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Oncogenic signaling pathways regulate gene expression in part through epigenetic modification of chromatin including DNA methylation and histone modification . Trimethylation of histone H3 at lysine-27 ( H3K27 ) , which correlates with transcriptional repression , is regulated by an oncogenic form of the small GTPase R...	Trimethylation of histone H3 at lysine-27 ( H3K27 ) has been associated with silencing of gene expression . Abnormalities of this modification are thought to contribute to the epigenetic silencing of tumor suppressor genes and are regarded as a hallmark of cancer . It has remained unclear , however , whether the produc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cancer", "genetics", "gene", "expression", "genetics", "epigenetics", "biology", "genomics", "histone", "modification" ]	2013	Ras-Induced Changes in H3K27me3 Occur after Those in Transcriptional Activity
The identification of MHC class II restricted peptide epitopes is an important goal in immunological research . A number of computational tools have been developed for this purpose , but there is a lack of large-scale systematic evaluation of their performance . Herein , we used a comprehensive dataset consisting of mo...	A critical step in developing immune response against pathogens is the recognition of antigenic peptides presented by MHC class II molecules . Since experiments for MHC class II binding peptide identification are expensive and time consuming , computational tools have been developed as fast alternatives but with inferi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology", "computational", "biology" ]	2008	A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach
HIV-infected individuals have deficient responses to Yellow Fever vaccine ( YFV ) and may be at higher risk for adverse events ( AE ) . Chronic immune activation–characterized by low CD4/CD8 ratio or high indoleamine 2 , 3-dioxygenase-1 ( IDO ) activity—may influence vaccine response in this population . We prospective...	Yellow Fever ( YF ) vaccine is considered one of the most effective vaccines ever produced . However , previous studies suggest that HIV impairs YF vaccine response . In this study , we assessed if HIV infection impacts the risk of adverse events and could reduce antibody response to YF vaccine . We explored if laborat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "retroviruses", "viruses", "immunodeficiency", "viruses", "preventive", "medicine", "vaccines", "rna", "viruses", "vac...	2016	CD4/CD8 Ratio and KT Ratio Predict Yellow Fever Vaccine Immunogenicity in HIV-Infected Patients
The intracellular bacterial pathogen Legionella pneumophila causes an inflammatory pneumonia called Legionnaires' Disease . For virulence , L . pneumophila requires a Dot/Icm type IV secretion system that translocates bacterial effectors to the host cytosol . L . pneumophila lacking the Dot/Icm system is recognized by ...	In animals , the innate immune system senses infection primarily through detection of conserved microbial molecules . It has been suggested , but not clearly established , that the immune system may also respond to pathogen-associated activities—i . e . , the manipulations of host cell processes that a pathogen employs...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "infectious", "diseases/bacterial", "infections", "immunology/immune", "response", "immunology/innate", "immunity" ]	2011	Secreted Bacterial Effectors That Inhibit Host Protein Synthesis Are Critical for Induction of the Innate Immune Response to Virulent Legionella pneumophila
Lignin is incorporated into plant cell walls to maintain plant architecture and to ensure long-distance water transport . Lignin composition affects the industrial value of plant material for forage , wood and paper production , and biofuel technologies . Industrial demands have resulted in an increase in the use of ge...	Lignin is an essential component of wood and the second most abundant terrestrial biopolymer . Plants synthesize lignin to strengthen cell walls and to resist pathogen attack . Because the technological value of plants is determined by the amount and composition of lignin , genetic engineering approaches frequently aim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chemical", "biology/small", "molecule", "chemistry", "microbiology/environmental", "microbiology", "microbiology/plant-biotic", "interactions", "plant", "biology/plant-biotic", "interactions", "plant", "biology/plant", "biochemistry", "and", "physiology", "plant", "biology/agricul...	2009	Imbalanced Lignin Biosynthesis Promotes the Sexual Reproduction of Homothallic Oomycete Pathogens
Amino-acid coevolution can be referred to mutational compensatory patterns preserving the function of a protein . Viral envelope glycoproteins , which mediate entry of enveloped viruses into their host cells , are shaped by coevolution signals that confer to viruses the plasticity to evade neutralizing antibodies witho...	Several virus-mediated molecular processes remain poorly described , which dampen the development of potent anti-viral therapies . Hence , new experimental strategies need to be undertaken to improve and accelerate our understanding of these processes . Here , as a proof of concept , we employ amino-acid coevolution as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "cell", "physiology", "enzyme-linked", "immunoassays", "microbiology", "viral", "structure", "membrane", "fusion", "coevolution", "immunologic", "techniques", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "se...	2018	A protein coevolution method uncovers critical features of the Hepatitis C Virus fusion mechanism
Across the mammalian nervous system , neurotrophins control synaptic plasticity , neuromodulation , and neuronal growth . The neurotrophin Brain-Derived Neurotrophic Factor ( BDNF ) is known to promote structural and functional synaptic plasticity in the hippocampus , the cerebral cortex , and many other brain areas . ...	Storing memory traces in the brain is essential for learning and memory formation , and it occurs through synaptic plasticity processes . Timing-dependent Long-Term Potentiation ( t-LTP ) is a physiologically relevant type of synaptic plasticity that results from the repeated sequential firing of action potentials ( AP...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "neurochemistry", "vesicles", "nervous", "system", "membrane", "potential", "electrophysiology", "neuroscience", "synaptic", "plasticity", "neurotransmitters", "cellular", "structures", "and", "organelles", "n...	2019	A kinetic model for Brain-Derived Neurotrophic Factor mediated spike timing-dependent LTP
The genetic component of complex disease risk in humans remains largely unexplained . A corollary is that the allelic spectrum of genetic variants contributing to complex disease risk is unknown . Theoretical models that relate population genetic processes to the maintenance of genetic variation for quantitative traits...	Gene action determines how mutations affect phenotype . When placed in an evolutionary context , the details of the genotype-to-phenotype model can impact the maintenance of genetic variation for complex traits . Likewise , non-equilibrium demographic history may affect patterns of genetic variation . Here , we explore...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "deletion", "mutation", "demography", "population", "genetics", "twins", "simulation", "and", "modeling", "developmental", "biology", "mutation", "genome", "analysis", "population", "biology", "research", "and", "analysis", "method...	2017	A Model of Compound Heterozygous, Loss-of-Function Alleles Is Broadly Consistent with Observations from Complex-Disease GWAS Datasets
Essential metabolic reactions are shaping constituents of metabolic networks , enabling viable and distinct phenotypes across diverse life forms . Here we analyse and compare modelling predictions of essential metabolic functions with experimental data and thereby identify core metabolic pathways in prokaryotes . Simul...	If we tried to list every known chemical reaction within an organism–human , plant or even bacteria–we would get quite a long and confusing read . But when this information is represented in so-called genome-scale metabolic networks , we have the means to access computationally each of those reactions and their interco...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "metabolic", "networks", "enzymology", "genomic", "databases", "prosthetic", "groups", "network", "analysis", "genome", "analysis", "enzyme", "chemistry", "research", "and", "analysis", "methods", "computer", "and", "information", "sciences", "biochemical", "cofactors", ...	2018	Metabolic models and gene essentiality data reveal essential and conserved metabolism in prokaryotes
Among other factors , changes in gene expression on the human evolutionary lineage have been suggested to play an important role in the establishment of human-specific phenotypes . However , the molecular mechanisms underlying these expression changes are largely unknown . Here , we have explored the role of microRNA (...	Humans are remarkably similar to apes and monkeys on the genome sequence level but remain remarkably distinct with respect to cognitive abilities . How could human cognition evolve within such a short evolutionary time ? Among many hypotheses , evolution in expression of a few key regulators affecting hundreds of their...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "sequence", "analysis", "organismal", "evolution", "genomics", "evolutionary", "biology", "human", "evolution", "biology", "computational", "biology" ]	2011	MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains
Dengue is a leading cause of morbidity throughout the tropics; however , accurate population-based estimates of mortality rates are not available . We established the Enhanced Fatal Acute Febrile Illness Surveillance System ( EFASS ) to estimate dengue mortality rates in Puerto Rico . Healthcare professionals submitted...	Dengue is a major public health problem in the tropics . Despite its global importance , population-based mortality rates attributable to dengue are largely unknown . Dengue vaccines are now in late stage clinical trials and one vaccine has been licensed in several countries . Evidence-based decisions regarding the fut...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "reverse", "transcriptase-polymerase", "chain", "reaction", "medicine", "and", "health", "sciences", "clinical", "laboratory", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "demography", "pathogens", "tropical", "diseases", "geo...	2016	Enhanced Surveillance for Fatal Dengue-Like Acute Febrile Illness in Puerto Rico, 2010-2012
Helminth infection is common in malaria endemic areas , and an interaction between the two would be of considerable public health importance . Animal models suggest that helminth infections may increase susceptibility to malaria , but epidemiological data has been limited and contradictory . In a vaccine trial , we stu...	Malaria infection and other parasitic infections are widespread in developing countries . There is evidence from some studies that intestinal worm infections may increase the risk of developing febrile malaria . However , the evidence is mixed , and some studies have found no effect or even protective effects . A vacci...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	Helminth Infection and Eosinophilia and the Risk of Plasmodium falciparum Malaria in 1- to 6-Year-Old Children in a Malaria Endemic Area
