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Denitrifying bacteria accumulate NO2− , NO , and N2O , the amounts depending on transcriptional regulation of core denitrification genes in response to O2-limiting conditions . The genes include nar , nir , nor and nosZ , encoding NO3− - , NO2− - , NO- and N2O reductase , respectively . We previously constructed a dyna...	Denitrifiers generally respire O2 , but if O2 becomes limiting , they may switch to anaerobic respiration ( denitrification ) by producing NO3− - , NO2− - , NO- and/or N2O reductase , encoded by nar , nir , nor , and nosZ genes , respectively . Denitrification causes transient accumulation of NO2− and NO/N2O emissions ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[]	2016	Transient Accumulation of NO2- and N2O during Denitrification Explained by Assuming Cell Diversification by Stochastic Transcription of Denitrification Genes
Our ability to detect target sounds in complex acoustic backgrounds is often limited not by the ear's resolution , but by the brain's information-processing capacity . The neural mechanisms and loci of this “informational masking” are unknown . We combined magnetoencephalography with simultaneous behavioral measures in...	Sounds that are well above the sensory threshold may sometimes fail to be perceived when they occur amid competing sounds , as often happens in everyday life . This phenomenon is generally referred to as “informational masking . ” We took advantage of this effect to isolate brain responses that correlate with conscious...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2008	Neural Correlates of Auditory Perceptual Awareness under Informational Masking
Following attachment to primary receptor heparan sulfate proteoglycans ( HSPG ) , human papillomavirus type 16 ( HPV16 ) particles undergo conformational changes affecting the major and minor capsid proteins , L1 and L2 , respectively . This results in exposure of the L2 N-terminus , transfer to uptake receptors , and ...	Human papillomaviruses ( HPV ) , especially HPV types 16 and 18 , are a major cause of cancer in women worldwide . HPV16 , like most genital HPV types , relies on heparan sulfate proteoglycans ( HSPGs ) to attach to host cells and to the extracellular matrix . Attachment is mediated by surface-exposed basic residues of...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/host", "invasion", "and", "cell", "entry", "virology" ]	2009	Target Cell Cyclophilins Facilitate Human Papillomavirus Type 16 Infection
Toxicity is an important factor in failed drug development , and its efficient identification and prediction is a major challenge in drug discovery . We have explored the potential of microscopy images of fluorescently labeled nuclei for the prediction of toxicity based on nucleus pattern recognition . Deep learning al...	Visualization of nuclei using different microscopic approaches has for decades allowed the identification of cells undergoing cell death , based on changes in morphology , nuclear density , etc . However , this human-based visual analysis has not been translated into quantitative tools able to objectively measure cytot...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "fluorescence", "imaging", "medicine", "and", "health", "sciences", "nuclear", "staining", "pathology", "and", "laboratory", "medicine", "engineering", "and", "technology", "signal", "processing", "drug", "screening", "toxicology", "toxicity", "pharmaceutics", "crops", ...	2018	Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening
The development of new adjuvants enables fine modulation of the elicited immune responses . Ideally , the use of one or more adjuvants should result in the induction of a protective immune response against the specific pathogen . We have evaluated the immune response and protection against Trypanosoma cruzi infection i...	Chagas disease is a parasitic disease caused by a protozoan parasite ( Trypanosoma cruzi ) which has a complex life cycle including insect vector and mammalians . In Latin America , 7–10 million people are infected , 100 million people are at risk of infection , and about 56 , 000 new infection cases and 12 , 000 death...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immunology", "parasitic", "diseases", "parasitic", "protozoans", "vaccines", "preventive", "medicine", "immunologic", "adjuvants", "protozoans", "infectious", "disease", "control", "vaccination", "an...	2017	Immunization with Tc52 or its amino terminal domain adjuvanted with c-di-AMP induces Th17+Th1 specific immune responses and confers protection against Trypanosoma cruzi
Gene Ontology ( GO ) has established itself as the undisputed standard for protein function annotation . Most annotations are inferred electronically , i . e . without individual curator supervision , but they are widely considered unreliable . At the same time , we crucially depend on those automated annotations , as ...	In the UniProt Gene Ontology Annotation database , the largest repository of functional annotations , over 98% of all function annotations are inferred in silico , without curator oversight . Yet these “electronic GO annotations” are generally perceived as unreliable; they are disregarded in many studies . In this arti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "functional", "genomics", "gene", "function", "genome", "analysis", "tools", "genome", "databases", "biology", "proteomics", "gene", "ontologies", "biochemistry", "proteomic", "databases", "genetics", "genomics", "computational", "biology", "genetics", "and", "genomics" ]	2012	Quality of Computationally Inferred Gene Ontology Annotations
Incremental learning , in which new knowledge is acquired gradually through trial and error , can be distinguished from one-shot learning , in which the brain learns rapidly from only a single pairing of a stimulus and a consequence . Very little is known about how the brain transitions between these two fundamentally ...	There are at least two distinct learning strategies for identifying the relationship between a cause and its consequence: ( 1 ) incremental learning , in which we gradually acquire knowledge through trial and error , and ( 2 ) one-shot learning , in which we rapidly learn from only a single pairing of a potential cause...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Neural Computations Mediating One-Shot Learning in the Human Brain
As a component of the Cytosolic Iron-sulfur cluster Assembly ( CIA ) pathway , DRE2 is essential in organisms from yeast to mammals . However , the roles of DRE2 remain incompletely understood largely due to the lack of viable dre2 mutants . In this study , we successfully created hypomorphic dre2 mutants using the CRI...	The Cytosolic Iron-sulfur cluster Assembly ( CIA ) pathway is essential for the maturation of Fe-S proteins localized in the cytosol and the nucleus . As an important component of the CIA pathway , DRE2 is essential from yeast to mammals . To study the CIA-related functions of DRE2 and further explore novel non-CIA rol...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "engineering", "and", "technology", "hormones", "dna", "damage", "plant", "science", "dna", "replication", "plant", "hormones", "genetically", "modified", "plants", "epigenetics", "dna", "seedlings", "molecular", "biology", "techniques", "plants", "dna"...	2019	Canonical cytosolic iron-sulfur cluster assembly and non-canonical functions of DRE2 in Arabidopsis
Buruli ulcer ( BU ) is a neglected tropical disease caused by Mycobacterium ulcerans . The tissue damage characteristic of BU lesions is known to be driven by the secretion of the potent lipidic exotoxin mycolactone . However , the molecular action of mycolactone on host cell biology mediating cytopathogenesis is not f...	Buruli Ulcer ( BU ) is a neglected tropical disease caused by Mycobacterium ulcerans infection . It has been recognized for many years that BU pathogenesis is mediated by the potent exotoxin mycolactone; however , the molecular action of this toxin on the host cell biology that drives its pathogenesis is not fully unde...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "tropical", "diseases", "bacterial", "diseases", "molecular", "motors", "emerging", "infectious", "diseases", "neglected", "tropical", "diseases", "cellular", "structures", "and", "or...	2014	Proteomic Analysis of the Action of the Mycobacterium ulcerans Toxin Mycolactone: Targeting Host Cells Cytoskeleton and Collagen
The tubular networks of the Drosophila respiratory system and our vasculature show distinct branching patterns and tube shapes in different body regions . These local variations are crucial for organ function and organismal fitness . Organotypic patterns and tube geometries in branched networks are typically controlled...	Tubes are common structural elements of many internal organs , facilitating fluid flow and material exchange . To meet the local needs of diverse tissues , the branching patterns and tube shapes vary regionally . Diametric tapering and specialized branch targeting to the brain represent two common examples of variation...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Intersection of the Extrinsic Hedgehog and WNT/Wingless Signals with the Intrinsic Hox Code Underpins Branching Pattern and Tube Shape Diversity in the Drosophila Airways
Replicative aging has been demonstrated in asymmetrically dividing unicellular organisms , seemingly caused by unequal damage partitioning . Although asymmetric segregation and inheritance of potential aging factors also occur in symmetrically dividing species , it nevertheless remains controversial whether this result...	Multicellular organisms universally senesce and must produce rejuvenated progenies in order to transmit life . Although similar age-related deterioration in physiological functions and reproduction is also found in unicellular organisms that divide asymmetrically to produce morphologically distinct aged and younger cel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "death", "rates", "cell", "death", "fluorescence", "imaging", "medicine", "and", "health", "sciences", "engineering", "and", "technology", "demography", "cell", "cycle", "and", "cell", "division", "protein", "aggregation", "cell", "processes", "physiological", "proces...	2017	Aging, mortality, and the fast growth trade-off of Schizosaccharomyces pombe
We present the genome sequences of a new clinical isolate of the important human pathogen , Aspergillus fumigatus , A1163 , and two closely related but rarely pathogenic species , Neosartorya fischeri NRRL181 and Aspergillus clavatus NRRL1 . Comparative genomic analysis of A1163 with the recently sequenced A . fumigatu...	Aspergillus is an extremely diverse genus of filamentous ascomycetous fungi ( molds ) found ubiquitously in soil and decomposing vegetation . Being supreme opportunists , aspergilli have adapted to overcome various chemical , physical , and biological stresses found in heterogeneous environments . While most species in...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "computational", "biology/population", "genetics", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "genetics", "and", "genomics/comparative", "genomics", "computational", "biology/comparative", "sequence", "analys...	2008	Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
