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article stringlengths 4.36k 149k	summary stringlengths 32 3.35k	section_headings listlengths 1 91	keywords listlengths 0 141	year stringclasses 13 values	title stringlengths 20 281
Sleep science is entering a new era , thanks to new data-driven analysis approaches that , combined with mouse gene–editing technologies , show a promise in functional genomics and translational research . However , the investigation of sleep is time consuming and not suitable for large-scale phenotypic datasets , main...	Sleep is a heterogeneous process determined by a number of genetic and epigenetic factors . To investigate the biology of sleep , animal models , such as mice , are extensively used in sleep studies , and large-scale phenotypic datasets are required to reach meaningful conclusions . Currently , manual annotations of el...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "sleep", "deprivation", "sleep", "brain", "electrophysiology", "electrophysiology", "neuroscience", "animal", "models", "physiological", "processes", "clinical", "medicine", "model", "organisms", "homeostasis", "brain", "mapping", ...	2018	A novel unsupervised analysis of electrophysiological signals reveals new sleep substages in mice
Porphyromonas gingivalis is the primary etiologic agent of periodontal disease that is associated with other human chronic inflammatory diseases , including atherosclerosis . The ability of P . gingivalis to invade and persist within human aortic endothelial cells ( HAEC ) has been postulated to contribute to a low to ...	A number of successful pathogens have evolved mechanisms to evade host defenses , thus establishing persistent and chronic infections . Although membrane-bound innate immune receptors including Toll-like receptors play a role in inflammation in response to the common oral pathogen Porphyromonas gingivalis , it is not k...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immunity", "to", "infections", "immunology", "microbiology", "host-pathogen", "interaction", "cardiovascular", "immune", "defense", "atherosclerosis", "bacterial", "pathogens", "oral", "diseases", "oral", "medicine", "medical", "microbiology", "biology", "gram"...	2012	Pathogen-Mediated Proteolysis of the Cell Death Regulator RIPK1 and the Host Defense Modulator RIPK2 in Human Aortic Endothelial Cells
Predicting novel microRNA ( miRNA ) -disease associations is clinically significant due to miRNAs’ potential roles of diagnostic biomarkers and therapeutic targets for various human diseases . Previous studies have demonstrated the viability of utilizing different types of biological data to computationally infer new d...	Discovering miRNA-disease associations promotes the understanding towards the molecular mechanisms of various human diseases at the miRNA level , and contributes to the development of diagnostic biomarkers and treatment tools for diseases . Computational models can make the discovery more efficient and experiments more...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cell", "death", "renal", "cell", "carcinoma", "medicine", "and", "health", "sciences", "linguistics", "gene", "regulation", "cell", "processes", "carcinomas", "cancers", "and", "neoplasms", "social", "sciences", "genitourinary", "tract", "tumors", "biomarkers", "onco...	2017	LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
Torque teno viruses ( TTVs ) are a group of viruses with small , circular DNA genomes . Members of this family are thought to ubiquitously infect humans , although causal disease associations are currently lacking . At present , there is no understanding of how infection with this diverse group of viruses is so prevale...	The torque teno viruses ( TTVs ) are a diverse group of viruses that ubiquitously infect humans and establish persistent infections . Despite their prevalence , TTVs lack concrete disease associations and remain among the most poorly characterized human viruses . Here we use computational and synthetic approaches to id...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	A Human Torque Teno Virus Encodes a MicroRNA That Inhibits Interferon Signaling
Dengue is an infection of increasing global importance , yet uncertainty remains regarding critical aspects of its virology , immunology and epidemiology . One unanswered question is how infection is controlled and cleared during a dengue infection . Antibody is thought to play a role , but little past work has examine...	Dengue is a globally important viral disease . Despite this , there is still much unknown about the immunology , virology and epidemiology of dengue . As for all viral infections , the interaction between virus and immune response is a complex one . Using data collected from patients , we model how the virus replicates...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "death", "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "cell", "processes", "microbiology", "mathematical", "models", ...	2016	Modelling Virus and Antibody Dynamics during Dengue Virus Infection Suggests a Role for Antibody in Virus Clearance
The largest outbreak of sporotrichosis occurred between 1938 and 1947 in the gold mines of Witwatersrand in South Africa . Here , we describe an outbreak of lymphocutaneous sporotrichosis that was investigated in a South African gold mine in 2011 . Employees working at a reopened section of the mine were recruited for ...	Sporotrichosis is a neglected tropical fungal disease . The subcutaneous form occurs following traumatic inoculation of organic matter contaminated with the fungus through the skin . Between 1938 and 1947 , the Witwatersrand gold mines in South Africa were the site of the largest outbreak of sporotrichosis worldwide . ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	An Outbreak of Lymphocutaneous Sporotrichosis among Mine-Workers in South Africa
Symbiosis has been among the most important evolutionary steps to generate biological complexity . The establishment of symbiosis required an intimate metabolic link between biological systems with different complexity levels . The strict endo-cellular symbiotic bacteria of insects are beautiful examples of the metabol...	Biological complexity has emerged on earth by the combination of living forms . This combination , called symbiosis , had to overcome the problems caused by the uncoupled metabolisms of the organisms involved . One way to do so was through the loss of genes that were no longer needed for the endosymbiont in the protect...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "genetics", "and", "genomics/comparative", "genomics", "genetics", "and", "genomics/bioinformatics", "computational", "biology/genomics" ]	2009	Genome-Wide Functional Divergence after the Symbiosis of Proteobacteria with Insects Unraveled through a Novel Computational Approach
Sosuga virus ( SOSV ) is a recently discovered zoonotic paramyxovirus isolated from a single human case in 2012; it has been ecologically and epidemiologically associated with transmission by the Egyptian rousette bat ( Rousettus aegyptiacus ) . Bats have long been recognized as sources of novel zoonotic pathogens , in...	Shortly after returning from a field trip to South Sudan and Uganda in 2012 , a wildlife researcher presented to the emergency room with high fever and muscle and joint pain , that later progressed to severe disease . Sosuga virus ( SOSV ) , a novel paramyxovirus , was identified as the etiological agent . Further epid...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "pathogens", "microbiology", "pulmonology", "plasmid", "construction", "viruses", "rna", "viruses", "genome", "analysis", "sequence", "motif", "analysis", ...	2018	Development of a reverse genetics system for Sosuga virus allows rapid screening of antiviral compounds
Human Enterovirus 71 ( EV71 ) commonly causes Hand , Foot and Mouth Disease in young children , and occasional occurrences of neurological complications can be fatal . In this study , a high-throughput cell-based screening on the serine/threonine kinase siRNA library was performed to identify potential antiviral agents...	Since its first isolation , human Enterovirus 71 ( EV71 ) has been known to cause hand , foot and mouth disease in children , with some cases developing severe neurologic complications , leading to death . In the recent years , outbreaks within the Asia-Pacific region have caused significant deaths , making EV71 a majo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Role of Misshapen NCK-related kinase (MINK), a Novel Ste20 Family Kinase, in the IRES-Mediated Protein Translation of Human Enterovirus 71
Monoamines provide chemical codes of behavioral states . However , the neural mechanisms of monoaminergic orchestration of behavior are poorly understood . Touch elicits an escape response in Caenorhabditis elegans where the animal moves backward and turns to change its direction of locomotion . We show that the tyrami...	How the nervous system controls complex behaviors has intrigued neurobiologists for decades . There are many examples where sequential motor patterns of specific behaviors have been described in great detail . However , the neural mechanisms that orchestrate a full behavioral sequence are poorly understood . Gentle tou...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "neuroscience", "animal", "genetics", "neural", "networks", "neuroscience", "neurotransmitter", "receptor", "signaling", "gene", "function", "animal", "models", "motor", "systems", "caenorhabditis", "elegans", "model", "organisms", "membrane", "receptor", "si...	2013	Monoaminergic Orchestration of Motor Programs in a Complex C. elegans Behavior
The emerging structural information about allosteric kinase complexes and the growing number of allosteric inhibitors call for a systematic strategy to delineate and classify mechanisms of allosteric regulation and long-range communication that control kinase activity . In this work , we have investigated mechanistic a...	Despite recent progress in computational and experimental studies of dynamic regulation in protein kinases , a mechanistic understanding of long-range communication and mechanisms of mutation-induced signaling controlling kinase activity remains largely qualitative . In this study , we have performed a systematic model...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "algorithms", "physics", "computer", "science", "computational", "chemistry", "computer", "modeling", "statistical", "mechanics", "chemistry", "biology", "computational", "biology", "biophysics" ]	2011	Computational Modeling of Allosteric Communication Reveals Organizing Principles of Mutation-Induced Signaling in ABL and EGFR Kinases
The positive-strand RNA virus Turnip yellow mosaic virus ( TYMV ) encodes an ovarian tumor ( OTU ) -like protease/deubiquitinase ( PRO/DUB ) protein domain involved both in proteolytic processing of the viral polyprotein through its PRO activity , and in removal of ubiquitin chains from ubiquitylated substrates through...	Viruses have much smaller genomes than their hosts . Consequently , they often encode proteins which are multifunctional . For instance , some viral proteases have a dual function , being also deubiquitinases , i . e . enzymes capable of removing ubiquitin tags grafted onto proteins and that often target them for destr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "plant", "anatomy", "microbial", "mutation", "crystal", "structure", "molecular", "dynamics", "condensed", "matter", "physics", "microbiology", "brassica", "crystals", "plant", "science", "model", "organisms", "materials", "science", "experimental", "organism", "systems",...	2017	A mobile loop near the active site acts as a switch between the dual activities of a viral protease/deubiquitinase