Infectious Leptospira colonize the kidneys of reservoir ( e . g . rats ) and accidental hosts such as humans . The renal response to persistent leptospiral colonization , as measured by urinary protein biosignatures , has not been systematically studied . Urinary exosomes--bioactive membrane-bound nanovesicles--contain...	Leptospirosis is a bacterial disease commonly transmitted from animals to humans . Though this disease affects more than three quarters of a million people every year and takes a disproportionate toll on the poor in in tropical regions , few virulence factors have been identified and very little is known regarding the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Proteomic Analysis of Urine Exosomes Reveals Renal Tubule Response to Leptospiral Colonization in Experimentally Infected Rats
At the interface between T cell and antigen-presenting cell ( APC ) , peptide antigen presented by MHC ( pMHC ) binds to the T cell receptor ( TCR ) and initiates signaling . The mechanism of TCR signal initiation , or triggering , remains unclear . An interesting aspect of this puzzle is that although soluble agonist ...	Using the T cell receptor ( TCR ) as a sensor , T cells of the immune system constantly migrate in lymphoid organs and probe the surface of antigen-presenting cells ( APCs ) for foreign antigens , a sign of pathogen infection . Antigen binding by TCRs leads to T cell activation and subsequent immune response to combat ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biotechnology", "biochemistry", "cell", "biology", "immunology", "biophysics" ]	2008	Surface-Anchored Monomeric Agonist pMHCs Alone Trigger TCR with High Sensitivity
The mechanisms by which the sensory environment influences metabolic homeostasis remains poorly understood . In this report , we show that oxygen , a potent environmental signal , is an important regulator of whole body lipid metabolism . C . elegans oxygen-sensing neurons reciprocally regulate peripheral lipid metabol...	We now appreciate that the sensory nervous systems of complex multicellular animals play a profound role in influencing energy balance , and body fat stores . Understanding the precise molecular mechanisms and neuroendocrine pathways by which the nervous system controls metabolic tissues has remained a tremendous chall...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "invertebrates", "medicine", "and", "health", "sciences", "caenorhabditis", "oxygen", "neuroscience", "animals", "animal", "models", "organisms", "oxygen", "metabolism", "caenorhabditis", "elegans", "model", "organisms", "experimental", "organism", "systems...	2018	Oxygen-sensing neurons reciprocally regulate peripheral lipid metabolism via neuropeptide signaling in Caenorhabditis elegans
The timing of spiking activity across neurons is a fundamental aspect of the neural population code . Individual neurons in the retina , thalamus , and cortex can have very precise and repeatable responses but exhibit degraded temporal precision in response to suboptimal stimuli . To investigate the functional implicat...	Neurons convey information about the world in the form of trains of action potentials ( spikes ) . These trains are highly repeatable when the same stimulus is presented multiple times , and this temporal precision across repetitions can be as fine as a few milliseconds . It is usually assumed that this time scale also...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Timing Precision in Population Coding of Natural Scenes in the Early Visual System
In C . elegans , efficient RNA silencing requires small RNA amplification mediated by RNA-dependent RNA polymerases ( RdRPs ) . RRF-1 , an RdRP , and other Mutator complex proteins localize to Mutator foci , which are perinuclear germline foci that associate with nuclear pores and P granules to facilitate small RNA amp...	Small RNAs are a driving force behind the regulation of both essential genes and deleterious transcripts . The Mutator complex is critical to the amplification of high levels of small RNAs and it requires the protein MUT-16 for its assembly . Here we investigate the function of MUT-16 by generating small deletions in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "deletion", "mutation", "rna", "interference", "caenorhabditis", "gene", "regulation", "animals", "animal", "models", "germ", "cells", "mutation", "caenorhabditis", "elegans", "model", "organisms", "immunoprecipitation", "experimental", "organism", "systems...	2018	Distinct regions of the intrinsically disordered protein MUT-16 mediate assembly of a small RNA amplification complex and promote phase separation of Mutator foci
Differential DNA methylation defects of H19/IGF2 are associated with congenital growth disorders characterized by opposite clinical pictures . Due to structural differences between human and mouse , the mechanisms by which mutations of the H19/IGF2 Imprinting Control region ( IC1 ) result in these diseases are undefine...	A humanized mouse line carrying a mutation of the H19/IGF2 imprinting control region demonstrates how tissue-specific and mosaic imprinting alterations result in growth disorders with opposite clinical pictures and asymmetric growth of bilateral organs .	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "disorders", "of", "imprinting", "animal", "models", "developmental", "biology", "model", "organisms", "methylation", "tongue", "experimental", "organism", "systems", "beckwith-wiedemann", "syndrome", "epigenetics", "dna", "embryos...	2018	Tissue-specific and mosaic imprinting defects underlie opposite congenital growth disorders in mice
In vertebrate definitive hematopoiesis , nascent hematopoietic stem/progenitor cells ( HSPCs ) migrate to and reside in proliferative hematopoietic microenvironment for transitory expansion . In this process , well-established DNA damage response pathways are vital to resolve the replication stress , which is deleterio...	The rapidly proliferating hematopoietic stem/progenitor cells ( HSPCs ) require well-established DNA damage response/repair pathways to resolve the DNA replication stress-induced DNA damage , which is deleterious for the genome stability and cell survival . Impairment of these pathways could lead to the progressive bon...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TopBP1 Governs Hematopoietic Stem/Progenitor Cells Survival in Zebrafish Definitive Hematopoiesis
Many components of Wnt/β-catenin signaling pathway also play critical roles in mammary tumor development , yet the role of the tumor suppressor gene APC ( adenomatous polyposis coli ) in breast oncongenesis is unclear . To better understand the role of Apc in mammary tumorigenesis , we introduced conditional Apc mutati...	Breast cancer is one of the most common malignanices in women in Western countries . Many components of Wnt/β-catenin signaling pathway are known to play critical roles in mammary tumor development , yet the role of the tumor suppressor gene APC ( adenomatous polyposis coli ) in breast oncongenesis is unclear . To stud...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/cancer", "genetics", "oncology/breast", "cancer" ]	2009	Genetic Mechanisms in Apc-Mediated Mammary Tumorigenesis
Vegetative phase change is regulated by a decrease in the abundance of the miRNAs , miR156 and miR157 , and the resulting increase in the expression of their targets , SQUAMOSA PROMOTER BINDING PROTEIN-LIKE ( SPL ) transcription factors . To determine how miR156/miR157 specify the quantitative and qualitative changes i...	Leaves produced at different stages in the development of an Arabidopsis shoot vary predictably in shape and size . Previous studies have shown that this phenomenon is regulated by variation in the abundance of the miRNAs , miR156 and miR157 , but how miR156/miR157 produce the changes in leaf morphology that occur duri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "plant", "anatomy", "trichomes", "molecular", "probe", "techniques", "gene", "regulation", "plant", "science", "micrornas", "molecular", "biology", "techniques", "seedlings", "rna", "sequencing", "plants", "research", "and", "analysis", "meth...	2018	Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana
Adaptive evolution in humans has rarely been characterized for its whole set of components , i . e . selective pressure , adaptive phenotype , beneficial alleles and realized fitness differential . We combined approaches for detecting polygenic adaptations and for mapping the genetic bases of physiological and fertilit...	The adaptations to high altitude environments in Tibetan populations have long been highlighted as an important case study of adaptive evolution in our species . Recent genetic studies found two genes , EGLN1 and EPAS1 , the genetic variants in which were swept to high frequency in Tibetans due to strong positive natur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "genome-wide", "association", "studies", "medicine", "and", "health", "sciences", "maternal", "health", "obstetrics", "and", "gynecology", "population", "genetics", "alleles", "ethnicities", "women's", "health", "pregnancy", "genome", "analysis", "population", "biology", ...	2018	Detecting past and ongoing natural selection among ethnically Tibetan women at high altitude in Nepal
MicroRNAs ( miRNAs ) are post-transcriptional regulatory RNAs that can modulate cell signaling and play key roles in cell state transitions . Epstein-Barr virus ( EBV ) expresses >40 viral miRNAs that manipulate both viral and cellular gene expression patterns and contribute to reprogramming of the host environment dur...	Understanding the molecular mechanisms regulating EBV latency and entry into the lytic replication cycle is important in developing therapies for viral disease . We demonstrate here that a subset of EBV miRNAs target host factors within the BCR signaling pathway and consequently , negatively regulate cellular responses...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "colorimetric", "assays", "medicine", "and", "health", "sciences", "luciferase", "immune", "cells", "pathology", "and", "laboratory", "medicine", "natural", "antisense", "transcripts", "gene", "regulation", "enzymes", "immunology", "pathogens", "microb...	2019	Epstein-Barr virus microRNAs regulate B cell receptor signal transduction and lytic reactivation
Replicating circular RNAs are independent plant pathogens known as viroids , or act to modulate the pathogenesis of plant and animal viruses as their satellite RNAs . The rate of discovery of these subviral pathogens was low over the past 40 years because the classical approaches are technical demanding and time-consum...	Viroids are a unique class of subviral pathogens found in plants , and they are difficult to identify since they are free circular non-coding RNAs and often replicate to low levels in host cells . We previously described the computational algorithm PFOR that discovers viroids by analyzing total small RNAs of the infect...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "science", "viroids", "plant", "pathogens", "plant", "pathology", "biology", "and", "life", "sciences" ]	2014	Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms
The transmission of hemorrhagic fever with renal syndrome ( HFRS ) is influenced by environmental determinants . This study aimed to explore the association between atmospheric moisture variability and the transmission of hemorrhagic fever with renal syndrome ( HFRS ) for the period of 1991–2010 in Changsha , China . W...	Hemorrhagic fever with renal syndrome ( HFRS ) , a rodentborne disease caused by Hantaviruses , is characterized by fever , haemorrhage , headache , back pain , abdominal pain , and acute kidney injury . At present , it is endemic in all 31 provinces , autonomous regions , and metropolitan areas in mainland China where...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "environmental", "health", "zoonoses", "hantavirus", "environmental", "epidemiology", "epidemiology", "infectious", "disease", "modeling", "public", "health" ]	2013	Atmospheric Moisture Variability and Transmission of Hemorrhagic Fever with Renal Syndrome in Changsha City, Mainland China, 1991–2010
