give Insight Into the Properties of Profilin
Wuchereria bancrofti ( Wb ) is the primary causative agent of lymphatic filariasis ( LF ) . Our studies of LF in Papua New Guinea ( PNG ) have shown that it is possible to reduce the prevalence of Wb in humans and mosquitoes through mass drug administration ( MDA; diethylcarbamazine with/without ivermectin ) . While MD...	The Global Program to Eliminate Lymphatic Filariasis ( LF ) , initiated by the World Health Organization ( WHO ) , aims to eliminate LF from endemic regions , where 1 . 34 billion people live at risk of this disease . The causative agent responsible for 90% of LF is the nematode parasite species Wuchereria bancrofti ( ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "epidemiology", "global", "health", "genetics", "neglected", "tropical", "diseases", "population", "biology", "biology", "parasitic", "diseases" ]	2013	Population Genetics of the Filarial Worm Wuchereria bancrofti in a Post-treatment Region of Papua New Guinea: Insights into Diversity and Life History
We studied cell death by apoptosis and necrosis in cardiac remodeling produced by Trypanosoma cruzi infection . In addition , we evaluated collagen I , III , IV ( CI , CIII and CIV ) deposition in cardiac tissue , and their relationship with serum levels of procollagen type I carboxy-terminal propeptide ( PICP ) and pr...	Chronic Chagas heart disease ( CHHD ) caused by the infection with the parasite Trypanosoma cruzi is the most important infectious heart disease in the world . The typical manifestations are dilated cardiomyopathy and congestive heart failure; they result from death of cardiomyocytes and their replacement by collagen ....	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "cell", "death", "immunology", "parasitic", "diseases", "cardiovascular", "animal", "models", "model", "organisms", "infectious", "diseases", "extracellular", "matrix", "connective", "tissue", "biology", "infectious", "disease", "modeling", "heart", "failure",...	2013	Cell Death and Serum Markers of Collagen Metabolism during Cardiac Remodeling in Cavia porcellus Experimentally Infected with Trypanosoma cruzi
Genomic instability drives tumorigenesis , but how it is initiated in sporadic neoplasias is unknown . In early preneoplasias , alterations at chromosome fragile sites arise due to DNA replication stress . A frequent , perhaps earliest , genetic alteration in preneoplasias is deletion within the fragile FRA3B/FHIT locu...	Normal cells have robust mechanisms to maintain the proper sequence of their DNA; in cancer cells these mechanisms are compromised , resulting in complex changes in the DNA of tumors . How this genome instability begins has not been defined , except in cases of familial cancers , which often have mutations in genes cal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2012	Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression
Wild bird movements and aggregations following spells of cold weather may have resulted in the spread of highly pathogenic avian influenza virus ( HPAIV ) H5N1 in Europe during the winter of 2005–2006 . Waterbirds are constrained in winter to areas where bodies of water remain unfrozen in order to feed . On the one han...	Highly pathogenic avian influenza virus of the H5N1 subtype emerged more than a decade ago in poultry in South-East Asia . In 2005 , it spread outside Asia infecting both poultry and wild birds in the Middle East , Europe and Africa . Both trade of poultry and movements of wild birds were likely implicated in the sprea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "public", "health", "and", "epidemiology/epidemiology", "infectious", "diseases/viral", "infections", "public", "health", "and", "epidemiology/infectious", "diseases", "ecology/spatial", "and", "landscape", "ecology", "ecology/population", "ecology", "infectious", "diseases/epi...	2010	Spatial and Temporal Association of Outbreaks of H5N1 Influenza Virus Infection in Wild Birds with the 0°C Isotherm
Mammalian X chromosome dosage compensation balances X-linked gene products between sexes and is coordinated by the long noncoding RNA ( lncRNA ) Xist . Multiple cis and trans-acting factors modulate Xist expression; however , the primary competence factor responsible for activating Xist remains a subject of dispute . T...	Long noncoding RNA ( lncRNA ) have been identified in all eukaryotes but mechanisms of lncRNA function remain challenging to study in vivo . A classic model of lncRNA function and mechanism is X-Chromosome Inactivation ( XCI ) : an essential process which balances X-linked gene expression between male and female mammal...	[ "Abstract", "Introduction", "Results", "Materials", "and", "methods" ]	[ "biotechnology", "medicine", "and", "health", "sciences", "x", "chromosome", "inactivation", "molecular", "probe", "techniques", "gene", "regulation", "long", "non-coding", "rnas", "animal", "models", "developmental", "biology", "model", "organisms", "x-linked", "traits...	2018	LncRNA Jpx induces Xist expression in mice using both trans and cis mechanisms
The molecular triggers leading to virulence of a number of human-adapted commensal bacteria such as Streptococcus gallolyticus are largely unknown . This opportunistic pathogen is responsible for endocarditis in the elderly and associated with colorectal cancer . Colonization of damaged host tissues with exposed collag...	Streptococcus gallolyticus ( formely known as S . bovis biotype I ) is an emerging cause of septicemia and endocarditis in the elderly . Intriguingly , epidemiological studies revealed a strong association , up to 65% , between endocarditis due to S . gallolyticus and colorectal malignancies . Whether S . gallolyticus ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "streptococci", "gene", "expression", "biology", "microbiology", "molecular", "cell", "biology", "bacterial", "pathogens", "gram", "positive" ]	2014	Single Cell Stochastic Regulation of Pilus Phase Variation by an Attenuation-like Mechanism