We hypothesized that a common SNP in the 3' untranslated region of the upstream transcription factor 1 ( USF1 ) , rs3737787 , may affect lipid traits by influencing gene expression levels , and we investigated this possibility utilizing the Mexican population , which has a high predisposition to dyslipidemia . We first...	By integrating a genetic polymorphism with genome-wide gene expression levels , we were able to attribute function to a genetic polymorphism in the USF1 gene . The USF1 gene has previously been associated with a common dyslipidemia , FCHL . FCHL is characterized by elevated levels of total cholesterol , triglycerides ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/gene", "expression" ]	2009	A Systems Genetics Approach Implicates USF1, FADS3, and Other Causal Candidate Genes for Familial Combined Hyperlipidemia
The study of gene and protein interaction networks has improved our understanding of the multiple , systemic levels of regulation found in eukaryotic and prokaryotic organisms . Here we carry out a large-scale analysis of the protein-protein interaction ( PPI ) network of fission yeast ( Schizosaccharomyces pombe ) and...	Analysis of protein interaction networks has been of use as a means to grapple with the complexity of the interactome of biological organisms . So far , network based approaches have only been used in a limited number of organisms due to the lack of high-throughput experiments . In this study , we investigate by graph ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cellular", "structures", "protein", "interactions", "signaling", "networks", "microbiology", "model", "organisms", "cell", "division", "cell", "growth", "cytokinesis", "cytoskeleton", "regulatory", "networks", "schizosaccharomyces", "pombe", "biology", "proteomics", "syste...	2012	Linkers of Cell Polarity and Cell Cycle Regulation in the Fission Yeast Protein Interaction Network
XopN is a type III effector protein from Xanthomonas campestris pathovar vesicatoria that suppresses PAMP-triggered immunity ( PTI ) in tomato . Previous work reported that XopN interacts with the tomato 14-3-3 isoform TFT1; however , TFT1's role in PTI and/or XopN virulence was not determined . Here we show that TFT1 ...	Bacterial pathogens of plants and animals employ the type III secretion system to secrete and translocate effector proteins into host cells to suppress defense responses . Biochemical analyses have revealed that several effector proteins mimic host enzyme activities to directly interfere with pathogen perception , defe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "protein", "interactions", "immunology", "microbiology", "host-pathogen", "interaction", "immune", "defense", "bacterial", "pathogens", "immune", "system", "proteins", "proteins", "microbial", "pathogens", "biology", "pathogenesis", "immune", "response", "biochemistry", "pl...	2012	Tomato TFT1 Is Required for PAMP-Triggered Immunity and Mutations that Prevent T3S Effector XopN from Binding to TFT1 Attenuate Xanthomonas Virulence
Twenty to thirty percent of persons with Trypanosoma cruzi infection eventually develop cardiomyopathy . If an early indicator were to be identified and validated in longitudinal studies , this could enable treatment to be prioritized for those at highest risk . We evaluated cardiac and extracellular matrix remodeling ...	In Chagas disease , a parasitic disease found primarily in Central and South America , individuals are chronically infected with the parasite Trypanosoma cruzi . A few decades after initial infection , 20–30% of infected individuals will develop cardiac disease . If we were able to predict which individuals would progr...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "parasitic", "diseases", "infectious", "diseases", "medicine", "and", "health", "sciences", "cardiology" ]	2014	Biomarkers in Trypanosoma cruzi-Infected and Uninfected Individuals with Varying Severity of Cardiomyopathy in Santa Cruz, Bolivia
The majority of new HIV infections occur in women as a result of heterosexual intercourse , overcoming multiple innate barriers to infection within the mucosa . However , the avenues through which infection is established , and the nature of bottlenecks to transmission , have been the source of considerable investigati...	There is currently a great effort world-wide to develop interventions such as vaccines and microbicides to decrease , or hopefully block , HIV transmission . To model the infection of women , the field utilizes the rhesus macaque vaginal transmission model . Understanding the initial events leading to infection after v...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "hiv", "prevention", "immune", "cells", "hiv", "immunopathogenesis", "immunology", "microbiology", "vertebrates", "animals", "mammals", "primates", "animal", "models", "immunodeficiency", "viruses", "preventive", ...	2014	Vaginal Challenge with an SIV-Based Dual Reporter System Reveals That Infection Can Occur throughout the Upper and Lower Female Reproductive Tract
Plasmodium sporozoites invade host hepatocytes and develop as liver stages ( LS ) before the onset of erythrocytic infection and malaria symptoms . LS are clinically silent , and constitute ideal targets for causal prophylactic drugs and vaccines . The molecular and cellular mechanisms underlying LS development remain ...	Plasmodium parasites , the causative agents of malaria , have a complex life cycle that alternates between a mosquito vector and a vertebrate host . Infected mosquitoes transmit Plasmodium forms called sporozoites , which rapidly migrate to the host liver , invade hepatocytes , and differentiate into replicative liver ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/protozoal", "infections", "microbiology/microbial", "growth", "and", "development", "microbiology/parasitology", "microbiology/immunity", "to", "infections" ]	2008	A Sporozoite Asparagine-Rich Protein Controls Initiation of Plasmodium Liver Stage Development
The Y-box proteins YBX2 and YBX3 bind RNA and DNA and are required for metazoan development and fertility . However , possible functional redundancy between YBX2 and YBX3 has prevented elucidation of their molecular function as RNA masking proteins and identification of their target RNAs . To investigate possible funct...	The Y-box proteins are evolutionary conserved across eukaryotes . This study focused on two Y-box proteins , YBX2 and YBX3 , expressed in testis and known be important for male fertility . Previous studies in male germ cells link YBX2 and YBX3 proteins to RNA masking , however , whether they function in translational r...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Compound Heterozygosity for Y Box Proteins Causes Sterility Due to Loss of Translational Repression
The leishmaniases are a group of vector-borne parasitic diseases that represent a major international public health problem; they belong to the most neglected tropical diseases and have one of the highest rates of morbidity and mortality . The clinical outcome of infection with Leishmania parasites depends on a variety...	It is well documented that ageing alters many aspects of immune responses; however , a causal relation between impaired immune functions in ageing individuals and the response to infection has not been established . Experimental leishmaniasis is an excellent model to analyse protective and pathological immune responses...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "immunology/immunity", "to", "infections" ]	2008	Age-Related Alteration of Arginase Activity Impacts on Severity of Leishmaniasis
We have used a transposon insertion sequencing ( TIS ) approach to establish the fitness landscape of the African Salmonella enterica serovar Typhimurium ST313 strain D23580 , to complement our previous comparative genomic and functional transcriptomic studies . We used a genome-wide transposon library with insertions ...	The success of a bacterial pathogen requires a trade-off between fitness and the need to produce the energy-demanding virulence systems that promote survival and growth in an infected host . Not only must the pathogen express the right virulence genes in the right place at the right time , but the repertoire of genes w...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "enzymes", "pathogens", "immunology", "microbiology", "enzymology", "salmonella", "typhi", "plasmid", "construction", "bacterial", "diseases", "en...	2019	The fitness landscape of the African Salmonella Typhimurium ST313 strain D23580 reveals unique properties of the pBT1 plasmid
The development of meningococcal disease , caused by the human pathogen Neisseria meningitidis , is preceded by the colonization of the epithelial layer in the nasopharynx . After initial adhesion to host cells meningococci form aggregates , through pilus-pilus interactions , termed microcolonies from which the bacteri...	The human restricted pathogen Neisseria meningitidis is a major cause of bacterial meningitis and sepsis worldwide . Colonization of the mucosal layer in the upper respiratory tract is essential to establish invasive disease . The initial interaction with host cells is characterized by bacterial proliferation and adhes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "chemical", "compounds", "viral", "transmission", "and", "infection", "oxygen", "pathogens", "microbiology", "neisseria", "gonorrhoeae", "carbohydrates", "organic", "compounds", "glucos...	2017	Host cell-derived lactate functions as an effector molecule in Neisseria meningitidis microcolony dispersal
Our previous genome-wide linkage analysis identified a susceptibility locus for generalized vitiligo on 22q12 . To search for susceptibility genes within the locus , we investigated a biological candidate gene , X-box binding protein 1 ( XBP1 ) . First , we sequenced all the exons , exon-intron boundaries as well as so...	Vitiligo is a genetically complex skin disorder that afflicts 0 . 1%–2% of the population throughout the world . Linkage and association studies in different populations have implicated several genomic regions and candidate genes that are linked to the development of vitiligo . Our previous genome-wide linkage analysis...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "dermatology/pigmentary", "disorders", "genetics", "and", "genomics/medical", "genetics" ]	2009	Genetic Variation of Promoter Sequence Modulates XBP1 Expression and Genetic Risk for Vitiligo
Sexual dimorphism results from sex-biased gene expression , which evolves when selection acts differently on males and females . While there is an intimate connection between sex-biased gene expression and sex-specific selection , few empirical studies have studied this relationship directly . Here we compare the two o...	Sexual dimorphism , which is evident in virtually all phenotypic traits , results from sex-biased gene expression . The evolution of sex-biased expression , in turn , results from selection that acts differently on males and females . We use genomic data from humans and flies to quantify the relation between ongoing se...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "heterozygosity", "medicine", "and", "health", "sciences", "population", "genetics", "alleles", "developmental", "biology", "mathematics", "algebra", "population", "biology", "sexual", "dimorphism", "morphogenesis", "polynomials", "gene", "expression", "exocrine", "glands",...	2016	Sex-Specific Selection and Sex-Biased Gene Expression in Humans and Flies
Homologous recombination in meiosis is initiated by the programmed induction of double strand breaks ( DSBs ) . Although the Drosophila Spo11 ortholog Mei-W68 is required for the induction of DSBs during meiotic prophase , only one other protein ( Mei-P22 ) has been shown to be required for Mei-W68 to exert this functi...	The ability of sexually reproducing organisms to produce viable offspring depends on their ability to faithfully execute meiosis . Meiosis is a specialized set of two cell divisions that ensures that each sperm and egg receives only one copy of each pair of chromosomes . Thus , in human females , although virtually all...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "gene", "identification", "and", "analysis", "genetics", "molecular", "genetics", "biology", "genetics", "and", "genomics" ]	2011	The Drosophila Zinc Finger Protein Trade Embargo Is Required for Double Strand Break Formation in Meiosis