The multiple-breath washout ( MBW ) is a lung function test that measures the degree of ventilation inhomogeneity ( VI ) . The test is used to identify small airway impairment in patients with lung diseases like cystic fibrosis . However , the physical and physiological factors that influence the test outcomes and diff...	Obstructive lung diseases , like cystic fibrosis or primary ciliary dyskinesia , lead to inhomogeneous ventilation . The degree of observed inhomogeneity represents a clinical measure for the progression of the disease . The multiple-breath washout ( MBW ) is a lung function test that measures this inhomogeneity in the...	[ "Abstract", "Introduction", "Methods", "Results", "&", "discussion" ]	[ "tissue", "mechanics", "medicine", "and", "health", "sciences", "classical", "mechanics", "fluid", "mechanics", "biomechanics", "pulmonology", "pleurae", "simulation", "and", "modeling", "respiratory", "system", "trachea", "research", "and", "analysis", "methods", "resp...	2019	A multi-scale model of gas transport in the lung to study heterogeneous lung ventilation during the multiple-breath washout test
Recognition of specific cell surface glycans , mediated by the VP8* domain of the spike protein VP4 , is the essential first step in rotavirus ( RV ) infection . Due to lack of direct structural information of virus-ligand interactions , the molecular basis of ligand-controlled host ranges of the major human RVs ( P[8]...	Rotaviruses ( RVs ) are diverse , infecting humans and/or animals . Significant advances in understanding ligand-associated RV host ranges have been made but how such host ligands drive RV evolution leading to the diverse genotypes/genogroups already identified remains unclear . In this study , through solving crystal ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "organismal", "evolution", "chemical", "bonding", "medicine", "and", "health", "sciences", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "condensed", "matter", "physics", "microbiology", "microbial", "evolution", "crystallography", "hydrogen", "bon...	2017	Structural basis of glycan specificity of P[19] VP8*: Implications for rotavirus zoonosis and evolution
The avian H7N9 influenza outbreak in 2013 resulted from an unprecedented incidence of influenza transmission to humans from infected poultry . The majority of human H7N9 isolates contained a hemagglutinin ( HA ) mutation ( Q226L ) that has previously been associated with a switch in receptor specificity from avian-type...	Influenza A virus of the H7N9 subtype continues to cross the species barrier from poultry to humans . This zoonotic ability is remarkable as the virus retains specificity to avian-type receptors . To effectively transmit between humans , the virus needs to acquire human-type receptor specificity . In this study , we sh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "h7n9", "chemical", "characterization", "medicine", "and", "health", "sciences", "microbial", "mutation", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "orthomyxoviruses", "animals", "viruses", "respiratory", "system", "h5n1", "...	2017	Three mutations switch H7N9 influenza to human-type receptor specificity
Bacterial cell-cell communication is mediated by small signaling molecules known as autoinducers . Importantly , autoinducer-2 ( AI-2 ) is synthesized via the enzyme LuxS in over 80 species , some of which mediate their pathogenicity by recognizing and transducing this signal in a cell density dependent manner . AI-2 m...	Bacteria communicate with each other through a network of small molecules that are secreted and perceived by nearest neighbors . In a process known as quorum sensing , bacteria communicate their cell density and certain behaviors emerge wherein the population of cells acts as a coordinated community . One small signali...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequence", "analysis", "bio-ontologies", "biology", "computational", "biology", "signaling", "networks" ]	2012	Gene Network Homology in Prokaryotes Using a Similarity Search Approach: Queries of Quorum Sensing Signal Transduction
Synaptic pathology is an early feature of prion as well as other neurodegenerative diseases . Although the self-templating process by which prions propagate is well established , the mechanisms by which prions cause synaptotoxicity are poorly understood , due largely to the absence of experimentally tractable cell cult...	Prion diseases are fatal neurodegenerative disorders that cause memory loss , impaired coordination , and abnormal movements . The molecular culprit in prion diseases is PrPSc , an infectious isoform of a host-encoded glycoprotein ( PrPC ) that can propagate itself by a self-templating mechanism . Whether PrPSc itself ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "animal", "diseases", "enzymes", "enzymology", "vertebrates", "neuroscience", "animals", "mammals", "organisms", "animal", "prion", "diseases", "gel", "electrophoresis", "zoology", "neuronal", "dendrites", "research", "and", "ana...	2016	A Neuronal Culture System to Detect Prion Synaptotoxicity
Dengue-related illness is a leading cause of hospitalization and death in Thailand and other Southeast Asian countries , imposing a major economic burden on households , health systems , and governments . This study aims to assess the economic impact of hospitalized dengue cases on households in Chachoengsao province i...	Dengue , an arbovirus infection with an explosive epidemic potential , is a major public health problem in Thailand and other developing countries in subtropical and tropical regions . Dengue illness often leads to school and work absenteeism , medical and non-medical expenditures , and foregone income . A growing lite...	[ "Abstract", "Introduction", "Material", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "education", "sociology", "tropical", "diseases", "geographical", "locations", "social", "sciences", "indirect", "costs", "health", "care", "pediatrics", "neglected", "tropical", "diseases", "patients", "public", "and", "occupati...	2017	Household costs of hospitalized dengue illness in semi-rural Thailand
We provide a novel method , DRISEE ( duplicate read inferred sequencing error estimation ) , to assess sequencing quality ( alternatively referred to as “noise” or “error” ) within and/or between sequencing samples . DRISEE provides positional error estimates that can be used to inform read trimming within a sample . I...	Sequence quality ( referred to alternatively as the level of sequencing error or noise ) is a primary concern to all sequence-dependent investigations . This is particularly true in the field of metagenomics where automated tools ( e . g . annotation pipelines like MG-RAST ) rely on high fidelity sequence data to deriv...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome", "sequencing", "genomics", "metagenomics", "mathematics", "statistics", "biology", "computational", "biology", "biostatistics" ]	2012	A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE
Nontuberculous mycobacterial pulmonary disease ( NTM-PD ) has become an emerging infectious disease and is responsible for more deaths than tuberculosis in industrialized countries . NTM-PD mortality remains high in some series reportedly ranging from 25% to 40% at five years and often due to unfavorable evolution of N...	Early predictive factors for a favorable development of nontuberculous mycobacterial pulmonary disease ( NTM-PD ) are important to improve management due to the high mortality of this infection at 5 years . The purpose of this study was to search for early factors that could predict at the first year , the favorable or...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "pulmonology", "signs", "and", "symptoms", "fungal", "evolution", "bacteria", "clinical", "microbiology", "sputum", "mycology", "mucus",...	2017	Predictive factors for a one-year improvement in nontuberculous mycobacterial pulmonary disease: An 11-year retrospective and multicenter study
The E3 ubiquitin ligase COP1 ( Constitutive Photomorphogenesis 1 ) is a well known component of the light-mediated plant development that acts as a repressor of photomorphogenesis . Here we show that COP1 positively regulates defense against turnip crinkle virus ( TCV ) and avrRPM1 bacteria by contributing to stability...	Plants must constantly regulate the allocation of resources between photomorphogenesis and defense signaling . Although light is known to influence plant defense , the underlying mechanisms remain largely unknown . Here we show that light plays specific and direct signaling roles in plant defense . Specifically , a pos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "plant", "anatomy", "rna", "interference", "protein", "interactions", "brassica", "plant", "physiology", "protein", "expression", "plant", "science", "model", "organisms", "genetically", "modified", "plants", "experimental", "organism", "systems", "molecu...	2018	COP1, a negative regulator of photomorphogenesis, positively regulates plant disease resistance via double-stranded RNA binding proteins
The shaping of individual cells requires a tight coordination of cell mechanics and growth . However , it is unclear how information about the mechanical state of the wall is relayed to the molecular processes building it , thereby enabling the coordination of cell wall expansion and assembly during morphogenesis . Com...	All morphogenesis processes , whether at the cell scale or tissue level , require the coordination of growth and mechanics to properly shape functional structures . However , the mechanisms that coordinate these two processes in the sculpting of individual cells , and especially in walled cells , remain unknown . Using...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "walls", "control", "theory", "engineering", "and", "technology", "plant", "cell", "biology", "cell", "processes", "plant", "cell", "walls", "control", "engineering", "viscosity", "plant", "science", "developmental", "biology", "systems", "science", "mathemati...	2018	Mechanical feedback coordinates cell wall expansion and assembly in yeast mating morphogenesis
Phenotypic screens can identify molecules that are at once penetrant and active on the integrated circuitry of a whole cell or organism . These advantages are offset by the need to identify the targets underlying the phenotypes . Additionally , logistical considerations limit screening for certain physiological and beh...	Many beneficial pharmacological interventions were first discovered by observing the effects of perturbation of intact biological systems by small organic molecules without a priori knowledge of their targets . This forward pharmacological approach has the advantage of directly identifying new pharmacological agents th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	In Silico Molecular Comparisons of C. elegans and Mammalian Pharmacology Identify Distinct Targets That Regulate Feeding
Identifying viral mutations that confer escape from antibodies is crucial for understanding the interplay between immunity and viral evolution . We describe a high-throughput approach to quantify the selection that monoclonal antibodies exert on all single amino-acid mutations to a viral protein . This approach , mutat...	Many viruses evolve rapidly , and this evolution sometimes enables them to escape antibodies that would otherwise neutralize their infectivity . An important aspect of studying this evolution is determining which viral mutations can mediate antibody escape . The classic way of identifying such mutations is to select or...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "organismal", "evolution", "medicine", "and", "health", "sciences", "microbial", "mutation", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "influenza", "pathogens", "immunology", "microbiology", "orthomyxoviruses", "viruses", "mutation", "rna", "vi...	2017	Complete mapping of viral escape from neutralizing antibodies