Most organs of multicellular organisms are built from epithelial tubes . To exert their functions , tubes rely on apico-basal polarity , on junctions , which form a barrier to separate the inside from the outside , and on a proper lumen , required for gas or liquid transport . Here we identify apnoia ( apn ) , a novel ...	Tubular organs , such as the fruitfly airways , comprise essential functional pipes through which gas and liquid are transported . They consist of highly polarized epithelial cells that form a barrier between air and the larval body . However , during larval development , these tubes , though very rigid due to the pres...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "invertebrates", "vesicles", "animals", "animal", "models", "membrane", "proteins", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "embryos", "cellular", "structures", "and", "or...	2019	The apical protein Apnoia interacts with Crumbs to regulate tracheal growth and inflation
Morphogen gradients are established by the localized production and subsequent diffusion of signaling molecules . It is generally assumed that cell fates are induced only after morphogen profiles have reached their steady state . Yet , patterning processes during early development occur rapidly , and tissue patterning ...	Subdivision of naive fields of cells into separate cell populations , distinguished by the unique combinations of genes they express , constitutes a major aspect of organism development . Classically , this involves the generation of gradients of signaling molecules ( morphogens ) , which induce distinct cell fates in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "computational", "biology", "drosophila", "genetics", "and", "genomics" ]	2007	Pre-Steady-State Decoding of the Bicoid Morphogen Gradient
Inherited photoreceptor degenerations ( IPDs ) are the most genetically heterogeneous of Mendelian diseases . Many IPDs exhibit substantial phenotypic variability , but the basis is usually unknown . Mutations in MERTK cause recessive IPD phenotypes associated with the RP38 locus . We have identified a murine genetic m...	Human inherited photoreceptor degenerations ( IPDs ) are genetically heterogeneous and exhibit significant unexplained phenotypic variability . Mutation of hundreds of known genes can cause these disorders , but variability still occurs among individuals with mutations in the same gene . Possible explanations include e...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Tyro3 Modulates Mertk-Associated Retinal Degeneration
During development , tissue-specific transcription factors regulate both protein-coding and non-coding genes to control differentiation . Recent studies have established a dual role for the transcription factor Pax6 as both an activator and repressor of gene expression in the eye , central nervous system , and pancreas...	The transcription factor Pax6 is reiteratively employed in space and time for the establishment of progenitor pools and the differentiation of neuronal and non-neuronal lineages of the CNS , pancreas , and eye . Execution of these diverse developmental programs depends on simultaneous activation and repression of gene ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Pax6 Regulates Gene Expression in the Vertebrate Lens through miR-204
Trans-sialidase ( TS ) , a virulence factor from Trypanosoma cruzi , is an enzyme playing key roles in the biology of this protozoan parasite . Absent from the mammalian host , it constitutes a potential target for the development of novel chemotherapeutic drugs , an urgent need to combat Chagas' disease . TS is involv...	Chagas' disease , or American trypanosomiasis , is an endemic illness that affects approximately 8 million people in Latin America . The etiologic agent is the protozoan parasite Trypanosoma cruzi . To survive in the mammalian host and invade its cells , leading to the chronic infection , the parasite incorporates a ch...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "microbiology", "host-pathogeninteraction", "parasitology", "neglectedtropicaldiseases", "chagasdisease", "proteins", "microbialpathogens", "biology", "pathogenesis", "proteinstructure", "parasiticdiseases", "protozoaninfections", "biochemistry", "infectiousdiseases", "prot...	2012	Trypanosoma cruzi trans-Sialidase in Complex with a Neutralizing Antibody: Structure/Function Studies towards the Rational Design of Inhibitors
Rabies is caused by lyssaviruses , and is one of the oldest known zoonoses . In recent years , more than 21 , 000 nucleotide sequences of rabies viruses ( RABV ) , from the prototype species rabies lyssavirus , have been deposited in public databases . Subsequent phylogenetic analyses in combination with metadata sugge...	Rabies is one of the oldest known zoonoses , caused by lyssaviruses . In recent years , more than 21 , 000 nucleotide sequences for rabies viruses ( RABV ) have been deposited in public databases . In this study , a novel mathematical approach called affinity propagation ( AP ) clustering , a highly powerful tool , to ...	[ "Abstract", "Introduction", "Methods", "Results", "and", "discussion" ]	[ "taxonomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "genome", "evolution", "pathogens", "microbiology", "vertebrates", "wolves", "animals", "mammals", "dogs", "viruses", "phylogenetics", "data", "management", "rna", "viruse...	2018	Defining objective clusters for rabies virus sequences using affinity propagation clustering