Highlighting the importance of proper intracellular organization , many muscle diseases are characterized by mispositioned myonuclei . Proper positioning of myonuclei is dependent upon the microtubule motor proteins , Kinesin-1 and cytoplasmic Dynein , and there are at least two distinct mechanisms by which Kinesin and...	A common pathology found in numerous cases of muscle diseases , including congenital myopathies and muscular dystrophies , is aberrantly located nuclei within individual multinucleated muscle cells . However , whether or not mispositioned myonuclei are a cause or consequence of muscle disease states is currently debate...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "kinesins", "microtubules", "animals", "gene", "function", "c-jun", "n-terminal", "kinase", "signaling", "cascade", "developmental", "biology", "drosophila", "melanogaster", "dyneins", "molecular", "motors", "molecular", "genetics", "cellular", "structures"...	2014	Syd/JIP3 and JNK Signaling Are Required for Myonuclear Positioning and Muscle Function
Bacteria glide across solid surfaces by mechanisms that have remained largely mysterious despite decades of research . In the deltaproteobacterium Myxococcus xanthus , this locomotion allows the formation stress-resistant fruiting bodies where sporulation takes place . However , despite the large number of genes identi...	Motility over solid surfaces ( gliding ) is an important bacterial mechanism that allows complex social behaviours and pathogenesis . Conflicting models have been suggested to explain this locomotion in the deltaproteobacterium Myxococcus xanthus: propulsion by polymer secretion at the rear of the cells as opposed to e...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "biology", "genomics", "evolutionary", "biology", "microbiology", "genetics", "and", "genomics" ]	2011	Emergence and Modular Evolution of a Novel Motility Machinery in Bacteria
Integrated analyses of functional genomics data have enormous potential for identifying phenotype-associated genes . Tissue-specificity is an important aspect of many genetic diseases , reflecting the potentially different roles of proteins and pathways in diverse cell lineages . Accounting for tissue specificity in gl...	Tissue specificity is an important aspect of many genetic diseases , reflecting the potentially different roles of proteins and pathways in diverse cell lineages . We propose an effective strategy to model tissue-specific functional relationship networks in the laboratory mouse . We integrated large scale genomics data...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genomics", "biology", "computational", "biology", "genetics", "and", "genomics" ]	2012	Tissue-Specific Functional Networks for Prioritizing Phenotype and Disease Genes
Bacteria possess networks of small RNAs ( sRNAs ) that are important for modulating gene expression . At the center of many of these sRNA networks is the Hfq protein . Hfq's role is to quickly match cognate sRNAs and target mRNAs from among a large number of possible combinations and anneal them to form duplexes . Here...	Bacteria have small RNAs ( sRNAs ) which are important modulators of gene expression . Many of these sRNAs require the Hfq protein to mediate their binding to specific target mRNAs which alters the translation and/or degradation of the mRNAs . The Hfq protein has a difficult task; it has to correctly pair cognate sRNAs...	[ "Abstract", "Introduction", "Results", "Discussion", "Model" ]	[ "rna", "interference", "synthetic", "biology", "microbiology", "microbial", "physiology", "gene", "expression", "biology", "molecular", "biology", "systems", "biology", "biochemistry", "rna", "nucleic", "acids", "genetics", "molecular", "cell", "biology", "gene", "netwo...	2011	Essential Requirements for Robust Signaling in Hfq Dependent Small RNA Networks
During the biogenesis of small ribosomal subunits in eukaryotes , the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm . The mechanisms underlying the nuclear export of these particles and its coordination with other biogenesis steps are mostly unknown . Here we show that yeast Rrp12 i...	During the synthesis of small ribosomal subunits in eukaryotes , the pre-40S particles formed in the nucleolus are rapidly transported to the cytoplasm . The mechanisms involved in the nuclear export of these particles and its coordination with other steps of the 40S synthesis pathway are mostly unknown . In this work ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "rna", "rna", "transport", "protein-protein", "interactions", "protein", "interactions", "ribosomal", "rna", "proteins", "rna", "processing", "cell", "biology", "gene", "expression", "ribonucleoproteins", "genetics", "biology", "and", "life", "sciences", ...	2014	Rrp12 and the Exportin Crm1 Participate in Late Assembly Events in the Nucleolus during 40S Ribosomal Subunit Biogenesis
Dok7 is a peripheral membrane protein that is associated with the MuSK receptor tyrosine kinase . Formation of the Dok7/MuSK/membrane complex is required for the activation of MuSK . This is a key step in the complex exchange of signals between neuron and muscle , which lead to neuromuscular junction formation , dysfun...	Neuromuscular junction formation and maintenance is an essential biological process , the disruption of which leads to congenital myasthenic syndromes and premature death . Dok7 is a key member in formation , maintenance and signaling in neuromuscular junctions . Dok7 is a peripheral membrane protein that is necessary ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "chemical", "bonding", "crystal", "structure", "condensed", "matter", "physics", "membrane", "proteins", "lipid", "structure", "crystallography", "cellular", "structures", "and", "organelles", "hydrogen", "bonding", "physical", "chemistry", "lipids", "solid", "state", "...	2016	Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes
Host colonization by lymphotropic γ-herpesviruses depends critically on expansion of viral genomes in germinal center ( GC ) B-cells . Myc is essential for the formation and maintenance of GCs . Yet , the role of Myc in the pathogenesis of γ-herpesviruses is still largely unknown . In this study , Myc was shown to be e...	Being obligatory intracellular parasites , it is not surprising that viruses have evolved mechanisms to induce cellular proliferation to promote their own life cycle . This is notorious in the case of γ-herpesviruses , such as Epstein-Barr virus ( EBV ) and Kaposi's sarcoma virus ( KSHV ) , which are human pathogens as...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "humoral", "immunity", "viral", "latency", "protein", "interactions", "viruses", "and", "cancer", "viral", "enzymes", "host-pathogen", "interaction", "microbiology", "signaling", "in", "selected", "disciplines", "cell", "division", "immunoregulation", "animal", "models", ...	2013	Stabilization of Myc through Heterotypic Poly-Ubiquitination by mLANA Is Critical for γ-Herpesvirus Lymphoproliferation
Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health . Constraint-based modeling , with flux balance analysis in particular , has been established as a key approach for studying microbial metabolism , wher...	In nature , organisms are typically found in near proximity to each other , forming symbiotic relationships . Particularly bacteria are often part of highly organized communities such as biofilms . In this study , we integrate the detailed knowledge about the metabolic capabilities of individual organisms into an indiv...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Methods" ]	[ "bacteriology", "biofilms", "cell", "physiology", "carbohydrate", "metabolism", "medicine", "and", "health", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "cell", "metabolism", "glucose", "metabolism", "pseudomona...	2017	BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
We report the first systems biology investigation of regulators controlling arterial plaque macrophage transcriptional changes in response to lipid lowering in vivo in two distinct mouse models of atherosclerosis regression . Transcriptome measurements from plaque macrophages from the Reversa mouse were integrated with...	Atherosclerosis , a progressive accumulation of lipid-rich plaque within arteries , is an inflammatory disease in which the response of macrophages ( a key cell type of the innate immune system ) to plasma lipoproteins plays a central role . In humans , the goal of significantly reducing already-established plaque thro...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "innate", "immune", "system", "medicine", "and", "health", "sciences", "immunology", "signaling", "networks", "network", "analysis", "genome", "analysis", "atherosclerosis", "bioassays", "and", "physiological", "analysis", "chromatin", "cardiology", "research", "and", "...	2014	Epigenome-Guided Analysis of the Transcriptome of Plaque Macrophages during Atherosclerosis Regression Reveals Activation of the Wnt Signaling Pathway
Plasmodesmata ( PD ) are essential but poorly understood structures in plant cell walls that provide symplastic continuity and intercellular communication pathways between adjacent cells and thus play fundamental roles in development and pathogenesis . Viruses encode movement proteins ( MPs ) that modify these tightly ...	In plants , spreading virus infection occurs via small pores in the cell wall named plasmodesmata that connect adjacent cells . Two decades have passed since the first discovery of specific viral proteins ( movement proteins; MP ) that assist this process . However , the manner by which these proteins adapt plasmodesma...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "plant", "biology/plant", "cell", "biology", "virology" ]	2010	A Family of Plasmodesmal Proteins with Receptor-Like Properties for Plant Viral Movement Proteins
The Trypanosoma cruzi satellite DNA ( satDNA ) OligoC-TesT is a standardised PCR format for diagnosis of Chagas disease . The sensitivity of the test is lower for discrete typing unit ( DTU ) TcI than for TcII-VI and the test has not been evaluated in chronic Chagas disease patients . We developed a new prototype of th...	Accurate diagnosis of Chagas disease is challenging due to the latent character of the infection and the low parasite load in the blood . Molecular tests such as the polymerase chain reaction ( PCR ) detect the parasite's DNA and are generally very sensitive and specific . In this study we evaluated two prototypes of a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "test", "evaluation", "chagas", "disease", "diagnostic", "medicine", "neglected", "tropical", "diseases" ]	2014	The Trypanosoma cruzi Satellite DNA OligoC-TesT and Trypanosoma cruzi Kinetoplast DNA OligoC-TesT for Diagnosis of Chagas Disease: A Multi-cohort Comparative Evaluation Study
One of the main characteristics of the transmissible isoform of the prion protein ( PrPSc ) is its partial resistance to proteinase K ( PK ) digestion . Diagnosis of prion disease typically relies upon immunodetection of PK-digested PrPSc following Western blot or ELISA . More recently , researchers determined that the...	Prion diseases are protein misfolding disorders . Different strains of prions are known to have variable resistance to proteinase K ( PK ) digestion . Furthermore , the same strain possesses both a PK sensitive ( sPrPSc ) and PK resistant ( rPrPSc ) aggregate of PrP . We developed methods to isolate the sPrPSc from rPr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "infectious", "diseases", "proteins", "biology", "prion", "diseases" ]	2012	PK-sensitive PrPSc Is Infectious and Shares Basic Structural Features with PK-resistant PrPSc