Taenia solium cysticercosis/taeniosis is emerging as a serious public health and economic problem in many developing countries . This study was conducted to determine prevalence and risk factors of human T . solium infections in Mbeya Region , Tanzania . A cross-sectional survey was conducted in 13 villages of Mbozi di...	Cysticercosis caused by the zoonotic pork tapeworm , Taenia solium , is emerging as a serious public health and agricultural problem in sub-Saharan Africa . Surveys have shown cysticercosis in pigs to be highly prevalent in multiple foci in Tanzania , and a hospital-based study in the northern highlands indicated neuro...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "neurocysticercosis", "parasitic", "diseases", "neglected", "tropical", "diseases", "veterinary", "science", "infectious", "diseases", "infectious", "diseases", "of", "the", "nervous", "system", "epilepsy", "zoonoses"...	2013	Prevalence and Risk Factors Associated with Human Taenia Solium Infections in Mbozi District, Mbeya Region, Tanzania
Constraint-based modeling techniques have become a standard tool for the in silico analysis of metabolic networks . To further improve their accuracy , recent methodological developments focused on integration of thermodynamic information in metabolic models to assess the feasibility of flux distributions by thermodyna...	When analyzing metabolic networks , one often searches for metabolic pathways with certain ( desired ) properties , for example , conversion routes that maximize the yield of a product from a given substrate . While those problems can be solved with established methods of constraint-based modeling , no algorithm is cur...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "carbohydrate", "metabolism", "ecology", "and", "environmental", "sciences", "chemical", "compounds", "atmospheric", "science", "carbohydrates", "glucose", "metabolism", "organic", "compounds", "glucose", "monomers", "(chemistry)", "metabolites", "thermodynamics", "polymer", ...	2018	OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli
LYST is a large cytosolic protein that influences the biogenesis of lysosome-related organelles , and mutation of the encoding gene , LYST , can cause Chediak-Higashi syndrome . Recently , Lyst-mutant mice were recognized to also exhibit an iris disease resembling exfoliation syndrome , a common cause of glaucoma in hu...	LYST is a poorly understood protein involved in hereditary disease . Mutations in the encoding gene cause Chediak-Higashi syndrome , a rare lethal disease affecting multiple tissues of the body . Mutations in Lyst also recapitulate features of exfoliation syndrome , a common disease affecting the anterior chamber of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/animal", "genetics", "cell", "biology/membranes", "and", "sorting", "genetics", "and", "genomics/disease", "models", "ophthalmology/inherited", "eye", "disorders", "ophthalmology/glaucoma" ]	2010	Elevated Oxidative Membrane Damage Associated with Genetic Modifiers of Lyst-Mutant Phenotypes
Conventional wisdom holds that the best way to treat infection with antibiotics is to ‘hit early and hit hard’ . A favoured strategy is to deploy two antibiotics that produce a stronger effect in combination than if either drug were used alone . But are such synergistic combinations necessarily optimal ? We combine mat...	We take an evolutionary approach to a problem from the medical sciences in seeking to understand how our knowledge of rapid bacterial evolution should shape the way we treat pathogens with antibiotic drugs . We pay particular attention to combinations of different drugs that are purposefully used to produce potent ther...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "control", "theory", "functional", "genomics", "applied", "mathematics", "population", "genetics", "genome", "sequencing", "mutation", "systems", "ecology", "mathematics", "theoretical", "ecology", "infectious", "diseases", "biology", "evolutionary", "theory", ...	2013	When the Most Potent Combination of Antibiotics Selects for the Greatest Bacterial Load: The Smile-Frown Transition
With increased global attention to neglected diseases , there has been a resurgence of interest in eliminating rabies from developing countries through mass dog vaccination . Tanzania recently embarked on an ambitious programme to repeatedly vaccinate dogs in 28 districts . To understand community perceptions and respo...	Mass vaccination of dogs is the most effective strategy to eliminate dog-mediated human rabies from developing countries . In 2009 , a large-scale elimination demonstration project was funded and coordinated by the Bill and Melinda Gates Foundation ( BMGF ) and the World Health Organisation ( WHO ) in three southern co...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "science", "policy", "biology", "and", "life", "sciences", "social", "sciences", "veterinary", "science" ]	2014	Eliminating Rabies in Tanzania? Local Understandings and Responses to Mass Dog Vaccination in Kilombero and Ulanga Districts
The prophage is one of the most important components of variable regions in bacterial genomes . Some prophages carry additional genes that may enhance the toxicity and survival ability of their host bacteria . This phenomenon is predominant in Staphylococcus aureus , a very common human pathogen . Bioinformatics analys...	Staphylococcus aureus is a widely distributed opportunistic pathogen causing numerous foreign-body-associated infections . A large group of virulence factors are encoded by genes of prophages integrated in the bacterial genome . Here we show a heretofore unrecognized mechanism whereby an alternative sigma factor is rec...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbiology/parasitology", "microbiology/medical", "microbiology", "microbiology" ]	2010	Alternative Sigma Factor σH Modulates Prophage Integration and Excision in Staphylococcus aureus
Patients with neonatal severe hyperparathyroidism ( NSHPT ) are homozygous for the calcium-sensing receptor ( CaR ) mutation and have very high circulating PTH , abundant parathyroid hyperplasia , and severe life-threatening hypercalcemia . Mice with homozygous deletion of CaR mimic the syndrome of NSHPT . To determine...	Mice with homozygous deletion of the calcium-sensing receptor ( CaR ) mimic the syndrome of neonatal severe hyperparathyroidism ( NSHPT ) in humans with very high circulating parathyroid hormone ( PTH ) and severe life-threatening hypercalcemia . To determine effects of CaR deficiency on skeletal development and intera...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "nutrition", "endocrinology", "vitamins", "diabetes", "and", "endocrinology", "endocrine", "physiology" ]	2011	The Abnormal Phenotypes of Cartilage and Bone in Calcium-Sensing Receptor Deficient Mice Are Dependent on the Actions of Calcium, Phosphorus, and PTH
Because cohesion prevents sister-chromatid separation and spindle elongation , cohesion dissolution may trigger these two events simultaneously . However , the relatively normal spindle elongation kinetics in yeast cohesin mutants indicates an additional mechanism for the temporal control of spindle elongation . Here w...	Before anaphase onset , the presence of securin Pds1 prevents the cleavage of cohesin , a protein complex that holds sister chromatids together , but the degradation of Pds1 leads to robust cohesion dissolution , resulting in synchronous separation of all chromosomes . Since sister chromatids are attached to spindle mi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics" ]	2013	Coordination of Chromatid Separation and Spindle Elongation by Antagonistic Activities of Mitotic and S-Phase CDKs
The thioredoxin and glutaredoxin pathways are responsible of recycling several enzymes which undergo intramolecular disulfide bond formation as part of their catalytic cycles such as the peroxide scavengers peroxiredoxins or the enzyme ribonucleotide reductase ( RNR ) . RNR , the rate-limiting enzyme of deoxyribonucleo...	The essential enzyme ribonucleotide reductase ( RNR ) , the rate-limiting enzyme of deoxyribonucleotide synthesis , relies on the thioredoxin and glutaredoxin electron flow cascades for recycling . RNR is tightly regulated in a cell cycle-dependent manner at different levels . Here , we show that cytosolic thioredoxin ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "chemical", "compounds", "oxides", "electron", "donors", "cell", "cycle", "and", "cell", "division", "cell", "processes", "dna", "transcription", "fungi", "model", "organisms", "dna", "replication", "experimental", "organism", "systems", "dna", "synthesis", "phase", ...	2017	Lack of a peroxiredoxin suppresses the lethality of cells devoid of electron donors by channelling electrons to oxidized ribonucleotide reductase
Functional MRI ( fMRI ) experiments rely on precise characterization of the blood oxygen level dependent ( BOLD ) signal . As the spatial resolution of fMRI reaches the sub-millimeter range , the need for quantitative modelling of spatiotemporal properties of this hemodynamic signal has become pressing . Here , we find...	Functional magnetic resonance imaging ( fMRI ) experiments have advanced our understanding of the structure and function of the human brain . Dynamic changes in the flow and concentration of oxygen in blood are observed experimentally in fMRI data via the blood oxygen level dependent ( BOLD ) signal . Since neuronal ac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "physics", "mathematics", "theoretical", "biology", "computational", "neuroscience", "interdisciplinary", "physics", "signal", "processing", "applied", "mathematics", "biology", "computational", "biology", "sensory", "systems", "biophysics", "neuroscience", "neuroimaging", "e...	2012	Hemodynamic Traveling Waves in Human Visual Cortex
Viruses that persist despite seemingly effective antiretroviral treatment ( ART ) and can reinitiate infection if treatment is stopped preclude definitive treatment of HIV-1 infected individuals , requiring lifelong ART . Among strategies proposed for targeting these viral reservoirs , the premise of the “shock and kil...	Antiretroviral therapy ( ART ) does not eradicate HIV-1 in infected individuals due to virus persistence in latently infected reservoir cells , despite apparently effective ART . The persistent virus and can rekindle infection when ART is interrupted . The goal of the “shock and kill” viral clearance strategy is to ind...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "antiviral", "therapy", "immune", "activation", "immunology", "microbiology", "preventive", "medicine", "developmental", "bio...	2016	Multi-dose Romidepsin Reactivates Replication Competent SIV in Post-antiretroviral Rhesus Macaque Controllers
Tsetse flies are obligate blood-feeding insects that transmit African trypanosomes responsible for human sleeping sickness and nagana in livestock . The tsetse salivary proteome contains a highly immunogenic family of the endonuclease-like Tsal proteins . In this study , a recombinant version of Tsal1 ( rTsal1 ) was ev...	Salivary proteins of hematophagous disease vectors represent potential biomarkers of exposure and could be used in serological assays that are complementary to entomological surveys . We illustrate that a recombinant version of the highly immunogenic Tsal1 protein of the savannah tsetse fly ( Glossina morsitans morsita...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary", "immunology", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "epidemiology", "african", "trypanosomiasis", "vector", "biology", "immunoassays", "biology", "and", "life", "sciences", "immunologic", "techniques", "trypanosomiasis"...	2014	Serological Responses and Biomarker Evaluation in Mice and Pigs Exposed to Tsetse Fly Bites