We have generated and made publicly available two very large networks of molecular interactions: 49 , 493 mouse-specific and 52 , 518 human-specific interactions . These networks were generated through automated analysis of 368 , 331 full-text research articles and 8 , 039 , 972 article abstracts from the PubMed databa...	We described and made publicly available the largest existing set of text-mined statements; we also presented its application to an important biological problem . We have extracted and purified two large molecular networks , one for humans and one for mouse . We characterized the data sets , described the methods we us...	[ "Abstract", "Introduction", "Results/Discussion", "Methods" ]	[ "computational", "biology/literature", "analysis", "neuroscience/neurodevelopment", "computational", "biology/systems", "biology" ]	2009	Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans
Heterosis describes the phenotypic superiority of hybrids over their parents in traits related to agronomic performance and fitness . Understanding and predicting nonadditive inheritance such as heterosis is crucial for evolutionary biology as well as for plant and animal breeding . However , the physiological bases of...	Hybrids often grow faster and produce more offspring than their parents . This phenomenon , called hybrid vigour or heterosis , has been extensively exploited in agriculture . Even though several hypotheses have been proposed to explain the genetic basis of hybrid superiority , there is still no unifying model able to ...	[ "Abstract", "Introduction", "Results", "Discussion", "Conclusions", "Material", "and", "methods" ]	[]	2019	Nonlinear phenotypic variation uncovers the emergence of heterosis in Arabidopsis thaliana
The two-component NS2B-NS3 proteases of West Nile and dengue viruses are essential for viral replication and established targets for drug development . In all crystal structures of the proteases to date , the NS2B cofactor is located far from the substrate binding site ( open conformation ) in the absence of inhibitor ...	Dengue and West Nile virus infections put an estimated 2 . 5 billion people at risk . Neither drugs nor vaccines are currently available against these diseases . The non-structural protein NS3 is a protease that , together with the cofactor NS2B , is essential for viral maturation . The NS2B-NS3 proteases of dengue and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biophysics/experimental", "biophysical", "methods", "virology/viral", "replication", "and", "gene", "regulation" ]	2009	NMR Analysis of the Dynamic Exchange of the NS2B Cofactor between Open and Closed Conformations of the West Nile Virus NS2B-NS3 Protease
In standard attractor neural network models , specific patterns of activity are stored in the synaptic matrix , so that they become fixed point attractors of the network dynamics . The storage capacity of such networks has been quantified in two ways: the maximal number of patterns that can be stored , and the stored i...	Two central hypotheses in neuroscience are that long-term memory is sustained by modifications of the connectivity of neural circuits , while short-term memory is sustained by persistent neuronal activity following the presentation of a stimulus . These two hypotheses have been substantiated by several decades of elect...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neural", "networks", "computational", "neuroscience", "biology", "and", "life", "sciences", "computational", "biology", "neuroscience", "learning", "and", "memory", "coding", "mechanisms" ]	2014	Memory Capacity of Networks with Stochastic Binary Synapses
Homeostatic maintenance of tissues is orchestrated by well tuned networks of cellular signaling . Such networks regulate , in a stochastic manner , fates of all cells within the respective lineages . Processes such as symmetric and asymmetric divisions , differentiation , de-differentiation , and death have to be contr...	Tissue stability is the basic property of healthy organs , and yet the mechanisms governing the stable , long-term maintenance of cell numbers in tissues are poorly understood . While more and more signaling pathways are being discovered , for the most part it remains unknown how they are being put together by differen...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "cell", "cycle", "and", "cell", "division", "population", "dynamics", "cell", "processes", "cell", "differentiation", "physiological", "processes", "developmental", "biology", "systems", "science", "mathematics", "homeostasis", "...	2016	Near Equilibrium Calculus of Stem Cells in Application to the Airway Epithelium Lineage
Dengue virus ( DENV ) is the most prevalent and burdensome arbovirus transmitted by Aedes mosquitoes , against which there is only a limited licensed vaccine and no approved drug treatment . A Chromobacterium species , C . sp . Panama , isolated from the midgut of A . aegypti is able to inhibit DENV replication within ...	The global burden of dengue cannot be overstated , and lack of effective control measures , besides avoiding contact with the mosquito vector , creates an urgent need to develop new strategies to control the disease . Here we elucidate the mechanism by which a natural soil bacterium inhibits DENV infection . Chromobact...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "viral", "transmission", "and", "infection", "enzymes", "pathogens", "geographical", "locations", "enzymology", "microbiology", "viral", "structure", "panama", "nor...	2018	Aminopeptidase secreted by Chromobacterium sp. Panama inhibits dengue virus infection by degrading the E protein
The reshaping and decorrelation of similar activity patterns by neuronal networks can enhance their discriminability , storage , and retrieval . How can such networks learn to decorrelate new complex patterns , as they arise in the olfactory system ? Using a computational network model for the dominant neural populatio...	The olfactory bulb is one of only two brain regions in which new neurons are added persistently in substantial numbers even in adult animals . This leads to an ongoing turnover of interneurons , in particular of the inhibitory granule cells , which constitute the largest cell population of the olfactory bulb . The func...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "neuroscience", "biology", "computational", "biology", "sensory", "systems", "neuroscience" ]	2012	Neurogenesis Drives Stimulus Decorrelation in a Model of the Olfactory Bulb
One of the crucial steps in endochondral bone formation is the replacement of a cartilage matrix produced by chondrocytes with bone trabeculae made by osteoblasts . However , the precise sources of osteoblasts responsible for trabecular bone formation have not been fully defined . To investigate whether cells derived f...	During endochondral bone formation , which is responsible for the generation of most bones in mammals and many other species , osteoblasts deposit a bone-specific matrix on the surface of cartilage scaffolds made by chondrocytes and hypertrophic chondrocytes . It has long been thought that the terminally differentiated...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biology", "and", "life", "sciences" ]	2014	Chondrocytes Transdifferentiate into Osteoblasts in Endochondral Bone during Development, Postnatal Growth and Fracture Healing in Mice
Phagocytosis and inflammation within the lungs is crucial for host defense during bacterial pneumonia . Triggering receptor expressed on myeloid cells ( TREM ) -2 was proposed to negatively regulate TLR-mediated responses and enhance phagocytosis by macrophages , but the role of TREM-2 in respiratory tract infections i...	Bacterial respiratory tract infections are a major cause of morbidity and mortality , and Streptococcus pneumoniae ( S . pneumoniae ) remains the main cause of community acquired pneumonia worldwide . The continued rise in antibiotic resistance stresses the need for better insights into the host defense mechanisms asso...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "medicine", "and", "health", "sciences", "biology", "and", "life", "sciences", "immunology", "microbiology", "pulmonology" ]	2014	The Triggering Receptor Expressed on Myeloid Cells 2 Inhibits Complement Component 1q Effector Mechanisms and Exerts Detrimental Effects during Pneumococcal Pneumonia
Plant guard cells gate CO2 uptake and transpirational water loss through stomatal pores . As a result of decades of experimental investigation , there is an abundance of information on the involvement of specific proteins and secondary messengers in the regulation of stomatal movements and on the pairwise relationships...	Stomata are microscopic pores surrounded and regulated by pairs of guard cells located on the surface of plant leaves . Stomata participate in CO2 uptake , O2 release and water vapor loss . Blue and red light induce stomatal opening ( enlargement of the pores ) , which allows the uptake of CO2 , providing the raw mater...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Computational", "implementation", "and", "tools" ]	[ "plant", "anatomy", "computer", "and", "information", "sciences", "plant", "science", "plant", "physiology", "simulation", "and", "modeling", "network", "analysis", "biology", "and", "life", "sciences", "signaling", "networks", "leaves", "stomata", "mathematical", "mo...	2014	Multi-level Modeling of Light-Induced Stomatal Opening Offers New Insights into Its Regulation by Drought
Dengue is a mosquito-borne viral disease endemic in many countries in the tropics and sub-tropics . The disease affects mainly children , but in recent years it is becoming more of an adult disease . Malaysia experienced a large dengue outbreak in 2006 to 2007 , involving mostly adults , with a high number of deaths . ...	Dengue continues to be a major mosquito-borne disease of serious public health concern . Children are usually the most affected group , but in recent decades , dengue and severe dengue have become more common among adults . Here we reviewed ten fatal dengue cases with a view to determine if there have been changes in t...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "clinical", "research", "design", "dengue", "fever", "neglected", "tropical", "diseases", "retrospective", "studies", "dengue", "viral", "diseases" ]	2013	Review of Dengue Hemorrhagic Fever Fatal Cases Seen Among Adults: A Retrospective Study
Despite having only begun ∼10 , 000 years ago , the process of domestication has resulted in a degree of phenotypic variation within individual species normally associated with much deeper evolutionary time scales . Though many variable traits found in domestic animals are the result of relatively recent human-mediated...	This study addresses why coat colors of domestic animals are so variable , while those of their wild ancestors are so uniform . Specifically , we asked whether this was the result of ( i ) relaxed purifying selection , ( ii ) that some mutations affect both coat color and another trait under strong selection ( for inst...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "evolutionary", "biology/evolutionary", "and", "comparative", "genetics" ]	2009	Contrasting Mode of Evolution at a Coat Color Locus in Wild and Domestic Pigs