Bacterial genotoxins , produced by several Gram-negative bacteria , induce DNA damage in the target cells . While the responses induced in the host cells have been extensively studied in vitro , the role of these effectors during the course of infection remains poorly characterized . To address this issue , we assessed...	Bacterial genotoxins cause DNA damage in the host cells , resulting in activation of the classical DNA damage response , similarly to other well-characterized genotoxic agents . Three types of bacterial genotoxins have been identified: the cytolethal distending toxin ( CDTs ) family , the typhoid toxin and the peptide-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "toxins", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "salmonellosis", "salmonella", "typhi", "toxicology", "toxic", "agents", "animal", "models", "dna", "damage", "bacterial", "diseases", "model", ...	2016	The Typhoid Toxin Promotes Host Survival and the Establishment of a Persistent Asymptomatic Infection
Many aspects of the historical relationships between populations in a species are reflected in genetic data . Inferring these relationships from genetic data , however , remains a challenging task . In this paper , we present a statistical model for inferring the patterns of population splits and mixtures in multiple p...	With modern genotyping technology , it is now possible to obtain large amounts of genetic data from many populations in a species . An important question that can be addressed with these data is: what is the history of these populations ? There is a long history in population genetics of inferring the relationships amo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "population", "genetics", "biology", "population", "biology", "gene", "flow", "genetics", "and", "genomics", "genetic", "drift" ]	2012	Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data
Pancreatic islets of Langerhans consist of endocrine cells , primarily α , β and δ cells , which secrete glucagon , insulin , and somatostatin , respectively , to regulate plasma glucose . β cells form irregular locally connected clusters within islets that act in concert to secrete insulin upon glucose stimulation . D...	High or low blood glucose levels are detrimental to human health . The hormone-secreting cells primarily responsible for maintaining glucose at physiologically appropriate levels are embedded in small clusters within the pancreas , the so-called islets of Langerhans . These islets have an irregular arrangement of cells...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	The Beta Cell in Its Cluster: Stochastic Graphs of Beta Cell Connectivity in the Islets of Langerhans
Clonorchis sinensis is the causative agent of the life-threatening disease endemic to China , Korea , and Vietnam . It is estimated that about 15 million people are infected with this fluke . C . sinensis provokes inflammation , epithelial hyperplasia , and periductal fibrosis in bile ducts , and may cause cholangiocar...	Clonorchis sinensis is a significant pathogen that causes clonorchiasis , which is endemic to East Asian countries . This fluke provokes acute inflammation and chronic hyperplasic changes in the biliary tracts . C . sinensis promotes cholangiocarcinoma , and has been classified as a Group 1 biological carcinogen , alon...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "and", "Discussion" ]	[ "medicine", "parasitic", "diseases", "sequence", "assembly", "tools", "genome", "sequencing", "genome", "analysis", "tools", "sequence", "analysis", "infectious", "diseases", "comparative", "genomics", "biology", "clonorchiasis", "gene", "ontologies", "transcriptomes", "g...	2011	Developmental Transcriptomic Features of the Carcinogenic Liver Fluke, Clonorchis sinensis
TORC1 , a central regulator of cell survival , growth , and metabolism , is activated in a variety of cancers . Loss of the tumor suppressors PTEN and Tsc1/2 results in hyperactivation of TORC1 . Tumors caused by the loss of PTEN , but not Tsc1/2 , are often malignant and have been shown to be insensitive to nutrient r...	Shortage of nutrients slows down cellular metabolism and protein synthesis , thereby restraining growth and proliferation of cells . Pre-cancerous cells deficient in specific tumor suppressors are resistant to these starvation-induced growth constraints , and instead gain a growth advantage over the surrounding tissue ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "cell", "death", "medicine", "and", "health", "sciences", "malignant", "tumors", "cell", "processes", "cancers", "and", "neoplasms", "cloning", "cell", "differentiation", "oncology", "developmental", "biology", "molecular", "biology", "techniques", "e...	2018	FoxO restricts growth and differentiation of cells with elevated TORC1 activity under nutrient restriction
Patterning of the cortical neuroepithelium occurs at early stages of embryonic development in response to secreted molecules from signaling centers . These signals have been shown to establish the graded expression of transcription factors in progenitors within the ventricular zone and to control the size and positioni...	Patterning of the cerebral cortex occurs early during embryonic development in response to secreted molecules or morphogens produced at signaling centers . These morphogens establish the graded expression of transcription factors ( TFs ) in progenitor cells and control the size and positioning of cortical areas in the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "developmental", "biology/pattern", "formation", "developmental", "biology/cell", "differentiation", "neuroscience/neurodevelopment", "developmental", "biology/neurodevelopment", "neuroscience/neuronal", "signaling", "mechanisms", "neuroscience" ]	2010	A Novel Role for Dbx1-Derived Cajal-Retzius Cells in Early Regionalization of the Cerebral Cortical Neuroepithelium
The spontaneous emergence of pattern formation is ubiquitous in nature , often arising as a collective phenomenon from interactions among a large number of individual constituents or sub-systems . Understanding , and controlling , collective behavior is dependent on determining the low-level dynamical principles from w...	The patterns exhibited by moving animal groups like flocks of birds and schools of fish are typical of self-organizing systems in which global structural and dynamical properties arise from local interactions between individuals . Despite their apparent complexity , such systems can often be described , and understood ...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "systems", "biology", "ecology", "biology", "computational", "biology", "genetics", "and", "genomics", "behavioral", "ecology" ]	2013	Collective States, Multistability and Transitional Behavior in Schooling Fish
The galectin 3 binding protein ( LGALS3BP , also known as 90K ) is a ubiquitous multifunctional secreted glycoprotein originally identified in cancer progression . It remains unclear how 90K functions in innate immunity during viral infections . In this study , we found that viral infections resulted in elevated levels...	The innate immune system detects the presence of viruses through germline-encoded pattern-recognition receptors ( PRRs ) and leads to the production of proinflammatory cytokines and interferons ( IFNs ) as the first line of defense against viral infections . Here , we identified a host protein , LGALS3BP , as a positiv...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "reverse", "transcriptase-polymerase", "chain", "reaction", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "vesicular", "stomatitis", "virus", "viral", "transmission...	2019	Inducible LGALS3BP/90K activates antiviral innate immune responses by targeting TRAF6 and TRAF3 complex
Marburg virus ( family Filoviridae ) causes sporadic outbreaks of severe hemorrhagic disease in sub-Saharan Africa . Bats have been implicated as likely natural reservoir hosts based most recently on an investigation of cases among miners infected in 2007 at the Kitaka mine , Uganda , which contained a large population...	Marburg virus , like its close relative Ebola virus , can cause large outbreaks of hemorrhagic fever with case fatalities nearing 90% . For decades the identity of the natural reservoir was unknown . However , in 2007 Marburg viruses were isolated directly from Egyptian fruit bats ( Rousettus aegyptiacus ) that inhabit...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "virology", "biology", "microbiology", "viral", "diseases" ]	2012	Seasonal Pulses of Marburg Virus Circulation in Juvenile Rousettus aegyptiacus Bats Coincide with Periods of Increased Risk of Human Infection
When both parasite species are co-endemic , Plasmodium vivax incidence peaks in younger children compared to P . falciparum . To identify differences in the number of blood stage infections of these species and its potential link to acquisition of immunity , we have estimated the molecular force of blood-stage infectio...	In areas where P . vivax and P . falciparum parasite species co-occur , immunity to P . vivax seems to be acquired more rapidly . This difference could be caused either by generic differences in the way immunity is acquired or by a relatively higher exposure to P . vivax blood-stage infections in early life . We found ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "plasmodium", "vivax", "molecular", "epidemiology", "infectious", "disease", "epidemiology", "global", "health", "epidemiology", "malaria", "parasitic", "diseases" ]	2013	A High Force of Plasmodium vivax Blood-Stage Infection Drives the Rapid Acquisition of Immunity in Papua New Guinean Children
AMP-activated protein kinase ( AMPK ) is an evolutionarily conserved master regulator of metabolism and a therapeutic target in type 2 diabetes . As an energy sensor , AMPK activity is responsive to both metabolic inputs , for instance the ratio of AMP to ATP , and numerous hormonal cues . As in mammals , each of two g...	While it is well appreciated that food availability has profound effects on behavior , physiology , and metabolism , the molecular systems that link these complex processes together still remain poorly understood . An ancient cellular sensor of energy is AMP-activated protein kinase , AMPK . Here we show that in the ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cell", "biology", "genetics", "biology", "and", "life", "sciences", "molecular", "cell", "biology", "neuroscience" ]	2014	Loss of a Neural AMP-Activated Kinase Mimics the Effects of Elevated Serotonin on Fat, Movement, and Hormonal Secretions
Latent membrane protein 1 ( LMP1 ) is the major transforming protein of Epstein-Barr virus ( EBV ) and is critical for EBV-induced B-cell transformation in vitro . Poly ( ADP-ribose ) polymerase 1 ( PARP1 ) regulates accessibility of chromatin , alters functions of transcriptional activators and repressors , and has be...	Epstein-Barr virus ( EBV ) is one of the most ubiquitous human viruses , with over 90% of adults worldwide harboring lifelong latent EBV infection in a small fraction of their B-lymphocytes . EBV is known to cause lymphoproliferative disorders and is associated with several other types of cancer , including Hodgkin's l...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "metabolic", "processes", "pathogens", "immunology", "dna-binding", "proteins", "microbiology", "glycolysis", "dna", "transc...	2018	Poly(ADP-ribose) polymerase 1 is necessary for coactivating hypoxia-inducible factor-1-dependent gene expression by Epstein-Barr virus latent membrane protein 1
Helicobacter pylori causes clinical disease primarily in those individuals infected with a strain that carries the cytotoxin associated gene pathogenicity island ( cagPAI ) . The cagPAI encodes a type IV secretion system ( T4SS ) that injects the CagA oncoprotein into epithelial cells and is required for induction of t...	Helicobacter pylori is a bacterium that colonizes the stomach of about half the world's population , most of whom are asymptomatic . However , some strains of H . pylori express a bacterial secretion system , a sort of molecular syringe that injects a bacterial protein inside the gastric cells and causes inflammation t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2013	Functional Plasticity in the Type IV Secretion System of Helicobacter pylori