The functions of many schistosome gene products remain to be characterized . A major step towards elucidating function of these genes would be in defining their sites of expression . This goal is rendered difficult to achieve by the generally small size of the parasites and the lack of a body cavity , which precludes a...	Schistosomes are parasitic worms responsible for important human diseases in tropical and developing nations . There is urgent need to develop new drugs and vaccines to augment current treatments for this disease . In recent years , concerted efforts by many laboratories have led to extensive genetic sequencing of the ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "molecular", "biology/bioinformatics", "infectious", "diseases/helminth", "infections", "molecular", "biology/molecular", "evolution", "infectious", "diseases/neglected", "tropical", "diseases" ]	2009	Tissue Specific Profiling of Females of Schistosoma japonicum by Integrated Laser Microdissection Microscopy and Microarray Analysis
Leishmania parasites replicate within the phagolysosome compartment of mammalian macrophages . Although Leishmania depend on sugars as a major carbon source during infections , the nutrient composition of the phagolysosome remains poorly described . To determine the origin of the sugar carbon source in macrophage phago...	Macrophages are the primary host cells for a number of important microbial pathogens , including protozoan parasites belonging to the genus Leishmania . With few exceptions , little is known about the nutrient composition of the vacuolar compartments occupied by these pathogens . Leishmania proliferate within the matur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Intracellular Survival of Leishmania major Depends on Uptake and Degradation of Extracellular Matrix Glycosaminoglycans by Macrophages
The spider family Sicariidae includes two genera , Sicarius and Loxosceles . Bites by Sicarius are uncommon in humans and , in Brazil , a single report is known of a 17-year old man bitten by a Sicarius species that developed a necrotic lesion similar to that caused by Loxosceles . Envenomation by Loxosceles spiders ca...	The spider family Sicariidae includes two genera , Sicarius and Loxosceles . These spiders' venoms share a common characteristic , i . e . , the presence of Sphingomyelinases D ( SMase D ) . This toxin is the main component responsible for the local and systemic effects observed in loxoscelism . In the present study , ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "zoology", "biochemistry", "immunology", "biology" ]	2013	Venom of the Brazilian Spider Sicarius ornatus (Araneae, Sicariidae) Contains Active Sphingomyelinase D: Potential for Toxicity after Envenomation
Flea-borne diseases have a wide distribution in the world . Studies on the identity , abundance , distribution and seasonality of the potential vectors of pathogenic agents ( e . g . Yersinia pestis , Francisella tularensis , and Rickettsia felis ) are necessary tools for controlling and preventing such diseases outbre...	The data about flea-borne emerging or re-emerging infections throughout Iran are limited . This paper showed that the flea fauna of Iran were dominated by seven families . Moreover flea-host association analysis indicates that rodents are common hosts of flea families and most vertebrates hosted fleas belonging to the ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "plagues", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "geographical", "locations", "microbiology", "vertebrates", "animals", "bacterial", "diseases", "...	2017	The Fleas (Siphonaptera) in Iran: Diversity, Host Range, and Medical Importance
The ability to integrate experiential information and recall it in the form of memory is observed in a wide range of taxa , and is a hallmark of highly derived nervous systems . Storage of past experiences is critical for adaptive behaviors that anticipate both adverse and positive environmental factors . The process o...	Long term memory formation is a complex process , and at different stages , requires regulation of transcription and protein synthesis . In a novel learning and memory paradigm , we examined transcriptional changes in the fly brain during and after memory formation . With RNA sequencing , we captured transcriptional wa...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetic", "networks", "chemical", "compounds", "gene", "regulation", "enzymes", "enzymology", "neuroscience", "organic", "compounds", "learning", "and", "memory", "cognition", "network", "analysis", "memory", "alcohols", "computer", "and", "information", "sciences", "p...	2017	A systems level approach to temporal expression dynamics in Drosophila reveals clusters of long term memory genes
It has long been known that multiple sclerosis ( MS ) is associated with an increased Epstein-Barr virus ( EBV ) seroprevalence and high immune reactivity to EBV and that infectious mononucleosis increases MS risk . This evidence led to postulate that EBV infection plays a role in MS etiopathogenesis , although the mec...	There is general consensus that multiple sclerosis ( MS ) is associated with Epstein-Barr virus ( EBV ) infection but the mechanistic links are still debated . EBV is a B-lymphotropic herpesvirus widespread in the human population and normally contained as a persistent , asymptomatic infection by immune surveillance . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunopathology", "virology", "immunology", "biology", "microbiology", "host-pathogen", "interaction", "immune", "response", "pathogenesis" ]	2013	Increased CD8+ T Cell Response to Epstein-Barr Virus Lytic Antigens in the Active Phase of Multiple Sclerosis
The exon junction complex ( EJC ) is an RNA binding complex comprised of the core components Magoh , Rbm8a , and Eif4a3 . Human mutations in EJC components cause neurodevelopmental pathologies . Further , mice heterozygous for either Magoh or Rbm8a exhibit aberrant neurogenesis and microcephaly . Yet despite the requir...	The mammalian neocortex is the brain structure responsible for higher cognition , abstract thought , and language . One process critical for brain development is neurogenesis , in which neural stem cell populations generate neurons . Alterations in neurogenesis can lead to neurodevelopmental disorders affecting brain s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "neurogenesis", "microcephaly", "neuroscience", "animal", "models", "developmental", "biology", "model", "organisms", "genome", "analysis", "morphogenesis", "cellular", "structures", "and", "organelles", "research", "and", "analysi...	2016	Haploinsufficiency for Core Exon Junction Complex Components Disrupts Embryonic Neurogenesis and Causes p53-Mediated Microcephaly
Patterns of disease co-occurrence that deviate from statistical independence may represent important constraints on biological mechanism , which sometimes can be explained by shared genetics . In this work we study the relationship between disease co-occurrence and commonly shared genetic architecture of disease . Reco...	Diseases do not always occur together at random , and patterns of disease association may reflect important biological constraints on disease mechanism . When a disease pair occurs more ( or less ) often than would be expected by chance given the frequencies of each disease separately , that may signal the presence of ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "bipolar", "disorder", "social", "sciences", "autism", "developmental", "psychology", "neuroscience", "diabetes", "mellitus", "endocrine", "disorders", "autism", "spectrum", "disorder", "mood", "disorders", "alcoholism", "public", ...	2016	Constraints on Biological Mechanism from Disease Comorbidity Using Electronic Medical Records and Database of Genetic Variants
Detection of Mycobacterium leprae in slit skin smear ( SSS ) is a gold standard technique for the leprosy diagnosis . Over recent years , molecular diagnosis by using PCR has been increasingly used as an alternative for its diagnosis due to its higher sensitivity . This study was carried out for comparative evaluation ...	Although leprosy has been eliminated at the national level , but region wise eastern Nepal has still the higher number of leprosy cases . Early diagnosis and then timely treatment is very crucial to prevent disabilities due to leprosy . Slit-skin smear ( SSS ) , the routine diagnostic method was compared with the molec...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "nervous", "system", "tropical", "diseases", "geographical", "locations", "bacterial", "diseases", "signs", "and", "symptoms", "neglected", "tropical", "dis...	2016	Evaluation of Polymerase Chain Reaction (PCR) with Slit Skin Smear Examination (SSS) to Confirm Clinical Diagnosis of Leprosy in Eastern Nepal
Complexity and heterogeneity are intrinsic to neurobiological systems , manifest in every process , at every scale , and are inextricably linked to the systems’ emergent collective behaviours and function . However , the majority of studies addressing the dynamics and computational properties of biologically inspired c...	Cortical microcircuits are highly inhomogeneous dynamical systems whose information processing capacity is determined by the characteristics of its heterogeneous components and their complex interactions . The high degree of variability that characterizes macroscopic population dynamics , both during ongoing , spontane...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "nervous", "system", "information", "processing", "electrical", "circuits", "population", "dynamics", "membrane", "potential", "electrophysiology", "neuroscience", "learning", "and", "memory", "c...	2019	Leveraging heterogeneity for neural computation with fading memory in layer 2/3 cortical microcircuits
Although the decision to proceed through cell division depends largely on the metabolic status or the size of the cell , the timing of cell division is often set by internal clocks such as the circadian clock . Light is a major cue for circadian clock entrainment , and for photosynthetic organisms it is also the main s...	Microalgae from phytoplankton play an essential role in the biogeochemical cycles through carbon dioxide assimilation in the oceans where they account for more than half of organic carbon production . Photosynthetic cells use light energy for cell growth , but light can also reset the circadian clock , which is involve...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology/plant", "genetics", "and", "gene", "expression", "cell", "biology/cell", "growth", "and", "division", "marine", "and", "aquatic", "sciences/genetics,", "genomics,", "and", "barcoding", "cell", "biology/cell", "signaling" ]	2010	Integration of Light Signals by the Retinoblastoma Pathway in the Control of S Phase Entry in the Picophytoplanktonic Cell Ostreococcus
Correlated neuronal activity is a natural consequence of network connectivity and shared inputs to pairs of neurons , but the task-dependent modulation of correlations in relation to behavior also hints at a functional role . Correlations influence the gain of postsynaptic neurons , the amount of information encoded in...	The co-occurrence of action potentials of pairs of neurons within short time intervals has been known for a long time . Such synchronous events can appear time-locked to the behavior of an animal , and also theoretical considerations argue for a functional role of synchrony . Early theoretical work tried to explain cor...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "physics", "neural", "networks", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience" ]	2014	The Correlation Structure of Local Neuronal Networks Intrinsically Results from Recurrent Dynamics
Coxiella burnetii is an intracellular pathogen that replicates in a lysosome-derived vacuole . The molecular mechanisms used by this bacterium to create a pathogen-occupied vacuole remain largely unknown . Here , we conducted a visual screen on an arrayed library of C . burnetii NMII transposon insertion mutants to ide...	Coxiella burnetii is the causative agent of the human disease Q fever . This bacterium uses the Dot/Icm type IV secretion system to deliver effectors into the cytosol of host cells . The Dot/Icm system is required for intracellular replication of C . burnetii . To determine the contribution of individual proteins to th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "host-pathogen", "interactions", "medical", "microbiology", "microbial", "pathogens", "biology", "and", "life", "sciences", "microbiology", "pathogenesis", "bacterial", ...	2014	A Screen of Coxiella burnetii Mutants Reveals Important Roles for Dot/Icm Effectors and Host Autophagy in Vacuole Biogenesis