The role of Type I interferon ( IFN ) during pathogenic HIV and SIV infections remains unclear , with conflicting observations suggesting protective versus immunopathological effects . We therefore examined the effect of IFNα/β on T cell death and viremia in HIV infection . Ex vivo analysis of eight pro- and anti-apopt...	Type I interferons ( IFNα/β ) are innate immune mediators that are produced by cells in response to viral infections . Although the protective effects of IFNα/β are well-established , it is not clear whether these cytokines are beneficial or deleterious during HIV-1 infection . We report that HIV-1 infection renders T ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Type I Interferon Upregulates Bak and Contributes to T Cell Loss during Human Immunodeficiency Virus (HIV) Infection
Members of the Rhizobiales ( class of α-proteobacteria ) display zonal peptidoglycan cell wall growth at one cell pole , contrasting with the dispersed mode of cell wall growth along the sidewalls of many other rod-shaped bacteria . Here we show that the seven-transmembrane receptor ( 7TMR ) protein RgsP ( SMc00074 ) ,...	Bacteria face the challenge of maintaining their peptidoglycan cell wall integrity during growth and division . The enzymes involved in cell wall biogenesis are tightly regulated and targeting of these enzymes by β-lactams cause cell death . In contrast to the well-characterized mode of dispersed cell wall formation in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "walls", "cell", "physiology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "microbiology", "light", "microscopy", "cell", "polarity", "plant", "science", "microscopy", "materials", "science", "cell", "growth", "cellular", "structures", "...	2018	Seven-transmembrane receptor protein RgsP and cell wall-binding protein RgsM promote unipolar growth in Rhizobiales
The COP9 signalosome ( CSN ) is a highly conserved multifunctional complex that has two major biochemical roles: cleaving NEDD8 from cullin proteins and maintaining the stability of CRL components . We used mutation analysis to confirm that the JAMM domain of the CSN-5 subunit is responsible for NEDD8 cleavage from cul...	Cullin-RING E3 ubiquitin ligases ( CRLs ) play important roles in regulating a wide range of processes , such as signal transduction , transcription , cell cycle progression , circadian rhythm , and development , via the ubiquitin-proteasome pathway . The activity and stability of CRLs is precisely controlled by the CO...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "neurospora", "crassa", "genetics", "yeast", "and", "fungal", "models", "biology", "microbial", "growth", "and", "development", "microbiology", "genetics", "and", "genomics", "gene", "function" ]	2012	Neurospora COP9 Signalosome Integrity Plays Major Roles for Hyphal Growth, Conidial Development, and Circadian Function
To facilitate viral infection and spread , HIV-1 Nef disrupts the surface expression of the viral receptor ( CD4 ) and molecules capable of presenting HIV antigens to the immune system ( MHC-I ) . To accomplish this , Nef binds to the cytoplasmic tails of both molecules and then , by mechanisms that are not well unders...	HIV is unique among viral pathogens in its capacity to cause chronic and progressive disease in almost all infected people . To accomplish this , HIV must evade the host immune response , especially cytotoxic T lymphocytes ( CTLs ) , which normally function to lyse virally infected cells . HIV encodes a factor , Nef , ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "immunology/immunity", "to", "infections", "virology/immune", "evasion" ]	2008	HIV-1 Nef Targets MHC-I and CD4 for Degradation Via a Final Common β-COP–Dependent Pathway in T Cells
Human African Trypanosomiasis ( HAT ) in West Africa is a lethal , neglected disease caused by Trypanosoma brucei gambiense transmitted by the tsetse Glossina palpalis gambiensis . Although the littoral part of Guinea with its typical mangrove habitat is the most prevalent area in West Africa , very few data are availa...	Human African Trypanosomiasis ( HAT ) in West Africa is a lethal , neglected disease caused by Trypanosoma brucei gambiense transmitted by the tsetse fly Glossina palpalis gambiensis . Although the littoral part of Guinea with its typical mangrove habitat is the most prevalent area in West Africa , very few data are av...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "public", "health", "and", "epidemiology", "infectious", "disease", "epidemiology", "african", "trypanosomiasis", "population", "genetics", "parasitic", "diseases", "effective", "population", "size", "neglected", "tropical", "diseases", "tsetse", "fly", "zoolo...	2012	Epidemiology of Sleeping Sickness in Boffa (Guinea): Where Are the Trypanosomes?
We investigated the relationship between bacterial load in Buruli ulcer ( BU ) lesions and the development of paradoxical reaction following initiation of antibiotic treatment . This was a longitudinal study involving BU patients from June 2013 to June 2017 . Fine needle aspirates ( FNA ) and swab samples were obtained...	Buruli ulcer is a neglected tropical skin disease caused by the third most common pathogenic mycobacterium: Mycobacterium ulcerans . Paradoxical reaction , a phenomenon observed in some patients is characterised by worsening of existing lesion ( s ) with attendant pain and occurrence of new lesions during or after anti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "drugs", "immunology", "tropical", "diseases", "microbiology", "bacterial", "diseases", "physiological", "processes", "signs", "and", "symptoms", "antibiotics", "ulcer...	2019	Paradoxical reactions in Buruli ulcer after initiation of antibiotic therapy: Relationship to bacterial load
Dispersal is a critical life history behavior for mosquitoes and is important for the spread of mosquito-borne disease . We implemented the first stable isotope mark-capture study to measure mosquito dispersal , focusing on Culex pipiens in southwest suburban Chicago , Illinois , a hotspot of West Nile virus ( WNV ) tr...	The distance and direction of adult mosquitoes movement on the landscape are important processes in the spread of mosquito-borne diseases , and are critical to understand to the development of effective intervention programs . Here we present a novel approach to study adult mosquito dispersal by using stable isotope en...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "veterinary", "diseases", "urban", "ecology", "ecology", "and", "environmental", "sciences", "ecology", "entomology", "veterinary", "virology", "biology", "and", "life", "sciences", "zoology", "veterinary", "science" ]	2014	Dispersal of Adult Culex Mosquitoes in an Urban West Nile Virus Hotspot: A Mark-Capture Study Incorporating Stable Isotope Enrichment of Natural Larval Habitats
Increased efforts in the assembly and analysis of connectome data are providing new insights into the principles underlying the connectivity of neural circuits . However , despite these considerable advances in connectomics , neuroanatomical data must be integrated with neurophysiological and behavioral data in order t...	Maps of the connections between neurons are being assembled for several organisms , including humans . But connectivity alone is insufficient for understanding the mechanisms of behavior . Nowhere is this more obvious than in the nematode C . elegans , where the nearly complete connectome has been available for over 25...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neural", "networks", "neuroscience", "animal", "behavior", "computational", "neuroscience", "theoretical", "biology", "biology", "connectomics", "computer", "science", "computer", "modeling", "neuroanatomy", "computational", "biology", "evolutionary", "biology", "behavioral"...	2013	Connecting a Connectome to Behavior: An Ensemble of Neuroanatomical Models of C. elegans Klinotaxis
Oral cholera vaccines ( OCVs ) are being increasingly employed , but current killed formulations generally require multiple doses and lack efficacy in young children . We recently developed a new live-attenuated OCV candidate ( HaitiV ) derived from a Vibrio cholerae strain isolated during the 2010 Haiti cholera epidem...	Oral cholera vaccines are increasingly used as public health tools for prevention of cholera and curtailing the spread of outbreaks . However , current killed vaccines provide minimal protection in young children , who are especially susceptible to this diarrheal disease , and require ~7–14 days between vaccination and...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "vibrio", "immunology", "tropical", "diseases", "microbiology", "vaccines", "bacterial", "diseases", "vibrio", "cholerae", "neglected", "tropical", ...	2019	Oral immunization with a probiotic cholera vaccine induces broad protective immunity against Vibrio cholerae colonization and disease in mice
B-1 cells play a critical role in early protection during influenza infections by producing natural IgM antibodies . However , the underlying mechanisms involved in regulating this process are largely unknown . Here we found that during influenza infection pleural cavity B-1a cells rapidly infiltrated lungs , where the...	Influenza infection is highly localized in respiratory tract where immune response is triggered to provide protection from primary infection . Although natural IgM antibodies produced by B-1a cells have long been recognized as first-line protection against influenza , it remains unclear whether B-1a cell response occur...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2016	IL-17A Promotes Pulmonary B-1a Cell Differentiation via Induction of Blimp-1 Expression during Influenza Virus Infection
Kinesin is a family of molecular motors that move unidirectionally along microtubules ( MT ) using ATP hydrolysis free energy . In the family , the conventional two-headed kinesin was experimentally characterized to move unidirectionally through “walking” in a hand-over-hand fashion by coordinated motions of the two he...	It is one of the major issues in biophysics how molecular motors such as conventional two-headed kinesin convert the chemical energy released at ATP hydrolysis into mechanical work . While most molecular motors move with more than one catalytic domain working in coordinated fashions , there are some motors that can mov...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "statistical", "mechanics", "theoretical", "biology", "biophysics", "theory", "biology", "biophysics", "simulations", "biophysics" ]	2013	Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin
Primate T-lymphotropic viruses type 1 ( PTLV-1 ) are complex retroviruses infecting both human ( HTLV-1 ) and simian ( STLV-1 ) hosts . They share common epidemiological , clinical and molecular features . In addition to the canonical gag , pol , env retroviral genes , PTLV-1 purportedly encodes regulatory ( i . e . Ta...	Primate T-lymphotropic viruses type 1 ( PTLV-1 ) are complex retroviruses infecting both human ( HTLV-1 ) and simian ( STLV-1 ) hosts . It has been shown that the persistence and pathogenesis of these viruses depend on the expression of small , accessory proteins . A bonnet macaque ( a monkey present in India ) was fou...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "taxonomy", "vertebrates", "animals", "mammals", "primates", "phylogenetics", "data", "management", "phylogenetic", "analysis", "genome", "analysis", "sequence", "motif", "analysis", "molecular", "biology", "techniques", "old", "world", "monkeys", "research", "and", "an...	2019	Absence of accessory genes in a divergent simian T-lymphotropic virus type 1 isolated from a bonnet macaque (Macaca radiata)
Tracking moving objects , including one’s own body , is a fundamental ability of higher organisms , playing a central role in many perceptual and motor tasks . While it is unknown how the brain learns to follow and predict the dynamics of objects , it is known that this process of state estimation can be learned purely...	A basic task for animals is to track objects—predators , prey , even their own limbs—as they move through the world . Because the position estimates provided by the senses are not error-free , higher levels of performance can be , and are , achieved when the velocity and acceleration , as well as the position , of the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Learning to Estimate Dynamical State with Probabilistic Population Codes
Gene expression during spore development in Bacillus subtilis is controlled by cell type-specific RNA polymerase sigma factors . σFand σE control early stages of development in the forespore and the mother cell , respectively . When , at an intermediate stage in development , the mother cell engulfs the forespore , σF ...	Precise temporal and cell-type specific regulation of gene expression is required for development of differentiated cells even in simple organisms . Endospore development by the bacterium Bacillus subtilis involves only two types of differentiated cells , a forespore that develops into the endospore , and a mother cell...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[]	2015	Dual-Specificity Anti-sigma Factor Reinforces Control of Cell-Type Specific Gene Expression in Bacillus subtilis
Cystic echinococcosis ( CE ) is one of the most widespread helminthic zoonoses and is caused by the tapeworm Echinococcus granulosus complex . CE diagnosis and monitoring primarily rely on imaging techniques , complemented by serology . This is usually approached by the detection of IgG antibodies against hydatid fluid...	Cystic echinococcosis ( CE ) is a helminthic zoonosis caused by Echinococcus granulosus sensu lato . CE diagnosis and monitoring is of paramount importance for the clinical management of patients and primarily rely on imaging techniques , complemented by serology . CE serology is usually based on the detection of antib...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "cystic", "echinococcosis", "medicine", "and", "health", "sciences", "enzyme-linked", "immunoassays", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "immunology", "tropical", "diseases", "parasitic", "diseases", "surgical", "and", "invasive", "medic...	2018	Evaluation of the recombinant antigens B2t and 2B2t, compared with hydatid fluid, in IgG-ELISA and immunostrips for the diagnosis and follow up of CE patients
Research on mate choice has primarily focused on preferences for quality indicators , assuming that all individuals show consensus about who is the most attractive . However , in some species , mating preferences seem largely individual-specific , suggesting that they might target genetic or behavioral compatibility . ...	The last half century has seen a tremendous interest in the study of mate choice and the evolution of traits that make individuals attractive to others . In some species , however , individuals can differ substantially in who they find attractive , and this variation has typically been interpreted as “mate choice for c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Fitness Benefits of Mate Choice for Compatibility in a Socially Monogamous Species
The 1000 Genomes Project data provides a natural background dataset for amino acid germline mutations in humans . Since the direction of mutation is known , the amino acid exchange matrix generated from the observed nucleotide variants is asymmetric and the mutabilities of the different amino acids are very different ....	In this paper we compare the differences between ‘natural’ and disease-associated amino acid variants at both sequence as well as structural levels . We used data from the 1000 Genomes Project ( 1 kG ) , the OMIM database and UniProtKB Humsavar . The results highlight the complex interplay of features from the level of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2013	Amino Acid Changes in Disease-Associated Variants Differ Radically from Variants Observed in the 1000 Genomes Project Dataset
Omics data integration is becoming necessary to investigate the genomic mechanisms involved in complex diseases . During the integration process , many challenges arise such as data heterogeneity , the smaller number of individuals in comparison to the number of parameters , multicollinearity , and interpretation and v...	At present , it is already possible to generate different type of omics–high throughput–data in the same individuals . However , we lack methodology to adequately combine them . Many challenges arise while the amount of data increases and we need to find the way to identify and understand the complex relationships when...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[]	2015	Integration Analysis of Three Omics Data Using Penalized Regression Methods: An Application to Bladder Cancer
The P2X4 receptor ( P2X4R ) is a member of a family of purinergic channels activated by extracellular ATP through three orthosteric binding sites and allosterically regulated by ivermectin ( IVM ) , a broad-spectrum antiparasitic agent . Treatment with IVM increases the efficacy of ATP to activate P2X4R , slows both re...	Ligand-gated ion channels play a crucial role in controlling many physiological and pathophysiological processes . Deciphering the gating kinetics of these channels is thus fundamental to understanding how these processes work . ATP-gated purinergic P2X receptors ( P2XRs ) are prototypic examples of such channels . The...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "allosteric", "regulation", "ion", "channel", "gating", "medicine", "and", "health", "sciences", "markov", "models", "ions", "enzymology", "social", "sciences", "electrophysiology", "permeability", "neuroscience", "simulation", "and", "modeling", "ion", "channels", "mat...	2017	Deciphering the regulation of P2X4 receptor channel gating by ivermectin using Markov models
Plant-associated microorganisms have been shown to critically affect host physiology and performance , suggesting that evolution and ecology of plants and animals can only be understood in a holobiont ( host and its associated organisms ) context . Host-associated microbial community structures are affected by abiotic ...	Under natural conditions , plant growth and behavior strongly depend on associated microbial communities called the microbiome . Much research has been performed to evaluate how the environment and plant genes help to determine the structure of the microbiome . Here , we show that interactions between microorganisms on...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "anatomy", "oomycetes", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "microbiome", "pathology", "and", "laboratory", "medicine", "community", "structure", "brassica", "microbiology", "fungi", "plant", "science", "model...	2016	Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation
Granule cells ( GCs ) are the major glutamatergic neurons in the cerebellum , and GC axon formation is an initial step in establishing functional cerebellar circuits . In the zebrafish cerebellum , GCs can be classified into rostromedial and caudolateral groups , according to the locations of their somata in the corres...	The cerebellum is involved in motor coordination and motor learning . Granule cells are the major excitatory neurons in the cerebellum . It is largely unknown how the formation of cerebellar neural circuits , including the elaboration of granule cell axons , is controlled . We investigated a zebrafish mutant shiomaneki...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Type IV Collagen Controls the Axogenesis of Cerebellar Granule Cells by Regulating Basement Membrane Integrity in Zebrafish
Most bacterial glycoproteins identified to date are virulence factors of pathogenic bacteria , i . e . adhesins and invasins . However , the impact of protein glycosylation on the major human pathogen Staphylococcus aureus remains incompletely understood . To study protein glycosylation in staphylococci , we analyzed l...	Staphylococcus aureus is a serious pathogen that causes life-threatening infections due to its ability to attach to surfaces , form biofilms , and persist inside the host . One of previously identified virulence factors in S . aureus pathogenesis is the plasmin-sensitive surface protein Pls . We here identified Pls as ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "biofilms", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "staphylococcus", "aureus", "plasmid", "construction", "methicillin-resistant", "staphylococcus", "aureus", "dna", "construction", ...	2017	The Plasmin-Sensitive Protein Pls in Methicillin-Resistant Staphylococcus aureus (MRSA) Is a Glycoprotein
Complex structural connectivity of the mammalian brain is believed to underlie the versatility of neural computations . Many previous studies have investigated properties of small subsystems or coarse connectivity among large brain regions that are often binarized and lack spatial information . Yet little is known abou...	In a previous study , a data-driven large-scale model of mouse brain connectivity was constructed . This mouse brain connectivity model is estimated by a simplified model which only takes in account anatomy and distance dependence of connection strength which is best fit by a power law . The distance dependence model c...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "built", "structures", "neural", "networks", "engineering", "and", "technology", "signal", "processing", "condensed", "matter", "physics", "neuroscience", "artificial", "neural", "networks", "artificial", "intelligence", "white", "noise", "brain", "mapping", "network", ...	2019	Synchronization dependent on spatial structures of a mesoscopic whole-brain network
The growth of plant organs is a complex process powered by osmosis that attracts water inside the cells; this influx induces simultaneously an elastic extension of the walls and pressure in the cells , called turgor pressure; above a threshold , the walls yield and the cells grow . Based on Lockhart’s seminal work , va...	Plant cells are surrounded by a rigid wall that prevents cell displacements and rearrangements as in animal tissues . Therefore , plant morphogenesis relies only on cell divisions , shape changes , and local modulation of growth rate . It has long been recognized that cell growth relies on the competition between osmos...	[ "Abstract", "Introduction", "Models", "and", "results", "Discussion" ]	[ "cell", "walls", "plant", "anatomy", "stem", "anatomy", "classical", "mechanics", "plant", "cell", "biology", "cell", "cycle", "and", "cell", "division", "cell", "processes", "plant", "physiology", "osmotic", "pressure", "shoot", "apical", "meristem", "plant", "ce...	2019	Coupling water fluxes with cell wall mechanics in a multicellular model of plant development