Laboratory models are often used to understand the interaction of related pathogens via host immunity . For example , recent experiments where ferrets were exposed to two influenza strains within a short period of time have shown how the effects of cross-immunity vary with the time between exposures and the specific st...	The resolution of an influenza infection requires different components of the immune response to work together . Despite recent advances in mathematical modelling , we do not well understand how much each broad immune component contributes to this process at a given time . In this study , we show that laboratory data o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "viral", "transmission", "and", "infection", "influenza", "immunology", "microbiology", "viral", "structure", "cytotoxic", "t", "cells", "viral", "load", "inf...	2019	Sequential infection experiments for quantifying innate and adaptive immunity during influenza infection
The cancer stem cell ( CSC ) concept is a highly debated topic in cancer research . While experimental evidence in favor of the cancer stem cell theory is apparently abundant , the results are often criticized as being difficult to interpret . An important reason for this is that most experimental data that support thi...	Cancer is in essence a genetic disease that leads to uncontrolled cell proliferation , invasion and metastasis . The cancer stem cell ( CSC ) hypothesis states that tumors are not just a mass of uniform malignant cells but they are hierarchically organized , like normal tissues . At the top of such a hierarchy are canc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "computer", "science/applications", "computational", "biology/molecular", "genetics", "evolutionary", "biology/genomics", "computational", "biology/evolutionary", "modeling", "molecular", "biology/dna", "methylation", "genetics", "and", "genomics/epigenetics" ]	2011	Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors
Translation initiation factor eIF4E mediates mRNA selection for protein synthesis via the mRNA 5’cap . A family of binding proteins , termed the 4E-BPs , interact with eIF4E to hinder ribosome recruitment . Mechanisms underlying mRNA specificity for 4E-BP control remain poorly understood . Saccharomyces cerevisiae 4E-B...	In eukaryotic cells protein synthesis initiation factor eIF4E controls mRNA selection by interacting with the mRNA 5’ cap . A family of binding proteins , termed the 4E-BPs , interact with eIF4E to hinder ribosome recruitment and repress translation of their target mRNAs . The yeast Saccharomyces cerevisiae has two 4E-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The 4E-BP Caf20p Mediates Both eIF4E-Dependent and Independent Repression of Translation
Microorganisms such as Pseudomonas putida play important roles in the mineralization of organic wastes and toxic compounds . To comprehensively and accurately elucidate key processes of nicotine degradation in Pseudomonas putida , we measured differential protein abundance levels with MS-based spectral counting in P . ...	Pseudomonas putida strains are among the microorganisms that have acquired the capability to use toxic and xenobiotic compounds , such as nicotine , for growth . Although nicotine degradation by Pseudomonas was first discovered more than 50 years ago , the underlying molecular mechanisms remain unclear . In the last fe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Systematic Unraveling of the Unsolved Pathway of Nicotine Degradation in Pseudomonas
Soil-transmitted helminth ( STH ) infections remain highly endemic across the Philippines , and are believed to be important contributors to delayed cognitive development of school-aged children . Identification of communities where children are at risk of functional illiteracy is important for the attainment of Sustai...	While previous studies in the Philippines indicated an association between STH infection and cognitive development measured by memory and school performance , the contribution of STH infections on the overall functional illiteracy burden in the Philippines is unknown . This study presents the first use of geographical ...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "invertebrates", "children", "medicine", "and", "health", "sciences", "parasite", "groups", "plasmodium", "helminths", "geographical", "locations", "tropical", "diseases", "social", "sciences", "parasitic", "diseases", "neuroscience", "animals", "parasitology", "health", ...	2019	Functional illiteracy burden in soil-transmitted helminth (STH) endemic regions of the Philippines: An ecological study and geographical prediction for 2017
Trypanosoma cruzi strains are currently classified into six discrete typing units ( DTUs ) named TcI to VI . It is known that these DTUs have different geographical distribution , as well as biological features . TcI and TcII are major DTUs found in patients from northern and southern Latin America , respectively . Our...	Chagas disease remains a major public health problem in Latin America with over 13 million people infected . It is believed that the host immune response and genetic diversity of the parasite play an important role in the progression of Chagas disease , which presents a variety of clinical forms ranging from indetermin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Differential Activation of Human Monocytes and Lymphocytes by Distinct Strains of Trypanosoma cruzi
In 2014 , the world witnessed the largest Ebolavirus outbreak in recorded history . The subsequent humanitarian effort spurred extensive research , significantly enhancing our understanding of ebolavirus replication and pathogenicity . The main functions of each ebolavirus protein have been studied extensively since th...	Between 2014 and 2016 , West Africa experienced the largest Ebolavirus outbreak in recorded history . The international containment effort spurred extensive research that is enhancing our understanding of ebolavirus replication and pathogenicity . Much has been learned about the main function of each ebolavirus protein...	[ "Abstract", "Introduction", "VP24", "VP35", "VP30", "VP40", "GP", "NP", "and", "L", "Conclusion" ]	[ "medicine", "and", "health", "sciences", "rna", "interference", "vesicles", "pathology", "and", "laboratory", "medicine", "gene", "regulation", "microbiology", "nucleocapsids", "viral", "structure", "review", "viral", "genome", "epigenetics", "cellular", "structures", "...	2018	Ebolaviruses: New roles for old proteins
Situations where individuals have to contribute to joint efforts or share scarce resources are ubiquitous . Yet , without proper mechanisms to ensure cooperation , the evolutionary pressure to maximize individual success tends to create a tragedy of the commons ( such as over-fishing or the destruction of our environme...	Why do friends spontaneously come up with mutually accepted rules , cooperation , and solidarity , while the creation of shared moral standards often fails in large communities ? In a “global village” , where everybody may interact with anybody else , it is not worthwhile to punish people who cheat . Moralists ( cooper...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "evolutionary", "biology" ]	2010	Evolutionary Establishment of Moral and Double Moral Standards through Spatial Interactions
Hedgehog ( Hh ) signaling controls embryonic development and adult tissue homeostasis through the G protein coupled receptor ( GPCR ) -family protein Smoothened ( Smo ) . Upon stimulation , Smo accumulates on the cell surface in Drosophila or primary cilia in vertebrates , which is thought to be essential for its activ...	The secreted glycoprotein Hedgehog ( Hh ) plays a conserved role in embryonic development and adult tissue homeostasis in species ranging from Drosophila to humans . Deregulation of Hh signal transduction contributes to a wide range of human disorders , including birth defects and cancer . The seven-transmembrane prote...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "rna", "interference", "cloning", "immunoprecipitation", "molecular", "biology", "techniques", "epigenetics", "cellular", "structures", "and", "organelles", "research", "and", "analysis", "methods", "specimen", "preparation", "and", "treatment", "staining...	2016	Regulation of Smoothened Phosphorylation and High-Level Hedgehog Signaling Activity by a Plasma Membrane Associated Kinase
Mastitis is an infectious disease mainly caused by bacteria invading the mammary gland . Genetic control of susceptibility to mastitis has been widely evidenced in dairy ruminants , but the genetic basis and underlying mechanisms are still largely unknown . We describe the discovery , fine mapping and functional charac...	Mastitis is an inflammation of the mammary gland mainly caused by invading bacteria . Ruminants show natural variability in their predisposition to mastitis , and therefore provide unique models for study of the genetics and physiology of host response to bacterial infection . A genome-wide association study was conduc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	A Point Mutation in Suppressor of Cytokine Signalling 2 (Socs2) Increases the Susceptibility to Inflammation of the Mammary Gland while Associated with Higher Body Weight and Size and Higher Milk Production in a Sheep Model
A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry . Much of the global resource in biology is present in universities , whereas the focus of medicinal chemistry is still largely within industry . Open source drug discovery , with sharing of i...	Malaria leads to the loss of over 440 , 000 lives annually; accelerating research to discover new candidate drugs is a priority . Medicines for Malaria Venture ( MMV ) has distilled over 25 , 000 compounds that kill malaria parasites in vitro into a group of 400 representative compounds , called the "Malaria Box" . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "and", "health", "sciences", "parasite", "groups", "medicinal", "chemistry", "pathology", "and", "laboratory", "medicine", "plasmodium", "gametocytes", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "toxicology", "g...	2016	Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond
Trypanosoma cruzi , the flagellate protozoan agent of Chagas disease or American trypanosomiasis , is unable to synthesize sialic acids de novo . Mucins and trans-sialidase ( TS ) are substrate and enzyme , respectively , of the glycobiological system that scavenges sialic acid from the host in a crucial interplay for ...	Trypanosoma cruzi is a flagellated protozoan parasite whose life cycle includes stages alternating between insect and mammal hosts . The membrane of the infective trypomastigote is equipped to allow survival in blood and to invade cells where it proliferates . Here we provide a novel description of the localization in ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "chemical", "compounds", "pathology", "and", "laboratory", "medicine", "sialic", "acids", "pathogens", "microbiology", "carbohydrates", "parasitic", "diseases", "parasitic", "protozoans", "protozoan", "life", "cycles", "organic", ...	2016	Sialic Acid Glycobiology Unveils Trypanosoma cruzi Trypomastigote Membrane Physiology
The Chinese national surveillance system showed that the risk of Schistosoma japonicum infection fluctuated temporally . This dynamical change might indicate periodicity of the disease , and its understanding could significantly improve targeted interventions to reduce the burden of schistosomiasis . The goal of this s...	We investigated changes in dynamics of schistosomiasis transmission over space and time in Anhui Province of East China . Parasitological data were obtained through repeated cross-sectional surveys that were carried out during 1997–2010 . A multivariate autoregressive model , combined with principal oscillation pattern...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Shifts in the Spatiotemporal Dynamics of Schistosomiasis: A Case Study in Anhui Province, China