Membrane proteins are critical functional molecules in the human body , constituting more than 30% of open reading frames in the human genome . Unfortunately , a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures . Computational to...	Over 30% of the human proteome consists of proteins embedded in biological membranes . These proteins are critical in many processes such as transport of materials in and out of the cell and transmitting signals to other cells in the body . They are implicated in a large number of diseases; in fact , they are targeted ...	[ "Abstract", "Introduction", "Discussion" ]	[]	2015	An Integrated Framework Advancing Membrane Protein Modeling and Design
Colorectal cancer ( CRC ) is believed to arise from mutant stem cells in colonic crypts that undergo a well-characterized progression involving benign adenoma , the precursor to invasive carcinoma . Although a number of ( epi ) genetic events have been identified as drivers of this process , little is known about the d...	The adenomatous polyp ( or adenoma ) is considered the common precursor lesion for colorectal cancer ( CRC ) . Although the natural history of adenomas is well-characterized in terms of their histopathology and ( epi ) genomic changes , little is known about their dynamics in the stage-wise progression from the first a...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "oncology", "medicine", "cancer", "detection", "and", "diagnosis", "stochastic", "processes", "mathematics", "cancer", "prevention", "cancers", "and", "neoplasms", "probability", "theory" ]	2011	Number and Size Distribution of Colorectal Adenomas under the Multistage Clonal Expansion Model of Cancer
Whooping cough caused by Bordetella pertussis is a re-emerging infectious disease despite the introduction of safer acellular pertussis vaccines ( Pa ) . One explanation for this is that Pa are less protective than the more reactogenic whole cell pertussis vaccines ( Pw ) that they replaced . Although Pa induce potent ...	The bacterium Bordetella pertussis causes whooping cough , a severe and often lethal respiratory infection in humans . The disease was largely controlled through vaccination with whole cell pertussis vaccines ( Pw ) . However , Pw had side effects and were replaced in developed countries in the 1990s with safer acellul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biology" ]	2013	Relative Contribution of Th1 and Th17 Cells in Adaptive Immunity to Bordetella pertussis: Towards the Rational Design of an Improved Acellular Pertussis Vaccine
An increasing number of neuroscience papers capitalize on the assumption published in this journal that visual speech would be typically 150 ms ahead of auditory speech . It happens that the estimation of audiovisual asynchrony in the reference paper is valid only in very specific cases , for isolated consonant-vowel s...	Since a paper was published in this journal , an increasing number of neuroscience papers capitalize on the assumption that visual speech would be typically 150 ms ahead of auditory speech . It happens that the estimation of audiovisual asynchrony in the mentioned paper is valid only in very specific cases , for isolat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "linguistics", "psychology", "biology", "and", "life", "sciences", "social", "sciences", "speech" ]	2014	No, There Is No 150 ms Lead of Visual Speech on Auditory Speech, but a Range of Audiovisual Asynchronies Varying from Small Audio Lead to Large Audio Lag
Katanin is an evolutionarily conserved microtubule-severing complex implicated in multiple aspects of microtubule dynamics . Katanin consists of a p60 severing enzyme and a p80 regulatory subunit . The p80 subunit is thought to regulate complex targeting and severing activity , but its precise role remains elusive . In...	Microtubules are critical components of cells , acting as a “scaffold” for the movement of organelles and proteins within the cytoplasm . The control of microtubule length , number , and movement is essential for many cellular processes , including division , architecture , and migration . We have defined the role of t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "urology", "developmental", "biology", "model", "organisms", "biology" ]	2012	An Essential Role for Katanin p80 and Microtubule Severing in Male Gamete Production
Erythropoiesis is one of the best understood examples of cellular differentiation . Morphologically , erythroid differentiation proceeds in a nearly identical fashion between humans and mice , but recent evidence has shown that networks of gene expression governing this process are divergent between species . We undert...	The process whereby blood progenitor cells differentiate into red blood cells , known as erythropoiesis , is very similar between mice and humans . Yet , while studies of this process in mouse have substantially improved our knowledge of human erythropoiesis , recent work has shown a significant divergence in global ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "medicine", "and", "health", "sciences", "genomics", "hematopoiesis", "gene", "regulatory", "networks", "molecular", "development", "gene", "expression", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "anemia", ...	2014	Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation
Active sensing organisms , such as bats , dolphins , and weakly electric fish , generate a 3-D space for active sensation by emitting self-generated energy into the environment . For a weakly electric fish , we demonstrate that the electrosensory space for prey detection has an unusual , omnidirectional shape . We comp...	Most animals , including humans , have sensory and motor capabilities that are biased in the forward direction . The black ghost knifefish , a nocturnal , weakly electric fish from the Amazon , is an interesting exception to this general rule . We demonstrate that these fish have sensing and motor capabilities that are...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "neuroscience", "computational", "biology" ]	2007	Omnidirectional Sensory and Motor Volumes in Electric Fish
The nuclear pore complex ( NPC ) is the gate to the nucleus . Recent determination of the configuration of proteins in the yeast NPC at ∼5 nm resolution permits us to study the NPC global dynamics using coarse-grained structural models . We investigate these large-scale motions by using an extended elastic network mode...	The nuclear pore complex ( NPC ) serves as the sole gateway to the cell nucleus , and its proper functioning is therefore crucial for gene expression and many vital signaling pathways . Although it is typically circular , the overall structure of the NPC has been observed to change in response to the presence of cargo ...	[ "Abstract", "Introduction" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "biophysics/theory", "and", "simulation" ]	2009	Global Motions of the Nuclear Pore Complex: Insights from Elastic Network Models
Unlike most eukaryotes , a kinetochore is fully assembled early in the cell cycle in budding yeasts Saccharomyces cerevisiae and Candida albicans . These kinetochores are clustered together throughout the cell cycle . Kinetochore assembly on point centromeres of S . cerevisiae is considered to be a step-wise process th...	The kinetochore , a macromolecular protein complex that assembles on centromere DNA , interacts with spindle microtubules to mediate faithful chromosome segregation . The sequence of centromere DNA , which varies from 125 bp long point centromere in Saccharomyces cerevisiae to a few Mb long regional centromeres in huma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology", "centromeres", "microbiology", "mitosis", "model", "organisms", "cell", "division", "dna", "chromatin", "chromosome", "biology", "biology", "molecular", "biology", "cell", "biology", "nucleic", "acids", "genetics", "yeast", "and", "fungal", ...	2012	A Coordinated Interdependent Protein Circuitry Stabilizes the Kinetochore Ensemble to Protect CENP-A in the Human Pathogenic Yeast Candida albicans
In the last several years , a number of studies have shown that spliceosome assembly and splicing catalysis can occur co-transcriptionally . However , it has been unclear which specific transcription factors play key roles in coupling splicing to transcription and the mechanisms through which they act . Here we report ...	Pre-messenger RNA splicing , the removal of non-coding RNA sequences ( introns ) that interrupt the protein-coding sequence of genes , is required for proper gene expression . While recent studies have revealed that intron recognition begins while the RNA is actively being synthesized by RNA polymerase II , little is k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/rna", "splicing" ]	2009	Acetylation by the Transcriptional Coactivator Gcn5 Plays a Novel Role in Co-Transcriptional Spliceosome Assembly
Shotgun metagenomic analysis of the human associated microbiome provides a rich set of microbial features for prediction and biomarker discovery in the context of human diseases and health conditions . However , the use of such high-resolution microbial features presents new challenges , and validated computational too...	The human microbiome–the entire set of microbial organisms associated with the human host–interacts closely with host immune and metabolic functions and is crucial for human health . Significant advances in the characterization of the microbiome associated with healthy and diseased individuals have been obtained throug...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Methods" ]	[ "body", "weight", "medicine", "and", "health", "sciences", "microbiome", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "neuroscience", "liver", "diseases", "group", "f", "streptococci", "organisms", "metagenomics", "physiological", "parameters...	2016	Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights
Meiotic recombination is required for proper homologous chromosome segregation in plants and other eukaryotes . The eukaryotic RAD51 gene family has seven ancient paralogs with important roles in mitotic and meiotic recombination . Mutations in mammalian RAD51 homologs RAD51C and XRCC3 lead to embryonic lethality . In ...	Meiotic recombination and sister chromatid cohesion are important for maintaining the association between homologous chromosomes and ensuring their accurate segregation . Meiotic recombination starts with a set of programmed DNA double-strand breaks ( DSBs ) , catalyzed by the SPO11 endonuclease . Processing of DSB end...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "homologous", "chromosomes", "chromosome", "structure", "and", "function", "centromeres", "metaphase", "cell", "cycle", "and", "cell", "division", "cell", "processes", "brassica", "pollen", "plant", "science", "model", "organisms", "experimental", ...	2017	Arabidopsis RAD51, RAD51C and XRCC3 proteins form a complex and facilitate RAD51 localization on chromosomes for meiotic recombination
Advances in genomic studies have led to significant progress in understanding the epigenetically controlled interplay between chromatin structure and nuclear functions . Epigenetic modifications were shown to play a key role in transcription regulation and genome activity during development and differentiation or in re...	Previous studies revealed spatially coherent and biological-meaningful chromatin mark combinations in human cells . Here , we analyze thirteen epigenetic mark maps in the human cell line K562 at 100 kb resolution of MRT data . The complexity of epigenetic data is reduced to four chromatin states that display remarkable...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[]	2013	Human Genome Replication Proceeds through Four Chromatin States