Expansions of trinucleotide GAA•TTC tracts are associated with the human disease Friedreich's ataxia , and long GAA•TTC tracts elevate genome instability in yeast . We show that tracts of ( GAA ) 230• ( TTC ) 230 stimulate mitotic crossovers in yeast about 10 , 000-fold relative to a “normal” DNA sequence; ( GAA ) n• (...	Although meiotic recombination has been much more studied than mitotic recombination , mitotic recombination is a universal property . Meiotic recombination rates are quite variable within the genome , with some chromosomal regions ( hotspots ) having much higher levels of exchange than other regions ( coldspots ) . Fo...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/chromosome", "biology" ]	2011	Friedreich's Ataxia (GAA)n•(TTC)n Repeats Strongly Stimulate Mitotic Crossovers in Saccharomyces cerevisae
During development , axons must integrate directional information encoded by multiple guidance cues and their receptors . Axon guidance receptors , such as UNC-40 ( DCC ) and SAX-3 ( Robo ) , can function individually or combinatorially with other guidance receptors to regulate downstream effectors . However , little i...	The nervous system is comprised of a complex network of axonal connections . This network is formed during development , when axons navigate to their target regions . Axon navigation requires multiple signaling pathways to detect and respond to extracellular guidance cues . Many of the guidance cues , receptors and sig...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	SYD-1C, UNC-40 (DCC) and SAX-3 (Robo) Function Interdependently to Promote Axon Guidance by Regulating the MIG-2 GTPase
Indirect reciprocity , in which individuals help others with a good reputation but not those with a bad reputation , is a mechanism for cooperation in social dilemma situations when individuals do not repeatedly interact with the same partners . In a relatively large society where indirect reciprocity is relevant , ind...	Humans and other animals often help others even when the helping behavior is costly . Several mechanisms can explain the emergence and maintenance of cooperation . In one such mechanism called indirect reciprocity , individuals are rated according to their past behavior toward others . Individuals help others with a go...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "theoretical", "biology", "evolutionary", "modeling", "biology", "computational", "biology" ]	2011	Indirect Reciprocity under Incomplete Observation
Neuronal synchronization reflected by oscillatory brain activity has been strongly implicated in the mechanisms supporting selective gating . We here aimed at identifying the anatomical pathways in humans supporting the top-down control of neuronal synchronization . We first collected diffusion imaging data using magne...	Directing attention to a part of visual space produces patterns of "brainwaves" or neuronal oscillations in the human visual cortex ( the part of the brain at the back that processes incoming information from the eyes ) ; oscillations at low frequencies are believed to help the brain block out irrelevant or distracting...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Frontoparietal Structural Connectivity Mediates the Top-Down Control of Neuronal Synchronization Associated with Selective Attention
Viruses have evolved strategies to protect infected cells from apoptotic clearance . We present evidence that HIV-1 possesses a mechanism to protect infected macrophages from the apoptotic effects of the death ligand TRAIL ( tumor necrosis factor–related apoptosis-inducing ligand ) . In HIV-1–infected macrophages , the...	Much of our understanding regarding mechanisms of HIV-1 persistence has been derived from studies with lymphocytes . However , mechanisms governing persistent infection of macrophages are less well understood . We investigated whether HIV-1 modulates macrophage function in a way that promotes their persist infection . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "cell", "biology", "macrophage", "virology", "in", "vitro", "hiv-1" ]	2007	Apoptotic Killing of HIV-1–Infected Macrophages Is Subverted by the Viral Envelope Glycoprotein
The space-filling fractal network in the human lung creates a remarkable distribution system for gas exchange . Landmark studies have illuminated how the fractal network guarantees minimum energy dissipation , slows air down with minimum hardware , maximizes the gas- exchange surface area , and creates respiratory flex...	The possibility of predicting oxygen currents in the human lung under varying conditions may give new understanding of the lung's operation , new therapeutic interventions , and new designs for non-biological transport systems . We introduce such a computation which requires only a pocket calculator and agrees with mea...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "physics", "mathematics", "physiology", "computational", "biology", "biophysics", "respiratory", "medicine" ]	2010	Reverse Engineering of Oxygen Transport in the Lung: Adaptation to Changing Demands and Resources through Space-Filling Networks
HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses . Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells . We used previously published data from five p...	Gaining a quantitative understanding of the development and turnover of different HIV-1-infected subpopulations of cells is crucial to improve the outcome of patients on combination antiretroviral therapy ( cART ) . The population of latently infected cells is of particular interest as they represent the major barrier ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "infectious", "diseases", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "medical", "microbiology", "hiv", "viral", "pathogens", "hiv", "clinical", "manifestations", "microbial", "pathogens", "biology", "and", "life", "...	2014	Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells
We reported previously that a proportion of natural CD25+ cells isolated from the PBMC of HCV patients can further upregulate CD25 expression in response to HCV peptide stimulation in vitro , and proposed that virus-specific regulatory T cells ( Treg ) were primed and expanded during the disease . Here we describe epig...	Hepatitis C virus persistently infects ∼3% of the world population , leading to life threatening liver diseases and liver failure . It is not well understood why the human immune system often fails to clear the virus , although it is likely multi-factorial . It is accepted that effector T cells are critical for clearin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunology/cellular", "microbiology", "and", "pathogenesis", "immunology/immunomodulation", "immunology", "immunology/immunity", "to", "infections" ]	2009	Analysis of FOXP3+ Regulatory T Cells That Display Apparent Viral Antigen Specificity during Chronic Hepatitis C Virus Infection
Leprosy remains a public health problem in Brazil . Although the overall number of new cases is declining , there are still areas with a high disease burden , such as Pará State in the north of the country . We aim to predict future trends in new case detection rate ( NCDR ) and explore the potential impact of contact ...	Leprosy remains a public health problem in Brazil . With over 30 , 000 new cases detected annually , it has the second-largest number of leprosy cases detected worldwide . Although the overall number of new cases is declining , there are still areas with a high disease burden , such as Pará State . In this study , we u...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "mycobacterium", "leprae", "medicine", "and", "health", "sciences", "immunology", "tropical", "diseases", "geographical", "locations", "india", "preventive", "medicine", "bacterial", "diseases", "mathematics", "extrapolation", "neglected", "tropical", "diseases", "vaccinati...	2016	Leprosy New Case Detection Trends and the Future Effect of Preventive Interventions in Pará State, Brazil: A Modelling Study
With the emergence of leishmaniasis in new regions around the world , molecular epidemiological methods with adequate discriminatory power , reproducibility , high throughput and inter-laboratory comparability are needed for outbreak investigation of this complex parasitic disease . As multilocus sequence analysis ( ML...	Molecular epidemiology of infectious diseases , which uses pathogen genetics to determine risk factors in the human population , is commonly employed to assist in outbreak investigation . While definitive genetic markers and techniques have been developed for several other bacterial , viral , and parasitic pathogens , ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "molecular", "epidemiology", "infectious", "disease", "epidemiology", "epidemiology", "genetics", "molecular", "genetics", "population", "genetics", "biology", "microbiology", "parasitology" ]	2014	Multilocus Sequence Analysis for Leishmania braziliensis Outbreak Investigation
The idea that most morphological adaptations can be attributed to changes in the cis-regulation of gene expression levels has been gaining increasing acceptance , despite the fact that only a handful of such cases have so far been demonstrated . Moreover , because each of these cases involves only one gene , we lack an...	Evolution can involve changes that are advantageous—known as adaptations—as well as changes that are neutral or slightly deleterious , which are established through a process of random drift . Discerning what specific differences between any two lineages are adaptive is a major goal of evolutionary biology . For gene e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "genetics", "biology", "computational", "biology", "evolutionary", "biology", "genetics", "and", "genomics" ]	2011	Systematic Detection of Polygenic cis-Regulatory Evolution
Symptoms and signs of leptospirosis are non-specific . Several diagnostic tests for leptospirosis are available and in some instances are being used prior to treatment of leptospirosis-suspected patients . There is therefore a need to evaluate the cost-effectiveness of the different treatment strategies in order to avo...	Symptoms and signs of leptospirosis are non-specific . A number of diagnostic tests for leptospirosis are available . We compared the cost-benefit of 5 management strategies: 1 ) no patients tested or given antibiotic treatment; 2 ) all patients given empirical doxycycline treatment; patients given doxycycline when a p...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2010	Strategies for Diagnosis and Treatment of Suspected Leptospirosis: A Cost-Benefit Analysis