Methicillin-resistant Staphylococcus aureus is estimated to cause more U . S . deaths annually than HIV/AIDS . The emergence of hypervirulent and multidrug-resistant strains has further amplified public health concern and accentuated the need for new classes of antibiotics . RNA degradation is a required cellular proce...	The last decade has witnessed a mass downsizing in pharmaceutical antibiotic drug discovery initiatives . This has posed a major healthcare issue that will likely worsen with time; antibiotic resistant bacteria continue to emerge while advances in new therapeutic options languish . In the current body of work , we show...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "molecular", "biology/post-translational", "regulation", "of", "gene", "expression", "infectious", "diseases", "molecular", "biology/mrna", "stability", "infectious", "diseases/bacterial", "infections", "microbiology/applied", "microbiology", "infectious", "diseases/antimicrobials"...	2011	Small Molecule Inhibitors of Staphylococcus aureus RnpA Alter Cellular mRNA Turnover, Exhibit Antimicrobial Activity, and Attenuate Pathogenesis
Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants . We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase , PI4Kγ5 , in Arabidopsis leaf margin development . PI4Kγ5 presents a dynamics expression pattern along with le...	Transcription factors ( TFs ) regulate the expression of target genes at nucleus , while interestingly , a few of TFs locate at plasma membrane or ER membrane , stored as resting precursors to secure a rapid response post endogenous or environmental stimuli . Membrane-bound TFs undergo post-translational processing to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "phosphorylation", "plant", "anatomy", "gene", "regulation", "cell", "cycle", "and", "cell", "division", "regulatory", "proteins", "cell", "processes", "brassica", "dna-binding", "proteins", "hormones", "plant", "science", "model", "organisms", "plant", "hormones", "t...	2016	Arabidopsis Type II Phosphatidylinositol 4-Kinase PI4Kγ5 Regulates Auxin Biosynthesis and Leaf Margin Development through Interacting with Membrane-Bound Transcription Factor ANAC078
Chemotaxis allows bacteria to colonize their environment more efficiently and to find optimal growth conditions , and is consequently under strong evolutionary selection . Theoretical and experimental analyses of bacterial chemotaxis suggested that the pathway has been evolutionarily optimized to produce robust output ...	All cellular networks are subject to fluctuations in the levels of their components . Robustness of the network output in the face of stochastic gene expression , or gene expression noise , is therefore essential to ensure proper function . Selection for robustness might thus have shaped much of the cellular evolution ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "evolutionary", "biology/microbial", "evolution", "and", "genomics", "cell", "biology/cell", "signaling", "microbiology", "computational", "biology/signaling", "networks", "computational", "biology/genomics", "molecular", "biology/translational", "regulation" ]	2009	Role of Translational Coupling in Robustness of Bacterial Chemotaxis Pathway
Chikungunya virus ( CHIKV ) is known to cause sporadic or explosive outbreaks . However , little is known about the endemic transmission of CHIKV . To ascertain the endemic occurrence of CHIKV transmission , we tested blood samples from patients with a non-dengue febrile illness who participated in a prospective cohort...	Chikungunya is one of the neglected diseases . It has only attracted attention during outbreaks , in particular , the large epidemics in the Indian Ocean in 2005–2006 . To our knowledge , there has never been any surveillance to determine the transmission of this virus among humans in non-outbreak settings . Such surve...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2013	Evidence for Endemic Chikungunya Virus Infections in Bandung, Indonesia
Recently , many researchers have used graph theory to study the aberrant brain structures in Alzheimer's disease ( AD ) and have made great progress . However , the characteristics of the cortical network in Mild Cognitive Impairment ( MCI ) are still largely unexplored . In this study , the gray matter volumes obtaine...	Understanding the progression of Alzheimer's disease ( AD ) is essential . We investigated networks of cortical connectivity along a continuum from normal to AD . Mild Cognitive Impairment ( MCI ) has been implicated as transitional between normal aging and AD . By investigating the characteristics of cortical networks...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neurological", "disorders/alzheimer", "disease", "radiology", "and", "medical", "imaging/magnetic", "resonance", "imaging", "neurological", "disorders/cognitive", "neurology", "and", "dementia", "neurological", "disorders/neuroimaging", "computational", "biology" ]	2010	Abnormal Cortical Networks in Mild Cognitive Impairment and Alzheimer's Disease
Social interactions in classic cognitive games like the ultimatum game or the prisoner's dilemma typically lead to Nash equilibria when multiple competitive decision makers with perfect knowledge select optimal strategies . However , in evolutionary game theory it has been shown that Nash equilibria can also arise as a...	Human motor interactions range from adversarial activities like judo and arm wrestling to more cooperative activities like tandem riding and tango dancing . In this study , we design a new methodology to study human sensorimotor interactions quantitatively based on game theory . We develop two motor tasks based on the ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "neuroscience/behavioral", "neuroscience", "neuroscience/motor", "systems", "neuroscience/cognitive", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2009	Nash Equilibria in Multi-Agent Motor Interactions
A central challenge in computational modeling of biological systems is the determination of the model parameters . Typically , only a fraction of the parameters ( such as kinetic rate constants ) are experimentally measured , while the rest are often fitted . The fitting process is usually based on experimental time co...	Parameter estimation is a key issue in systems biology , as it represents the crucial step to obtaining predictions from computational models of biological systems . This issue is usually addressed by “fitting” the model simulations to the observed experimental data . Such approach does not take the measurement noise i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mathematics/statistics", "computer", "science/systems", "and", "control", "theory", "computational", "biology/systems", "biology" ]	2010	Parameter Estimation and Model Selection in Computational Biology
Cell cycle of Entamoeba histolytica , the etiological agent of amoebiasis , follows a novel pathway , which includes nuclear division without the nuclear membrane disassembly . We report a nuclear localized Ca2+-binding protein from E . histolytica ( abbreviated hereafter as EhCaBP6 ) , which is associated with microtu...	E . histolytica , the etiological agent of amoebiasis , is a protozoan parasite responsible for around 100 , 000 deaths per year in developing nations . Though the organism has been identified more than 100 years back , there is not much understanding about the biology of this organism . Calcium signaling plays an impo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "microtubules", "parasitic", "cell", "cycles", "cell", "cycle", "and", "cell", "division", "drugs", "cell", "processes", "microbiology", "parasitic", "protozoans", "parasitology", "developmental", "biology", "pr...	2017	Structure of Ca2+-binding protein-6 from Entamoeba histolytica and its involvement in trophozoite proliferation regulation
Invasive non-typhoidal Salmonella ( iNTS ) are an important cause of septicemia in children under the age of five years in sub-Saharan Africa . A novel genotype of Salmonella enterica subsp . enterica serovar Typhimurium ( multi-locus sequence type [ST] 313 ) circulating in this geographic region is genetically differe...	Non-typhoidal Salmonella , such as Salmonella Typhimurium , generally cause self-limiting gastroenteritis . However , in sub-Saharan Africa , a novel genotype called sequence type ( ST ) 313 is circulating and causes bloodstream infections in infants and HIV-infected individuals . In contrast , the most common genotype...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "biology", "and", "life", "sciences", "microbiology", "medicine", "and", "health", "sciences" ]	2015	Invasive Salmonella Typhimurium ST313 with Naturally Attenuated Flagellin Elicits Reduced Inflammation and Replicates within Macrophages
Visceral leishmaniasis ( VL ) caused by Leishmania infantum is an ongoing health problem in southern Europe , where dogs are considered the main reservoirs of the disease . Current data point to a northward spread of VL and canine leishmaniasis ( CanL ) in Italy , with new foci in northern regions previously regarded a...	Visceral leishmaniasis is a sand fly-borne disease caused by protozoan parasites of the genus Leishmania . Leishmania infantum is the only parasitic species circulating in Italy and dogs are considered the main reservoirs of the disease . In this study , 55 L . infantum strains obtained from humans , dogs and sand flie...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "european", "union", "evolutionary", "biology", "italian", "people", "population", "genetics", "geographical", "locations", "tropical", "diseases", "vertebrates", "sand", "flies", "parasitic", "diseases", "parasitic", "protozoans",...	2018	Multilocus microsatellite typing (MLMT) reveals host-related population structure in Leishmania infantum from northeastern Italy
LEDGF/p75 can tether over-expressed lentiviral integrase proteins to chromatin but how this underlies its integration cofactor role for these retroviruses is unclear . While a single integrase binding domain ( IBD ) binds integrase , a complex N-terminal domain ensemble ( NDE ) interacts with unknown chromatin ligands ...	Like other retroviruses , HIV-1 integrates a DNA copy of its genome into a host cell chromosome in each replication cycle . The resulting integrated proviruses are the basis for two important clinical problems: the inability to eradicate HIV-1 from the body and the permanent archiving of drug-resistant viruses . The DN...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/immunodeficiency", "viruses", "virology/viral", "replication", "and", "gene", "regulation", "virology" ]	2009	LEDGF/p75 Proteins with Alternative Chromatin Tethers Are Functional HIV-1 Cofactors
Scrub typhus is an acute febrile disease caused by Orientia tsutsugamushi infection . Recently , the rapid increase of scrub typhus incidence in several countries within the endemic region has become a serious public health issue . Despite the wide range of preventative approaches that have been attempted in the past 7...	Scrub typhus , caused by Orientia tsutsugamushi infection , is one of the common febrile illness in the Asia-Pacific region , accounting for up to 20% of febrile hospital admissions in rural areas of southern Asia . It has been estimated that one billion people are at risk and one million cases occur annually in the As...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Immunization with an Autotransporter Protein of Orientia tsutsugamushi Provides Protective Immunity against Scrub Typhus