The Drosophila melanogaster gene archipelago ( ago ) encodes the F-box/WD-repeat protein substrate specificity factor for an SCF ( Skp/Cullin/F-box ) -type polyubiquitin ligase that inhibits tumor-like growth by targeting proteins for degradation by the proteasome . The Ago protein is expressed widely in the fly embryo...	Cells in multicellular animals must adapt to changing environmental conditions in order to ensure survival of the larger organism . One key challenge they face is fluctuation in the availability of dissolved oxygen . As cells get low on oxygen , they respond by turning on a program of gene expression that helps them su...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "growth", "control", "cellular", "stress", "responses", "cancer", "genetics", "developmental", "biology", "morphogenesis", "gene", "expression", "biology", "molecular", "biology", "signal", "transduction", "cell", "biology", "cell", "migration", "genetics", "molecular", ...	2013	The Archipelago Ubiquitin Ligase Subunit Acts in Target Tissue to Restrict Tracheal Terminal Cell Branching and Hypoxic-Induced Gene Expression
The guanine nucleotide exchange factor Vav1 is essential for transducing T cell antigen receptor signals and therefore plays an important role in T cell development and activation . Our previous genetic studies identified a locus on rat chromosome 9 that controls the susceptibility to neuroinflammation and contains a n...	The understanding of the physiological role of Vav1 , a key regulator of T cell receptor signaling , was primarily inferred from studies using Vav1-deficient mice . Such models , however , provide little insight on how polymorphisms leading to quantitative changes in Vav1 activity could affect immune system functions ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "t", "helper", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "immunology", "animal", "models", "developmental", "biology", "model", "organisms", "stem", "cell...	2016	A Natural Variant of the T Cell Receptor-Signaling Molecule Vav1 Reduces Both Effector T Cell Functions and Susceptibility to Neuroinflammation
Scaling up of insecticide treated nets has contributed to a substantial malaria decline . However , some malaria vectors , and most arbovirus vectors , bite outdoors and in the early evening . Therefore , topically applied insect repellents may provide crucial additional protection against mosquito-borne pathogens . Am...	Malaria and arboviruses are transmitted by several mosquitoes . Targeting these mosquitoes instead of the pathogens can contribute to prevention of these diseases . For mosquitoes biting throughout the night , mosquito nets ( preferably impregnated with insecticides ) are very effective for mosquito control . However ,...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "dengue", "fever", "neglected", "tropical", "diseases", "tropical", "diseases", "viral", "diseases" ]	2014	Field Evaluation of Picaridin Repellents Reveals Differences in Repellent Sensitivity between Southeast Asian Vectors of Malaria and Arboviruses
Trypanosoma cruzi is the causative agent of Chagas disease , which affects more than 9 million people in Latin America . We have generated a draft genome sequence of the TcI strain Sylvio X10/1 and compared it to the TcVI reference strain CL Brener to identify lineage-specific features . We found virtually no differenc...	Chagas disease is a major health problem in Latin America and it is caused by the protozoan parasite Trypanosoma cruzi . The genome sequence of the T . cruzi strain CL Brener ( TcVI ) has revealed a genome with large repertoires of genes for surface antigens , among other features . In the present study , we sequenced ...	[ "Abstract", "Introduction", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases", "genetics", "and", "genomics" ]	2011	Shotgun Sequencing Analysis of Trypanosoma cruzi I Sylvio X10/1 and Comparison with T. cruzi VI CL Brener
In Caenorhabditis elegans , the dosage compensation complex ( DCC ) specifically binds to and represses transcription from both X chromosomes in hermaphrodites . The DCC is composed of an X-specific condensin complex that interacts with several proteins . During embryogenesis , DCC starts localizing to the X chromosome...	In many animals , males have a single X and females have two X chromosomes , creating an X chromosomal gene dosage imbalance between sexes . This imbalance is corrected by dosage compensation mechanisms , which are essential for development in mammals , flies and worms . The timing and the molecular mechanisms of dosag...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Developmental Dynamics of X-Chromosome Dosage Compensation by the DCC and H4K20me1 in C. elegans
Co-evolution of transcriptional regulatory proteins and their sites of action has been often hypothesized but rarely demonstrated . Here we provide experimental evidence of such co-evolution in yeast silent chromatin , a finding that emerged from studies of hybrids formed between two closely related Saccharomyces speci...	As eukaryotic species evolve , transcriptionally silent portions of their genomes—termed “heterochromatin”—mutate rapidly . To maintain the “off” state of certain genes in silenced regions , regulatory DNA sequences called silencers , which reside within a rapidly mutating region , must co-evolve with the regulatory pr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "expression", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics", "molecular", "biology/molecular", "evolution", "evolutionary", "biology/genomics", "genetics", "and", "genomics/gene", "function", "genetics", "and", "g...	2010	Co-Evolution of Transcriptional Silencing Proteins and the DNA Elements Specifying Their Assembly
There is a critical need to better use existing antibiotics due to the urgent threat of antibiotic resistant bacteria coupled with the reduced effort in developing new antibiotics . β-lactam antibiotics represent one of the most commonly used classes of antibiotics to treat a broad spectrum of Gram-positive and -negati...	Antibiotic resistance is a growing problem that the World Health Organization describes as “one of the top three threats to global health . ” To date , bacteria have developed resistance to all antibiotics used in clinical settings . Unfortunately , the evolution of antibiotic resistant bacteria is accelerating , as an...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Bacterial Temporal Dynamics Enable Optimal Design of Antibiotic Treatment
Tether proteins attach the endoplasmic reticulum ( ER ) to other cellular membranes , thereby creating contact sites that are proposed to form platforms for regulating lipid homeostasis and facilitating non-vesicular lipid exchange . Sterols are synthesized in the ER and transported by non-vesicular mechanisms to the p...	Almost half of the inner surface area of the yeast plasma membrane ( PM ) is covered with closely associated cortical endoplasmic reticulum ( ER ) . In yeast and human cells , it has been proposed that ER-anchored tether proteins staple the ER to the PM , creating membrane contact sites at which lipid transport between...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "b", "vitamins", "chemical", "compounds", "endoplasmic", "reticulum", "cell", "processes", "organic", "compounds", "cholines", "membrane", "proteins", "fungi", "cellular", "structures", "and", "organelles", "lipids", "chemistry", "vitamins", "sterols", "cell", "membrane...	2018	Endoplasmic reticulum-plasma membrane contact sites integrate sterol and phospholipid regulation
Numerous gene fusions have been uncovered across multiple cancer types . Although the ability to target several of these fusions has led to the development of some successful anti-cancer drugs , most of them are not druggable . Understanding the molecular pathways of a fusion is important in determining its function in...	We present a computational framework , FusionPathway , to infer the oncogenesis pathways of a fusion and help develop therapeutic strategies in these pathways for patients harboring the fusion . In this work , we successfully validated the capabilities of this approach through its application to the well-studied BCR-AB...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "protein", "interactions", "cancer", "treatment", "protein", "interaction", "networks", "cancers", "and", "neoplasms", "oncology", "ewing", "sarcoma", "network", "analysis", "molecular", "biology", "techniqu...	2018	FusionPathway: Prediction of pathways and therapeutic targets associated with gene fusions in cancer
Circadian clocks are aligned to the environment via synchronizing signals , or Zeitgebers , such as daily light and temperature cycles , food availability , and social behavior . In this study , we found that genome-wide expression profiles from temperature-entrained flies show a dramatic difference in the presence or ...	A key adaptation to life on Earth is provided by internal daily time-keeping mechanisms that allow anticipation of the alternations between night and day . To act as reliable time-keeping mechanisms , circadian clocks have to be able to synchronize to environmental time cues , maintain ∼24-h rhythms under constant cond...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "biochemistry", "none", "cell", "biology", "neuroscience", "drosophila", "genetics", "and", "genomics" ]	2007	Integration of Light and Temperature in the Regulation of Circadian Gene Expression in Drosophila
Invariant natural killer T ( iNKT ) cells are an evolutionary conserved T cell population characterized by features of both the innate and adaptive immune response . Studies have shown that iNKT cells are required for protective responses to Gram-positive pathogens such as Streptococcus pneumoniae , and that these cell...	Invariant natural killer T ( iNKT ) cells are an evolutionarily conserved population of immune cells that recognize lipid antigens . A protein called a T cell receptor for antigen ( TCR ) on the surface of these iNKT cells recognizes lipids bound to a protein called CD1d on the surface of antigen-presenting cells . Her...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "immunology", "biology" ]	2011	Unique Interplay between Sugar and Lipid in Determining the Antigenic Potency of Bacterial Antigens for NKT Cells
The effect of drugs , disease and other perturbations on mRNA levels are studied using gene expression microarrays or RNA-seq , with the goal of understanding molecular effects arising from the perturbation . Previous comparisons of reproducibility across laboratories have been limited in scale and focused on a single ...	Gene expression studies in model systems are widely used for understanding the mechanism of drugs and other perturbations in biological systems . Other researchers have examined the reproducibility of microarray studies between laboratories , or comparing microarrays and/or RNA sequencing . However , no large scale stu...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "liver", "vertebrates", "animals", "mammals", "dna", "transcription", "animal", "models", "model", "organisms", "pharmaceutics", "genome", "analysis", "bioassays", "and", "physiological", "analysis", "research", "and", "analysis"...	2016	Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes
Genome-wide association studies have successfully identified thousands of loci for a range of human complex traits and diseases . The proportion of phenotypic variance explained by significant associations is , however , limited . Given the same dense SNP panels , mixed model analyses capture a greater proportion of ph...	Unravelling overall trait architecture of complex traits and diseases is important for phenotype prediction and disease prevention and correct modelling of the trait will further aid discovery of causative loci . Here we take advantage of genome-wide data and a large family-based study to examine the role of common gen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "chemical", "compounds", "social", "sciences", "biomarkers", "anthropology", "organic", "compounds", "carbohydrates", "glucose", "simulation", "and", "modeling", "genome", "analysis", "research", "and", "analysis", "methods", "anth...	2016	Pedigree- and SNP-Associated Genetics and Recent Environment are the Major Contributors to Anthropometric and Cardiometabolic Trait Variation