LINE-1 ( L1 ) retrotransposons can mobilize ( retrotranspose ) within the human genome , and mutagenic de novo L1 insertions can lead to human diseases , including cancers . As a result , cells are actively engaged in preventing L1 retrotransposition . This work reveals that the human Condensin II complex restricts L1 ...	LINE-1 ( L1 ) retrotransposons mobilize within the human genome and L1 insertions are implicated in the development of various cancers . This work identifies the Condensin II complex as a novel repressor of L1 expression and retrotransposition in human primary and transformed epithelial cells . Proteomics analyses reve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "retrotransposons", "molecular", "probe", "techniques", "gene", "regulation", "rna", "extraction", "immunoblotting", "epithelial", "cells", "immunoprecipitation", "genetic", "elements", "molecular", "biology", "techniques", "extracti...	2017	Condensin II and GAIT complexes cooperate to restrict LINE-1 retrotransposition in epithelial cells
Technological advances make it possible to use high-throughput sequencing as a primary discovery tool of medical genetics , specifically for assaying rare variation . Still this approach faces the analytic challenge that the influence of very rare variants can only be evaluated effectively as a group . A further compli...	Developments in sequencing technology now enable us to assay all genetic variation , much of which is extremely rare . We propose to test the distribution of rare variants we observe in cases versus controls . To do so , we present a novel application of the C-alpha statistic to test these rare variants . C-alpha aims ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "disease", "computational", "biology/genomics", "mathematics/statistics", "genetics", "and", "genomics/medical", "genetics" ]	2011	Testing for an Unusual Distribution of Rare Variants
Plasmodium falciparum mediates adhesion of infected red blood cells ( RBCs ) to blood vessel walls by assembling a multi-protein complex at the RBC surface . This virulence-mediating structure , called the knob , acts as a scaffold for the presentation of the major virulence antigen , P . falciparum Erythrocyte Membran...	The human malaria parasite Plasmodium falciparum causes severe disease , which is initiated by the adhesion of parasite-infected RBCs to receptors on the walls of the host’s capillaries . Adhesion is mediated by a structure called the knob , which acts as a scaffold for the presentation of the virulence protein , P . f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "fluorescence", "microbeads", "parasitic", "diseases", "electromagnetic", "radiation", "spectrins", "microscopy", "materials", "science", "protein", "structure", "macromolecules", "research", "and", "analys...	2019	The knob protein KAHRP assembles into a ring-shaped structure that underpins virulence complex assembly
Although incidence of leprosy in Spain has declined steadily over the years , the fivefold increase in immigration since the turn of the century—much of it from countries where leprosy is still prevalent—has been linked to an uptick in registered cases . To describe the epidemiologic trends of incident leprosy cases de...	Most of cases of leprosy that are diagnosed in Europe come from other parts of the world . This study describes the epidemiologic trends of incident leprosy cases detected in Spain among Spanish- and foreign-born population groups from 2003 to 2013 . We show that new cases of leprosy will continue to appear in the coun...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "paraguay", "spanish", "people", "medicine", "and", "health", "sciences", "geographical", "locations", "tropical", "diseases", "epidemiological", "methods", "and", "statistics", "ethnicities", "bacterial", "diseases", "neglected", "tropical", "diseases", "africa", "infect...	2016	Epidemiology of Leprosy in Spain: The Role of the International Migration
Much remains unknown of molecular events controlling the plant hypersensitive defense response ( HR ) , a rapid localized cell death that limits pathogen spread and is mediated by resistance ( R- ) genes . Genetic control of the HR is hard to quantify due to its microscopic and rapid nature . Natural modifiers of the e...	The hypersensitive pathogen defense response ( HR ) in plants typically consists of a rapid , localized cell death around the point of attempted pathogen penetration . It is found in all plant species and is associated with high levels of resistance to a wide range of pathogens and pests including bacteria , fungi , vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "cereal", "crops", "plant", "science", "crop", "science", "genome", "analysis", "crops", "genetics", "plant", "genetics", "biology", "and", "life", "sciences", "plant", "pathology", "crop", "diseases", "computational", "biology...	2014	A Genome-Wide Association Study of the Maize Hypersensitive Defense Response Identifies Genes That Cluster in Related Pathways
By using fluorescence imaging , we provide a time-resolved single-cell view on coupled defects in transcription , translation , and growth during expression of heterologous membrane proteins in Lactococcus lactis . Transcripts encoding poorly produced membrane proteins accumulate in mRNA-dense bodies at the cell poles ...	Malfunctioning of particular membrane proteins lies at the heart of some detrimental human diseases . The discovery and correction of bottlenecks in the cellular production of high quantities of membrane proteins for structure/function or drug discovery studies is a huge challenge . Single-cell studies have drastically...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "lactococcus", "lactis", "cell", "physiology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "messenger", "rna", "microbiology", "light", "microscopy", "cell", "polarity", "membrane", "proteins", "microscopy", "cellu...	2016	On the Spatial Organization of mRNA, Plasmids, and Ribosomes in a Bacterial Host Overexpressing Membrane Proteins

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