Giardia duodenalis ( synonyms G . lamblia and G . intestinalis ) is an enteric protozoan parasite of a wide range of mammalian hosts , including humans and various domestic and wild animals . There is considerable genetic variability in G . duodenalis and isolates of this parasite have been divided into eight genetic a...	Giardia duodenalis is a protozoan parasite that causes giardiasis , a disease that affects millions of people worldwide and a wide range of mammalian hosts . G . duodenalis presents considerable genetic variability and there is an increasing demand for the development of new molecular markers . This study aimed to iden...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "giardia", "population", "genetics", "parasitic", "protozoans", "microsatellite", "loci", "protozoans", "genome", "analysis", "gene", "types", "sequence", "motif", "analysis", "population", "biology", "research", "and", "analysis", "methods", "sequence", "analysis", "ge...	2018	Molecular genotyping, diversity studies and high-resolution molecular markers unveiled by microsatellites in Giardia duodenalis
Eukaryotic genomes are regulated by epigenetic marks that act to modulate transcriptional control as well as to regulate DNA replication and repair . In Arabidopsis thaliana , mutation of the ATXR5 and ATXR6 histone methyltransferases causes reduction in histone H3 lysine 27 monomethylation , transcriptional upregulati...	In eukaryotic genomes cellular processes such as transcription and replication need to be tightly controlled in order to promote genomic stability and prevent deleterious mutations . In Arabidopsis thaliana , two redundant histone methyltransferases , ATXR5 and ATXR6 , are responsible for the deposition of a silencing ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "plant", "growth", "and", "development", "plant", "embryo", "anatomy", "dna", "transcription", "dna", "damage", "developmental", "biology", "plant", "science", "dna", "replication", "genetic", "elements", "dna", "epigenetics", "dna", "methylation",...	2016	Identification of Multiple Proteins Coupling Transcriptional Gene Silencing to Genome Stability in Arabidopsis thaliana
Highly specific transcriptional regulation depends on the cooperative association of transcription factors into enhanceosomes . Usually , their DNA-binding cooperativity originates from either direct interactions or DNA-mediated allostery . Here , we performed unbiased molecular simulations followed by simulations of p...	Pluripotent stem cells can give rise to all somatic lineages . When taken out of the context of the embryo they can be maintained and for this a core transcriptional regulatory circuitry is crucial . OCT4 and SOX2 , two factors of this network , are also critical for the induction of pluripotency in somatic cells . In ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
Leishmania donovani is a protozoan parasite , a primary causative agent of visceral leishmaniasis . Sterol produced via the mevalonate pathway , show differences in composition across biological kingdoms . The specific occurrence of Δ22-unsaturated sterols , containing a double bond at the C-22 position in the side cha...	The cytochromes P450 ( P450s ) are ubiquitous heme-containing enzymes that affect a vast range of oxidation reactions in nature . Cytochrome P450s ( CYPs ) play an essential role in the metabolism of endogenous or xenobiotic compounds and steroid . The sterol compositions among biological kingdoms differ in the specifi...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "microbiology", "parasitic", "protozoans", "protozoan", "life", "cycles", "developmental", "biology", "protozoans", "leishmania", "sequence", "motif", "analysis", "promastigotes", "research", "and", "analysis", "methods", "sequence", "analysis", "lipids", "bioinformatics", ...	2019	A Plant like Cytochrome P450 Subfamily CYP710C1 Gene in Leishmania donovani Encodes Sterol C-22 Desaturase and its Over-expression Leads to Resistance to Amphotericin B
Apoptosis plays an important role in the pathogenesis of reovirus encephalitis . Reovirus outer-capsid protein μ1 , which functions to penetrate host cell membranes during viral entry , is the primary regulator of apoptosis following reovirus infection . Ectopic expression of full-length and truncated forms of μ1 indic...	Many viruses produce central nervous system disease by infecting and systematically killing host neurons via a process known as programmed cell death , or apoptosis . However , for most viruses , it is not understood how viral invasion is detected by host cells nor how this recognition triggers a signaling cascade that...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry", "virology/virulence", "factors", "and", "mechanisms", "virology/animal", "models", "of", "infection", "virology" ]	2008	Independent Regulation of Reovirus Membrane Penetration and Apoptosis by the μ1 φ Domain
Neuropathic pain ( NP ) can occur as a chronic complication of leprosy neuropathy . NP epidemiology and its impact on patients have not been well documented . This study investigates NP prevalence and impact in the years after patients are declared “released from treatment” ( RFT ) following multidrug therapy ( MDT ) c...	Leprosy could present with chronic neuropathic pain , which might severely disturb daily life and mental health of leprosy-infected patients . This complication could also occur even years after antibiotics therapy completion , and we noticed that it is associated with recent leprosy reactions and nerve tenderness on p...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "somatosensory", "system", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "nervous", "system", "tropical", "diseases", "geographical", "locations", "neuroscience", "bacterial", "diseases", "signs", "and", "symptoms", "neglected", ...	2018	Diagnosis and impact of neuropathic pain in leprosy patients in Nepal after completion of multidrug therapy
Branching is an important mechanism by which axons navigate to their targets during neural development . For instance , in the developing zebrafish retinotectal system , selective branching plays a critical role during both initial pathfinding and subsequent arborisation once the target zone has been reached . Here we ...	The complex morphologies of neurons present challenges for analysis . Large data sets can be gathered , but extracting meaningful data from the hundreds of branches from one axon over a few hundred time points can be difficult . One problem in particular is matching a single unique branch through several images , when ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "death", "rates", "medicine", "and", "health", "sciences", "demography", "brain", "vertebrates", "animals", "animal", "models", "osteichthyes", "developmental", "biology", "model", "organisms", "mathematics", "ganglion", "cells", "statistics", "(mathematics)", "nerve", ...	2016	Quantitative Analysis of Axonal Branch Dynamics in the Developing Nervous System
Hox transcription factors specify distinct cell types along the anterior-posterior axis of metazoans by regulating target genes that modulate signaling pathways . A well-established example is the induction of Epidermal Growth Factor ( EGF ) signaling by an Abdominal-A ( Abd-A ) Hox complex during the specification of ...	Hox genes encode a conserved family of transcription factors that regulate unique cell types within the distinct morphological structures that arise along the body plan of animals . Hox transcription factors specify different cell fates by regulating the expression of downstream genes , many of which are part of cell s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "gene", "regulation", "regulatory", "proteins", "dna-binding", "proteins", "precursor", "cells", "animals", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "transcrip...	2017	A Hox complex activates and potentiates the Epidermal Growth Factor signaling pathway to specify Drosophila oenocytes
Domestic dog breeds display significant diversity in both body mass and skeletal size , resulting from intensive selective pressure during the formation and maintenance of modern breeds . While previous studies focused on the identification of alleles that contribute to small skeletal size , little is known about the u...	Modern dog breeds display significant variation in body size and mass resulting from selective breeding practices . A genome-wide association study ( GWAS ) of 170 , 000 SNPs genotyped on a panel of 855 dogs from 88 breeds revealed two loci on the canine X chromosome that were strongly associated with the large Standar...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genome-wide", "association", "studies", "animal", "types", "medicine", "and", "health", "sciences", "variant", "genotypes", "vertebrates", "pets", "and", "companion", "animals", "dogs", "mammals", "alleles", "animals", "genetic", "mapping", "physiological", "parameters...	2017	Analysis of large versus small dogs reveals three genes on the canine X chromosome associated with body weight, muscling and back fat thickness
The bulk polar movement of the plant signaling molecule auxin through the stem is a long-recognized but poorly understood phenomenon . Here we show that the highly polar , high conductance polar auxin transport stream ( PATS ) is only part of a multimodal auxin transport network in the stem . The dynamics of auxin move...	The growing shoot tips of a plant can communicate and influence each other’s growth . This is most obvious in the phenomenon of apical dominance , in which the leading shoot in a shoot system inhibits the growth of buds in the axils of the leaves below it . Removing the leading shoot results in the activation of these ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "plant", "anatomy", "stem", "anatomy", "medicine", "and", "health", "sciences", "internodes", "vascular", "bundles", "buds", "plant", "physiology", "hormones", "cell", "polarity", "endocrine", "physiology", "xylem", "hormone", "transport", "plant...	2016	Connective Auxin Transport in the Shoot Facilitates Communication between Shoot Apices
Meiotic recombination involves the repair of double-strand break ( DSB ) precursors as crossovers ( COs ) or noncrossovers ( NCOs ) . The proper number and distribution of COs is critical for successful chromosome segregation and formation of viable gametes . In budding yeast the majority of COs occurs through a pathwa...	Meiosis is the type of cell division used by sexually reproducing organisms to create gametes ( eggs and sperm , in animals ) . During meiosis , the two copies of each chromosome swap segments of DNA , forming reciprocal exchanges called crossovers . Crossovers are needed to help ensure that each gamete inherits a copy...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Reduced Crossover Interference and Increased ZMM-Independent Recombination in the Absence of Tel1/ATM
Cell size scales with ploidy in a great range of eukaryotes , but the underlying mechanisms remain unknown . Using various orthogonal single-cell approaches , we show that cell size increases linearly with centromere ( CEN ) copy number in budding yeast . This effect is due to a G1 delay mediated by increased degradati...	It has been known for a long time that cells increase their size with the amount of DNA across the whole evolutionary scale . Moreover , within a given species and differentiation status , cells increase their size in an exquisitely proportional manner to the number of chromosomes . This correlation has been observed i...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Materials", "and", "methods" ]	[ "chromosome", "structure", "and", "function", "centromeres", "cell", "cycle", "and", "cell", "division", "cell", "processes", "population", "genetics", "ploidy", "plasmid", "construction", "fungi", "model", "organisms", "experimental", "organism", "systems", "chaperone"...	2018	Centromeric signaling proteins boost G1 cyclin degradation and modulate cell size in budding yeast