Target-based screening is one of the major approaches in drug discovery . Besides the intended target , unexpected drug off-target interactions often occur , and many of them have not been recognized and characterized . The off-target interactions can be responsible for either therapeutic or side effects . Thus , ident...	High-throughput techniques have generated vast amounts of diverse omics and phenotypic data . However , these sets of data have not yet been fully explored to improve the effectiveness and efficiency of drug discovery , a process which has traditionally adopted a one-drug-one-gene paradigm . Consequently , the cost of ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "applied", "mathematics", "cancer", "treatment", "enzymology", "simulation", "and", "modeling", "oncology", "algorithms", "genomic", "databases", "tyrosine", "kinase", "inhibitors", "mathematics", "forecasting", "statistics", "(mat...	2016	Large-Scale Off-Target Identification Using Fast and Accurate Dual Regularized One-Class Collaborative Filtering and Its Application to Drug Repurposing
Sensory information about the state of the world is generally ambiguous . Understanding how the nervous system resolves such ambiguities to infer the actual state of the world is a central quest for sensory neuroscience . However , the computational principles of perceptual disambiguation are still poorly understood: W...	Sensory information is generally ambiguous , and a single sensory modality most often cannot provide enough information to univocally specify the actual state of the world . A primary task for the brain is therefore to resolve perceptual ambiguity . Here we use a dynamic audiovisual ambiguous display embedded in noise ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "decision", "making", "engineering", "and", "technology", "signal", "processing", "social", "sciences", "light", "neuroscience", "learning", "and", "memory", "electromagnetic", "radiation", "perception", "cognitive", "psychology", "luminance", "cognition", "memory", "visi...	2017	Noise, multisensory integration, and previous response in perceptual disambiguation
Viruses are usually thought to form parasitic associations with hosts , but all members of the family Polydnaviridae are obligate mutualists of insects called parasitoid wasps . Phylogenetic data founded on sequence comparisons of viral genes indicate that polydnaviruses in the genus Bracovirus ( BV ) are closely relat...	Microorganisms form symbiotic associations with animals and plants that range from parasitic ( pathogens ) to beneficial ( mutualists ) . Although numerous examples of obligate , mutualistic bacteria , fungi , and protozoans exist , viruses are almost always considered to be pathogens . An exception is the family Polyd...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "dna", "viruses", "viral", "classification", "virology", "biology", "microbiology" ]	2013	Mutualistic Polydnaviruses Share Essential Replication Gene Functions with Pathogenic Ancestors
ATR activation is dependent on temporal and spatial interactions with partner proteins . In the budding yeast model , three proteins – Dpb11TopBP1 , Ddc1Rad9 and Dna2 - all interact with and activate Mec1ATR . Each contains an ATR activation domain ( ADD ) that interacts directly with the Mec1ATR:Ddc2ATRIP complex . An...	DNA damage checkpoint signalling is an essential component of the DNA damage response . Many of the key proteins initiating the checkpoint signal have been identified and characterised in yeast . Here we explore the role of the ATR activating domain ( AAD ) of TopBP1 in embryonic development , cell growth and checkpoin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	An Essential Function for the ATR-Activation-Domain (AAD) of TopBP1 in Mouse Development and Cellular Senescence
The collagen binding integrin α2β1 plays a crucial role in hemostasis , fibrosis , and cancer progression amongst others . It is specifically inhibited by rhodocetin ( RC ) , a C-type lectin-related protein ( CLRP ) found in Malayan pit viper ( Calloselasma rhodostoma ) venom . The structure of RC alone reveals a heter...	In animals , collagen-mediated platelet aggregation is an essential component of the blood’s clotting response following vascular injury . A small group of snake venom toxins belonging to the C-type lectin protein family exert their harmful effects by directly targeting this pathway . Rhodocetin ( RC ) is a heterotetra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "crystal", "structure", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "aliphatic", "amino", "acids", "condensed", "matter", "physics", "organic", "compounds", "toxicology", "toxic", "agents", ...	2017	Dramatic and concerted conformational changes enable rhodocetin to block α2β1 integrin selectively
Chromosomal insertions are genomic rearrangements with a chromosome segment inserted into a non-homologous chromosome or a non-adjacent locus on the same chromosome or the other homologue , constituting ~2% of nonrecurrent copy-number gains . Little is known about the molecular mechanisms of their formation . We identi...	By traditional cytogenetic techniques , the incidence of microscopically visible chromosomal insertions was estimated to be 1 in 80 , 000 live births . More recently , by aCGH in conjunction with FISH confirmation of the aCGH findings , insertion events were demonstrated to occur much more frequently ( 1 in ~500 indivi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "probe", "techniques", "dna", "replication", "molecular", "biology", "techniques", "translocations", "dna", "duplications", "research", "and", "analysis", "methods", "genome", "complexity", "probe", "hybridization", "chromosome", "biology", "chromosomal", "ab...	2016	Mechanisms for Complex Chromosomal Insertions
Traditionally microorganisms were considered to be autonomous organisms that could be studied in isolation . However , over the last decades cell-to-cell communication has been found to be ubiquitous . By secreting molecular signals in the extracellular environment microorganisms can indirectly assess the cell density ...	Biological systems are characterized by communication; humans talk , insects produce pheromones and birds sing . Over the last decades it has been shown that even the simplest organisms on earth , the bacteria , communicate . Despite the prevalence of communication , it is often hard to explain how communicative system...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "bacteriology", "signaling", "networks", "evolutionary", "selection", "microbiology", "cell", "differentiation", "developmental", "biology", "microbial", "evolution", "molecular", "development", "microbial", "growth", "and", "development", "theoretical", "biology", "evolution...	2012	The Evolution of Cell-to-Cell Communication in a Sporulating Bacterium
Convergent extension , the simultaneous extension and narrowing of tissues , is a crucial event in the formation of the main body axis during embryonic development . It involves processes on multiple scales: the sub-cellular , cellular and tissue level , which interact via explicit or intrinsic feedback mechanisms . Co...	The process of convergent extension is a major contributor to the formation of the anterior-posterior body axis in the early embryo . Convergent extension refers to the directed movement of cells that leads to the extension of tissue in one direction and narrowing of the tissue in the perpendicular direction . Often , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Segment-Specific Adhesion as a Driver of Convergent Extension
In colonies of the honeybee Apis mellifera , the queen is usually the only reproductive female , which produces new females ( queens and workers ) by laying fertilized eggs . However , in one subspecies of A . mellifera , known as the Cape bee ( A . m . capensis ) , worker bees reproduce asexually by thelytoky , an abn...	Honeybee colonies are mainly composed of female worker bees that are unable to lay eggs and reproduce; a task that is performed by a single queen bee . However , in a subspecies of the Western honeybee ( Apis mellifera ) known as the Cape bee ( A . m . capensis ) , worker bees can lay eggs produced by an abnormal form ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "ecology", "and", "environmental", "sciences", "honey", "bees", "population", "genetics", "invertebrate", "genomics", "animals", "population", "biology", "bees", "genomic", "signal", "processing", "hymenoptera", "parasitism", "genetic", "loci", "animal", ...	2016	Identification of Multiple Loci Associated with Social Parasitism in Honeybees
Nipah virus targets human endothelial cells via NiV-F and NiV-G envelope glycoproteins , resulting in endothelial syncytia formation and vascular compromise . Endothelial cells respond to viral infection by releasing innate immune effectors , including galectins , which are secreted proteins that bind to specific glyca...	Nipah virus ( NiV ) is classified as a “priority pathogen” by the NIH . NiV infection of humans results in multi-organ hemorrhage due to endothelial syncytia formation , and also causes fatal encephalitis in up to 70% of patients . As there are no effective vaccines or therapeutics for NiV , understanding the mechanism...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "antiviral", "responses", "virology/emerging", "viral", "diseases", "pathology/pathophysiology", "immunology/innate", "immunity" ]	2010	Endothelial Galectin-1 Binds to Specific Glycans on Nipah Virus Fusion Protein and Inhibits Maturation, Mobility, and Function to Block Syncytia Formation
Influenza A virus ( IAV ) neuraminidase ( NA ) receptor-destroying activity and hemagglutinin ( HA ) receptor-binding affinity need to be balanced with the host receptor repertoire for optimal viral fitness . NAs of avian , but not human viruses , contain a functional 2nd sialic acid ( SIA ) -binding site ( 2SBS ) adja...	Influenza A viruses infect birds and mammals . They contain receptor-binding ( HA ) and receptor-destroying ( NA ) proteins , which are crucial determinants of host tropism and pathogenesis . It is generally accepted that the functional properties of HA and NA need to be well balanced to enable virion penetration of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "characterization", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "vertebrates", "viral", "structure", "orthomyxoviruses", "animals", "viruses", "rna", "viruses", "research", "and", "analysi...	2019	The 2nd sialic acid-binding site of influenza A virus neuraminidase is an important determinant of the hemagglutinin-neuraminidase-receptor balance
Although little is known about the role of the cystic fibrosis transmembrane regulator ( CFTR ) gene in reproductive physiology , numerous variants in this gene have been implicated in etiology of male infertility due to congenital bilateral absence of the vas deferens ( CBAVD ) . Here , we studied the fertility effect...	Cystic fibrosis ( CF ) is the most common lethal recessive disorder in European-derived populations and is characterized by clinical heterogeneity that involves multiple organ systems . Over 1 , 600 disease-causing mutations have been identified in the cystic fibrosis transmembrane regulator ( CFTR ) gene , but our und...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/human", "evolution", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/medical", "genetics", "genetics", "and", "genomics/population", "genetics" ]	2010	The CFTR Met 470 Allele Is Associated with Lower Birth Rates in Fertile Men from a Population Isolate

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