Visceral Leishmaniasis ( VL ) has spread to many urban centers worldwide . Dogs are considered the main reservoir of VL , because canine cases often precede the occurrence of human cases . Detection and euthanasia of serologically positive dogs is one of the primary VL control measures utilized in some countries , incl...	Visceral Leishmaniasis ( VL ) is a major public health problem . Its control is based on detection and culling of positive dogs , treatment of human cases and vector control . Canine cases often precede the occurrence of human cases; hence , disease control in dogs is important . Use of accurate diagnostic tests is req...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	The Rapid Test Based on Leishmania infantum Chimeric rK28 Protein Improves the Diagnosis of Canine Visceral Leishmaniasis by Reducing the Detection of False-Positive Dogs
Parasitic nematodes impose a debilitating health and economic burden across much of the world . Nematode resistance to anthelmintic drugs threatens parasite control efforts in both human and veterinary medicine . Despite this threat , the genetic landscape of potential resistance mechanisms to these critical drugs rema...	The treatment of roundworm ( nematode ) infections in both humans and animals relies on a small number of anti-parasitic drugs . Resistance to these drugs has appeared in veterinary parasite populations and is a growing concern in human medicine . A better understanding of the genetic basis for parasite drug resistance...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "and", "discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "chemical", "compounds", "quantitative", "trait", "loci", "caenorhabditis", "animals", "organic", "compounds", "parasitology", "animal", "models", "caenorhabditis", "elegans", "model", "organisms", "experimental", ...	2018	Discovery of genomic intervals that underlie nematode responses to benzimidazoles
Plants respond to different stresses by inducing or repressing transcription of partially overlapping sets of genes . In Arabidopsis , the PHR1 transcription factor ( TF ) has an important role in the control of phosphate ( Pi ) starvation stress responses . Using transcriptomic analysis of Pi starvation in phr1 , and ...	As sessile organisms , plants are often exposed to stress conditions , and have evolved adaptive responses to protect themselves from different types of stress . Some responses are stress type-specific whereas others are common to different stress types . Understanding how these responses are controlled is crucial for ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-environment", "interactions", "genetics", "and", "genomics/plant", "genetics", "and", "gene", "expression", "plant", "biology/plant", "biochemistry", "and", "physiology" ]	2010	A Central Regulatory System Largely Controls Transcriptional Activation and Repression Responses to Phosphate Starvation in Arabidopsis
Interspecies transmission of prions is a well-established phenomenon , both experimentally and under field conditions . Upon passage through new hosts , prion strains have proven their capacity to change their properties and this is a source of strain diversity which needs to be considered when assessing the potential ...	Prions , the infectious agents responsible for causing mad cow disease , amongst other diseases , can transmit from one species to another . For example , Bovine Spongiform Encephalopathy can transmit to humans resulting in invariably fatal variant Creutzfeldt-Jakob Disease . We wanted to study the susceptibility of ra...	[ "Abstract", "Introduction", "Results", "Materials", "and", "Methods", "Discussion" ]	[]	2015	Transgenic Mouse Bioassay: Evidence That Rabbits Are Susceptible to a Variety of Prion Isolates
Fungi , such as Candida spp . , are commonly found on the skin and at mucosal surfaces . Yet , they rarely cause invasive infections in immunocompetent individuals , an observation reflecting the ability of our innate immune system to control potentially invasive microbes found at biological boundaries . Antimicrobial ...	It has been estimated that humans contain about 1 kg of microbes , an observation that reflects our coexistence with colonizing microbes such as bacteria and fungi . The fungal species Candida is present as a commensal at mucosal surfaces and on skin . Although it may cause life-threatening infections , such as sepsis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases/fungal", "infections", "immunology/innate", "immunity", "dermatology/skin", "infections" ]	2008	Histidine-Rich Glycoprotein Protects from Systemic Candida Infection
The splicing regulator Polypyrimidine Tract Binding Protein ( PTBP1 ) has four RNA binding domains that each binds a short pyrimidine element , allowing recognition of diverse pyrimidine-rich sequences . This variation makes it difficult to evaluate PTBP1 binding to particular sites based on sequence alone and thus to ...	A key step in the regulation of mammalian genes is the splicing of the messenger RNA precursor to produce a mature mRNA that can be translated into a particular protein needed by the cell . Through the process of alternative splicing , mRNAs encoding different proteins can be derived from the same primary gene transcri...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "sequence", "analysis", "biochemistry", "rna", "rna", "processing", "nucleic", "acids", "gene", "regulation", "gene", "expression", "genetics", "molecular", "genetics", "gene", "splicing", "biology", "computational", "biology" ]	2014	De Novo Prediction of PTBP1 Binding and Splicing Targets Reveals Unexpected Features of Its RNA Recognition and Function
Transcription in mammalian nuclei is highly compartmentalized in RNA polymerase II-enriched nuclear foci known as transcription factories . Genes in cis and trans can share the same factory , suggesting that genes migrate to preassembled transcription sites . We used fluorescent in situ hybridization to investigate the...	Many different types of cancer result from gene translocations . Specifically , two different chromosomes can be joined that fuse growth control genes with powerful regulatory elements , leading to unrestricted control of cell growth . Translocation partner genes must physically encounter each other in the nucleus to u...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "oncology", "cell", "biology", "mammals", "immunology", "mus", "(mouse)", "molecular", "biology", "genetics", "and", "genomics", "hematology" ]	2007	Myc Dynamically and Preferentially Relocates to a Transcription Factory Occupied by Igh
Implantable electrode arrays are widely used in therapeutic stimulation of the nervous system ( e . g . cochlear , retinal , and cortical implants ) . Currently , most neural prostheses use serial stimulation ( i . e . one electrode at a time ) despite this severely limiting the repertoire of stimuli that can be applie...	Implantable multi-electrode arrays ( MEAs ) are used to record neurological signals and stimulate the nervous system to restore lost function ( e . g . cochlear implants ) . MEAs that can combine both sensing and stimulation will revolutionize the development of the next generation of devices . Simple models that can a...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "engineering", "and", "technology", "signal", "processing", "membrane", "potential", "ocular", "anatomy", "retinal", "ganglion", "cells", "electrophysiology", "neuroscience", "surgical", "and", "invasive", ...	2016	A Simple and Accurate Model to Predict Responses to Multi-electrode Stimulation in the Retina
Many neurodegenerative diseases have a hallmark regional and cellular pathology . Gene expression analysis of healthy tissues may provide clues to the differences that distinguish resistant and sensitive tissues and cell types . Comparative analysis of gene expression in healthy mouse and human brain provides a framewo...	Animal models of human neurodegenerative and psychiatric disorders , particularly mouse models , have assumed a central role in biomedical research aimed at discovering the causes of disease and generating novel , mechanism-based treatments . But to what degree can a mouse brain serve as a model for a human brain ? Her...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "neuroscience", "homo", "(human)", "mus", "(mouse)" ]	2007	Conservation of Regional Gene Expression in Mouse and Human Brain
An important goal in researching the biology of olfaction is to link the perception of smells to the chemistry of odorants . In other words , why do some odorants smell like fruits and others like flowers ? While the so-called stimulus-percept issue was resolved in the field of color vision some time ago , the relation...	An important issue in olfaction sciences deals with the question of how a chemical information can be translated into percepts . This is known as the stimulus-percept problem . Here , we set out to better understand this issue by combining knowledge about the chemistry and cognition of smells with computational olfacti...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "smell", "chemical", "compounds", "statistics", "social", "sciences", "neuroscience", "data", "mining", "perception", "physicochemical", "properties", "cognitive", "psychology", "scientists", "forecasting", "odorants", "mathematics", "materials", "science", "information", "...	2019	Chemical features mining provides new descriptive structure-odor relationships
Cells typically vary in their response to extracellular ligands . Receptor transport processes modulate ligand-receptor induced signal transduction and impact the variability in cellular responses . Here , we quantitatively characterized cellular variability in erythropoietin receptor ( EpoR ) trafficking at the single...	Cell surface receptors translate extracellular ligand concentrations to intracellular responses . Receptor transport between the plasma membrane and other cellular compartments regulates the number of accessible receptors at the plasma membrane that determines the strength of downstream pathway activation at a given li...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "medicine", "and", "health", "sciences", "vesicles", "endocrine", "physiology", "hormone", "transport", "membrane", "receptor", "signaling", "cellular", "structures", "and", "organelles", "intracellular", "receptors", "proteins", "endocrinology", "me...	2017	Correlated receptor transport processes buffer single-cell heterogeneity
The precision with which visual information can be recalled from working memory declines as the number of items in memory increases . This finding has been explained in terms of the distribution of a limited representational resource between items . Here we investigated how the sensory strength of memoranda affects res...	Investigations of visual short-term memory typically involve memorising clearly visible objects with elementary features , such as monochromatic disks or oriented bars . Results of such studies indicate that memory is allocated like a limited resource , i . e . shared out between objects . However , in daily life we ar...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "engineering", "and", "technology", "signal", "processing", "social", "sciences", "neuroscience", "learning", "and", "memory", "noise", "reduction", "cognitive", "neuroscience", "cognition", "computational", "neuroscience", "memory", "vision", "neuronal", "tuning", "codin...	2018	Internal but not external noise frees working memory resources