Burden of disease estimates are widely used for priority setting in public health and disability-adjusted life years are a powerful “currency” nowadays . However , disability weights , which capture the disability incurred by a typical patient of a certain condition , are fundamental to such burden calculation and thei...	In public health , "burden" estimates should capture the human suffering caused by certain health states , and the estimates are often used for priority setting . However , such "burden" estimates need to assess not only the number of affected people by certain conditions , but also the disability incurred by the avera...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "behavioral", "and", "social", "aspects", "of", "health", "infectious", "disease", "epidemiology", "parasitic", "diseases", "helminth", "infection", "social", "epidemiology", "hookworm", "infection", "neglected", "t...	2012	Schistosomiasis, Soil-Transmitted Helminthiasis, and Sociodemographic Factors Influence Quality of Life of Adults in Côte d'Ivoire
The immune system rapidly responds to intracellular infections by detecting MHC class I restricted T-cell epitopes presented on infected cells . It was originally thought that viral peptides are liberated during constitutive protein turnover , but this conflicts with the observation that viral epitopes are detected wit...	To defend the host from an infection , the immune system continuously scans cell surfaces for foreign objects . Specifically , a virus inside a cell exploits the host to make copies of its proteins; viral proteins are broken up into peptide fragments; and the fragments are displayed on the infected cell's surface , the...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequence", "analysis", "biochemistry", "proteomics", "biology" ]	2013	Positional Bias of MHC Class I Restricted T-Cell Epitopes in Viral Antigens Is Likely due to a Bias in Conservation
A life-shortening strain of the obligate intracellular bacteria Wolbachia , called wMelPop , is seen as a promising new tool for the control of Aedes aegypti . However , developing a vector control strategy based on the release of mosquitoes transinfected with wMelPop requires detailed knowledge of the demographics of ...	Prevention of dengue disease relies predominantly on controlling the mosquito Aedes aegypti . A new control strategy is being developed based on the use of a life-shortening strain of the intracellular bacteria Wolbachia , which has been microinjected into Ae . aegypti in the laboratory . This strategy aims to eliminat...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases", "ecology/population", "ecology", "ecology", "ecology/spatial", "and", "landscape", "ecology" ]	2009	Characterizing the Aedes aegypti Population in a Vietnamese Village in Preparation for a Wolbachia-Based Mosquito Control Strategy to Eliminate Dengue
Mammalian cytosolic Hsp110 family , in concert with the Hsc70:J-protein complex , functions as a disaggregation machinery to rectify protein misfolding problems . Here we uncover a novel role of this machinery in driving membrane translocation during viral entry . The non-enveloped virus SV40 penetrates the endoplasmic...	How non-enveloped viruses penetrate a host membrane to enter cells and cause disease remains an enigmatic step . To infect cells , the non-enveloped SV40 must transport across the ER membrane to reach the cytosol . In this study , we report that a cellular Hsp105-powered disaggregation machinery pulls SV40 into the cyt...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Non-enveloped Virus Hijacks Host Disaggregation Machinery to Translocate across the Endoplasmic Reticulum Membrane
Trichomes are leaf hairs that are formed by single cells on the leaf surface . They are known to be involved in pathogen resistance . Their patterning is considered to emerge from a field of initially equivalent cells through the action of a gene regulatory network involving trichome fate promoting and inhibiting facto...	The patterning of trichomes ( leaf hair ) on the surface of a leaf is a paradigm for studying gene regulation in developmental processes . The statistical analysis of trichome patterning requires automated methods for the location of trichomes on a curved leaf surface . This is particularly challenging for young , stro...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "software", "design", "computer", "science", "plant", "science", "plant", "morphology", "plant", "physiology", "leafs", "plant", "growth", "and", "development", "software", "tools", "software", "engineering", "botany", "biology", "plants", "flowering", "plants" ]	2013	Semi-automated 3D Leaf Reconstruction and Analysis of Trichome Patterning from Light Microscopic Images
African swine fever virus ( ASFV ) can cause highly lethal disease in pigs and is becoming a global threat . ASFV DNA Polymerase X ( AsfvPolX ) is the most distinctive DNA polymerase identified to date; it lacks two DNA-binding domains ( the thumb domain and 8-KD domain ) conserved in the homologous proteins . AsfvPolX...	African swine fever virus ( ASFV ) is highly contagious and can cause lethal disease in pigs . AsfvPolX catalyzes the gap-filling reaction during the DNA repair process of the virus genome; it is highly error prone and plays an important role in the strategic mutagenesis of the virus genome . Unlike the homologous prot...	[ "Abstract", "Introduction", "Results", "and", "discussion", "Unique", "substrate", "binding", "mode", "Conclusions", "Materials", "and", "methods" ]	[ "crystal", "structure", "condensed", "matter", "physics", "dna-binding", "proteins", "polymerases", "protein", "structure", "dna", "structure", "dna", "crystallography", "solid", "state", "physics", "proteins", "chemistry", "molecular", "biology", "physics", "protein", ...	2017	Unique 5′-P recognition and basis for dG:dGTP misincorporation of ASFV DNA polymerase X
Rabies is a fatal zoonotic disease that causes a heavy burden on societies . Namibia , a country in southern Africa , is aiming at controlling the disease in its main reservoir , the domestic dog . To facilitate the implementation comprehensive information on the ecology and epidemiology of the disease and surveillance...	Rabies is a fatal zoonotic disease . It has been recorded in southern Africa including Namibia since the early 19th century . At present , Namibia is aiming at controlling the disease in its main reservoir , the domestic dog . This study assessed the baseline data for rabies surveillance in Namibia from 2011–2017 . The...	[ "Abstract", "Introduction", "Material", "&", "methods", "Results", "Discussion" ]	[ "animal", "types", "livestock", "medicine", "and", "health", "sciences", "namibia", "tropical", "diseases", "geographical", "locations", "vertebrates", "animals", "mammals", "dogs", "rabies", "neglected", "tropical", "diseases", "population", "biology", "zoology", "afri...	2019	Ecology and epidemiology of rabies in humans, domestic animals and wildlife in Namibia, 2011-2017
Plant-parasitic nematodes are destructive plant pathogens that cause significant yield losses . They induce highly specialized feeding sites ( NFS ) in infected plant roots from which they withdraw nutrients . In order to establish these NFS , it is thought that the nematodes manipulate the molecular and physiological ...	Sedentary plant-parasitic nematodes are major agricultural pests worldwide . They establish an intimate relationship with their host and force the latter to induce specialized structures from which they feed . Due to the withdrawal of nutrients together with the damage they cause to the hosts roots , plant-parasitic ne...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions" ]	2009	Parasitic Nematodes Modulate PIN-Mediated Auxin Transport to Facilitate Infection
Rapid conduction of nerve impulses requires coating of axons by myelin . To function as an electrical insulator , myelin is generated as a tightly packed , lipid-rich multilayered membrane sheath . Knowledge about the mechanisms that govern myelin membrane biogenesis is required to understand myelin disassembly as it o...	Myelin is a specialized membrane that covers axons and serves as an insulator to enable the fast conduction of the action potentials . The importance of myelin membrane is highlighted in demyelinating diseases such as multiple sclerosis , which lead to severe neurological disability . Here , we describe a physicochemic...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "cellular", "structures", "developmental", "neuroscience", "membranes", "and", "sorting", "biology", "molecular", "cell", "biology", "morphogenesis", "neuroscience", "cell", "differentiation" ]	2013	Myelin Membrane Assembly Is Driven by a Phase Transition of Myelin Basic Proteins Into a Cohesive Protein Meshwork
The different environments that humans experience are likely to impact physiology and disease susceptibility . In order to estimate the magnitude of the impact of environment on transcript abundance , we examined gene expression in peripheral blood leukocyte samples from 46 desert nomadic , mountain agrarian and coasta...	The incidence of complex diseases such as diabetes , asthma , and depression is almost epidemic in many countries and coincides with transition in lifestyles . Clearly this is a result of interaction between modern cultural and environmental factors with the genetic legacy of human history . To estimate the extent of t...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/genetics", "of", "the", "immune", "system", "genetics", "and", "genomics/gene", "expression" ]	2008	A Genome-Wide Gene Expression Signature of Environmental Geography in Leukocytes of Moroccan Amazighs
How the brain stores information about a sensory stimulus in working memory is not completely known . Clues about the mechanisms responsible for working memory can be gleaned by recording from neurons during the performance of a delayed response task . I focus on the data recorded during such an experiment , a classic ...	The ability to retain stimulus information after the stimulus has ceased is important for survival . The term “working memory” refers to storage of stimulus information for a short period of time , so that this information can be recalled for a decision making process . A common way to probe for the cellular basis of w...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "neuroscience", "theoretical", "biology", "biology" ]	2014	Timing over Tuning: Overcoming the Shortcomings of a Line Attractor during a Working Memory Task
Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens . Virulence of the human gastric pathogen Helicobacter pylori is dependent on nickel , cofactor of two enzymes essential for in vivo colonization , urease and [N...	Helicobacter pylori is a bacterium that persistently colonizes the stomach of half of the human population . Infection by H . pylori is associated with gastritis , peptic ulcer disease and adenocarcinoma . To resist gastric acidity and proliferate in the stomach , H . pylori relies on urease , an enzyme that contains a...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization
Determining the factors underlying the long-range spatial spread of infectious diseases is a key issue regarding their control . Dengue is the most important arboviral disease worldwide and a major public health problem in tropical areas . However the determinants shaping its dynamics at a national scale remain poorly ...	Dengue fever is a mosquito borne viral infection . It has become a major public health problem during the past decades: only 9 countries were affected in the 1970s; dengue is now endemic in more than 100 countries . In the absence of any vaccine or specific treatment , control of dengue fever is currently limited to ve...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "statistics", "mathematics", "neglected", "tropical", "diseases", "biostatistics", "epidemiological", "methods", "infectious", "disease", "control", "infectious", "diseases", "di...	2012	Can Human Movements Explain Heterogeneous Propagation of Dengue Fever in Cambodia?

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