Plant viruses move through plasmodesmata to infect new cells . The plant endoplasmic reticulum ( ER ) is interconnected among cells via the ER desmotubule in the plasmodesma across the cell wall , forming a continuous ER network throughout the entire plant . This ER continuity is unique to plants and has been postulate...	Plant viruses may use different host cell transport machineries to move from one cell to another through plasmodesmata . The contribution of host cell transport systems to the intercellular movement of multipartite negative-strand RNA plant viruses including tospoviruses is poorly understood . We used Tomato spotted wi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "physiology", "plant", "anatomy", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "endoplasmic", "reticulum", "cell", "processes", "microbiology", "brassica", "viruses", "membrane", "proteins", "plant", "scienc...	2016	The ER-Membrane Transport System Is Critical for Intercellular Trafficking of the NSm Movement Protein and Tomato Spotted Wilt Tospovirus
The putative link between gene expression of brain regions and their neural connectivity patterns is a fundamental question in neuroscience . Here this question is addressed in the first large scale study of a prototypical mammalian rodent brain , using a combination of rat brain regional connectivity data with gene ex...	Brain connectivity is believed to be associated with gene expression levels in the developing and the adult animal . Recently , this association has been explored in two model animals: the worm C . elegans at the level of single neurons; and the mouse , where specific subpopulations of neurons in the hippocampus were s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genomics", "computational", "neuroscience", "biology", "computational", "biology", "neuroscience", "genetics", "and", "genomics" ]	2011	Gene Expression in the Rodent Brain is Associated with Its Regional Connectivity
Lactoferrin is a multifunctional mammalian immunity protein that limits microbial growth through sequestration of nutrient iron . Additionally , lactoferrin possesses cationic protein domains that directly bind and inhibit diverse microbes . The implications for these dual functions on lactoferrin evolution and genetic...	Immunity genes can evolve rapidly in response to antagonism by microbial pathogens , but how the emergence of new protein functions impacts such evolutionary conflicts remains unclear . Here we have traced the evolutionary history of the lactoferrin gene in primates , which in addition to an ancient iron-binding functi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "antimicrobials", "organismal", "evolution", "medicine", "and", "health", "sciences", "drugs", "population", "genetics", "microbiology", "vertebrates", "animals", "mammals", "primates", "microbial", "evolution", "pharmacology", "population", "biology", "evol...	2016	Antimicrobial Functions of Lactoferrin Promote Genetic Conflicts in Ancient Primates and Modern Humans
RNA-binding proteins ( RBPs ) have roles in the regulation of many post-transcriptional steps in gene expression , but relatively few RBPs have been systematically studied . We searched for the RNA targets of 40 proteins in the yeast Saccharomyces cerevisiae: a selective sample of the approximately 600 annotated and pr...	Regulation of gene transcription has been extensively studied , but much less is known about how the fates of the resulting mRNA transcripts are regulated . We were intrigued by the fact that while most eukaryotic genomes encode hundreds of RNA-binding proteins ( RBPs ) , the targets and regulatory roles of only a smal...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology", "genetics", "and", "genomics" ]	2008	Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System
Oligomers of length k , or k-mers , are convenient and widely used features for modeling the properties and functions of DNA and protein sequences . However , k-mers suffer from the inherent limitation that if the parameter k is increased to resolve longer features , the probability of observing any specific k-mer beco...	Genomic regulatory elements ( enhancers , promoters , and insulators ) control the expression of their target genes and are widely believed to play a key role in human development and disease by altering protein concentrations . A fundamental step in understanding enhancers is the development of DNA sequence-based mode...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "sequence", "analysis", "computer", "and", "information", "sciences", "functional", "genomics", "molecular", "biology", "network", "analysis", "genetics", "regulatory", "networks", "biology", "and", "life", "sciences", "molecular", "biology", ...	2014	Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
The exclusive localization of the histone H3 variant CENP-A to centromeres is essential for accurate chromosome segregation . Ubiquitin-mediated proteolysis helps to ensure that CENP-A does not mislocalize to euchromatin , which can lead to genomic instability . Consistent with this , overexpression of the budding yeas...	Chromosomes carry the genetic material in cells . When cells divide , each daughter cell must inherit a single copy of each chromosome . The centromere is the locus on each chromosome that ensures the equal distribution of chromosomes during cell division . One essential protein involved in this task is CENP-ACse4 , wh...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "chromosome", "structure", "and", "function", "molecular", "probe", "techniques", "centromeres", "dna-binding", "proteins", "immunoblotting", "dna", "transcription", "fungi", "model", "organisms", "genome", "analysis", "epigenetics", "molecular", "biology", "techniques", ...	2016	Regulation of Budding Yeast CENP-A levels Prevents Misincorporation at Promoter Nucleosomes and Transcriptional Defects
Ovulation is critical for successful reproduction and correlates with ovarian cancer risk , yet genetic studies of ovulation have been limited . It has long been thought that the mechanism controlling ovulation is highly divergent due to speciation and fast evolution . Using genetic tools available in Drosophila , we n...	Sexual reproduction is thought to be a highly divergent process due to fast evolution and speciation . For example , sperm from one species can seldom fertilize eggs from another species , indicating that different molecular machinery for fertilization is applied in different species . In contrast to this divergent vie...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Matrix Metalloproteinase 2 Is Required for Ovulation and Corpus Luteum Formation in Drosophila
Activation-induced cytidine deaminase ( AID ) is required for initiation of Ig class switch recombination ( CSR ) and somatic hypermutation ( SHM ) of antibody genes during immune responses . AID has also been shown to induce chromosomal translocations , mutations , and DNA double-strand breaks ( DSBs ) involving non-I...	Activation-induced cytidine deaminase ( AID ) is required for diversifying antibodies during immune responses , and it does this by introducing mutations and DNA breaks into antibody genes . How AID is targeted is not understood , and it induces chromosomal translocations , mutations , and double-strand breaks ( DSBs )...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Nbs1 ChIP-Seq Identifies Off-Target DNA Double-Strand Breaks Induced by AID in Activated Splenic B Cells
Annual influenza epidemics and occasional pandemics pose a severe threat to human health . Host cell factors required for viral spread but not for cellular survival are attractive targets for novel approaches to antiviral intervention . The cleavage activation of the influenza virus hemagglutinin ( HA ) by host cell pr...	Seasonal influenza epidemics and pandemics represent a serious health threat to the human population . Resistance to presently available anti-viral drugs is frequently observed . Therefore , identification of new targets for anti-viral therapy is an urgent need . Host proteases are required for processing of the virus ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Tmprss2 Is Essential for Influenza H1N1 Virus Pathogenesis in Mice
Viral diseases of the respiratory tract , which include influenza pandemic , children acute bronchiolitis , and viral pneumonia of the elderly , represent major health problems . Plasmacytoid dendritic cells play an important role in anti-viral immunity , and these cells were recently shown to express ChemR23 , the rec...	Infections of the lower respiratory tract by single-stranded RNA viruses represent a major health problem worldwide . Animal models indicate that the severity of infections caused by these viruses is due essentially to an excessive primary immune response of the host , rather than the direct cytopathogenicity of the vi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "respiratory", "infections", "immunity", "to", "infections", "immunology", "pulmonology", "viral", "pneumonia", "infectious", "diseases", "inflammation", "respiratory", "syncytial", "virus", "infection", "immune", "response", "clinical", "immunology", "immunity"...	2011	ChemR23 Dampens Lung Inflammation and Enhances Anti-viral Immunity in a Mouse Model of Acute Viral Pneumonia
In the murine model of Leishmania major infection , resistance or susceptibility to the parasite has been associated with the development of a Th1 or Th2 type of immune response . Recently , however , the immunosuppressive effects of IL-10 have been ascribed a crucial role in the development of the different clinical c...	The clinical symptoms caused by infections with Leishmania parasites range from self-healing cutaneous to uncontrolled visceral disease and depend not only on the parasite species but also on the type of the host's immune response . It is estimated that 350 million people worldwide are at risk , with a global incidence...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "clinical", "immunology" ]	2013	T Cell-Derived IL-10 Determines Leishmaniasis Disease Outcome and Is Suppressed by a Dendritic Cell Based Vaccine
Epidemic transitions are an important feature of infectious disease systems . As the transmissibility of a pathogen increases , the dynamics of disease spread shifts from limited stuttering chains of transmission to potentially large scale outbreaks . One proposed method to anticipate this transition are early-warning ...	Anticipating disease emergence is a challenging problem , however the public health ramifications are clear . A proposed tool to help meet this challenge are early-warning signals ( EWS ) , summary statistics which undergo characteristic changes before dynamical transitions . While previous theoretical studies are prom...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "infectious", "disease", "epidemiology", "pathogens", "mathematical", "models", "epidemiological", "methods", "and", "statistics", "probability", "distribution", "mathematics", "stochasti...	2018	Anticipating epidemic transitions with imperfect data
Breast cancer mortality is primarily due to metastasis rather than primary tumors , yet relatively little is understood regarding the etiology of metastatic breast cancer . Previously , using a mouse genetics approach , we demonstrated that inherited germline polymorphisms contribute to metastatic disease , and that th...	Estrogen receptor-negative ( ER- ) breast cancer is a highly malignant form of breast cancer with poor prognosis . Like most solid tumors , the mortality associated with ER- breast cancer is due to the development of secondary tumors , or metastases , in vital organs distant from the original breast tumor . ER- breast ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "breast", "tumors", "quantitative", "trait", "loci", "cancers", "and", "neoplasms", "basic", "cancer", "research", "oncology", "chronobiology", "mammalian", "genomics", "epigenetics", "chromosome", "6", "chromatin", "chromosome",...	2016	The Circadian Rhythm Gene Arntl2 Is a Metastasis Susceptibility Gene for Estrogen Receptor-Negative Breast Cancer
Knockdown resistance ( kdr ) to dichlorodiphenyltrichloroethane ( DDT ) and pyrethroids is known to link amino acid substitutions in the voltage-gated sodium channel ( VGSC ) in Aedes aegypti . Dengue fever primarily transmitted by Ae . aegypti is an annual public health issue in Taiwan . Accordingly , pyrethroid insec...	VGSC mutations of Aedes aegypti threaten vector control programs and have been brought to attention in dengue endemic areas . Taiwan has suffered dengue outbreaks , which usually begin from an imported case . Pyrethroid insecticides were used to kill infectious females and adults in the surrounding environment of each ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "geographical", "locations", "animals", "genetic", "mapping", "mutation", "insect", "vectors", "infectious", "diseases", "genome", "complexity", "agrochemicals", "taiwan", "aedes", "aegypti", "disease", "vectors", ...	2019	Voltage-gated sodium channel intron polymorphism and four mutations comprise six haplotypes in an Aedes aegypti population in Taiwan
Bone and lung metastases are responsible for the majority of deaths in patients with breast cancer . Following treatment of the primary cancer , emotional and psychosocial factors within this population precipitate time to recurrence and death , however the underlying mechanism ( s ) remain unclear . Using a mouse mode...	Improved detection programs and better drugs to eradicate breast tumors have increased survival in women with breast cancer . However , pain and metastasis to distant organs , including bone , remain significant clinical problems . Understanding why and how metastatic cancer cells colonize specific organs is therefore ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "cancer", "treatment", "anatomy", "and", "physiology", "oncology", "bone", "signaling", "pathways", "adrenergic", "signal", "transduction", "musculoskeletal", "system", "biology", "molecular", "biology", "autonomic", "nervous", "system", "signal", "transductio...	2012	Stimulation of Host Bone Marrow Stromal Cells by Sympathetic Nerves Promotes Breast Cancer Bone Metastasis in Mice
Therapeutics with novel modes of action and a low risk of generating resistance are urgently needed to combat drug-resistant Plasmodium falciparum malaria . Here , we report that the peptide vinyl sulfones WLL-vs ( WLL ) and WLW-vs ( WLW ) , highly selective covalent inhibitors of the P . falciparum proteasome , potent...	The spread of artemisinin-resistant Plasmodium falciparum malaria across Southeast Asia creates an imperative to develop new treatment options with compounds that are not susceptible to existing mechanisms of antimalarial drug resistance . Recent work has identified the P . falciparum proteasome as a promising drug tar...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "trophozoites", "parasite", "groups", "medicine", "and", "health", "sciences", "chemical", "compounds", "plasmodium", "methylenes", "cancer", "treatment", "drugs", "microbiology", "parasitology", "antimalarials", "oncology", "mutation", "apicomplexa", "methylene", "blue", ...	2019	Covalent Plasmodium falciparum-selective proteasome inhibitors exhibit a low propensity for generating resistance in vitro and synergize with multiple antimalarial agents
The DNA uptake of naturally competent bacteria has been attributed to the action of DNA uptake machineries resembling type IV pilus complexes . However , the protein ( s ) for pulling the DNA across the outer membrane of Gram-negative bacteria remain speculative . Here we show that the competence protein ComEA binds in...	Horizontal gene transfer ( HGT ) plays a key role in transferring genetic information from one organism to another . Natural competence for transformation is one of three modes of HGT used by bacteria to promote the uptake of free DNA from the surrounding . The human pathogen Vibrio cholerae enters such a competence st...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "microbial", "evolution", "protein", "structure", "microbial", "pathogens", "microbiology", "biology", "computational", "biology", "macromolecular", "structure", "analysis" ]	2014	ComEA Is Essential for the Transfer of External DNA into the Periplasm in Naturally Transformable Vibrio cholerae Cells
Cognitive and behavioral disorders are thought to be a result of neuronal dysfunction , but the underlying molecular defects remain largely unknown . An important signaling pathway involved in the regulation of neuronal function is the cyclic AMP/Protein kinase A pathway . We here show an essential role for coronin 1 ,...	Memory and behavior depend on the proper transduction of signals in the brain , but the underlying molecular mechanisms remain largely unknown . Coronin 1 is a member of a highly conserved family of proteins , and although its gene lies in a chromosome region associated with neurobehavioral dysfunction in mice and men ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "signaling", "signal", "transduction", "molecular", "neuroscience", "cell", "biology", "biology", "and", "life", "sciences", "neuroscience" ]	2014	Coronin 1 Regulates Cognition and Behavior through Modulation of cAMP/Protein Kinase A Signaling
DNA repair mechanisms in mitotically proliferating cells avoid generating crossovers , which can contribute to genome instability . Most models for the production of crossovers involve an intermediate with one or more four-stranded Holliday junctions ( HJs ) , which are resolved into duplex molecules through cleavage b...	The maintenance of a stable genome is crucial to organismal survival . Genome stability is perpetually threatened by spontaneous DNA damage , and DNA repair proteins are required to accurately and efficiently repair DNA damage in ways that minimize genome alterations . Some repair pathways are linked to increased risk ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "cell", "biology", "cell", "biology", "chromosome", "biology", "genetics", "molecular", "genetics", "biology", "genomics", "genetics", "and", "genomics" ]	2011	Three Structure-Selective Endonucleases Are Essential in the Absence of BLM Helicase in Drosophila
Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking . For clonal species , a single allele can theoretically define a population . For non-clonal species such as Burkholderia pseudomallei , however , shared allelic states between distantly related ...	Burkholderia pseudomallei is a soil-dwelling bacterium that can infect a large range of hosts . In humans , B . pseudomallei causes melioidosis , and typical routes of entry include open wounds , inhalation , or ingestion . Clinical features are diverse , although pneumonia and abscess formation are common . High rates...	[ "Abstract", "Introduction", "Methods", "Results", "and", "Discussion" ]	[ "emerging", "infectious", "diseases", "population", "genetics", "biology", "evolutionary", "biology", "microbiology", "bacterial", "pathogens" ]	2011	Epidemiological Tracking and Population Assignment of the Non-Clonal Bacterium, Burkholderia pseudomallei
Cyclosporin A ( CsA ) has important anti-microbial activity against parasites of the genus Leishmania , suggesting CsA-binding cyclophilins ( CyPs ) as potential drug targets . However , no information is available on the genetic diversity of this important protein family , and the mechanisms underlying the cytotoxic e...	Visceral leishmanisasis , also known as Kala Azar , is caused by the protozoan parasite Leishmania donovani . The L . donovani infectious cycle comprises two developmental stages , a motile promastigote stage that proliferates inside the digestive tract of the phlebotomine insect host , and a non-motile amastigote stag...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "computational", "biology/sequence", "motif", "analysis", "cell", "biology/cellular", "death", "and", "stress", "responses", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases/protozoal", "infections", "infectious", "diseases/antimicrobials", "a...	2010	Cyclosporin A Treatment of Leishmania donovani Reveals Stage-Specific Functions of Cyclophilins in Parasite Proliferation and Viability
Albeit genetically highly heterogeneous , muscular dystrophies ( MDs ) share a convergent pathology leading to muscle wasting accompanied by proliferation of fibrous and fatty tissue , suggesting a common MD–pathomechanism . Here we show that mutations in muscular dystrophy genes ( Dmd , Dysf , Capn3 , Large ) lead to ...	All kinds of muscular dystrophies ( MDs ) are characterized by progressive muscle wasting due to life-long proliferation of precursor cells of myo- ( muscle ) , fibro- ( connective tissue ) , and lipogenic ( fat ) origin . Despite discovery of many MD genes over the past 25 years , MDs still represent debilitating , in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "animal", "genetics", "cancer", "genetics", "genetic", "mutation", "duchenne", "muscular", "dystrophy", "cytogenetic", "analysis", "animal", "models", "genetics", "of", "disease", "model", "organisms", "biology", "mouse", "x-linked", "congenital", "hereditary", "myopath...	2011	DNA Damage, Somatic Aneuploidy, and Malignant Sarcoma Susceptibility in Muscular Dystrophies
Insulin-like growth factor I receptor ( Igf1r ) signaling controls proliferation , differentiation , growth , and cell survival in many tissues; and its deregulated activity is involved in tumorigenesis . Although important during fetal growth and postnatal life , a function for the Igf pathway during preimplantation d...	One of the most important steps during mammalian development is the formation of a blastocyst before implantation . Proper blastocyst development is fundamentally reliant on the function of the E-cadherin adhesion molecule , which cannot be replaced by another highly related member of the cadherin family . We have addr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetic", "mutation", "mechanisms", "of", "signal", "transduction", "animal", "models", "developmental", "biology", "model", "organisms", "molecular", "development", "signaling", "pathways", "signaling", "in", "cellular", "processes", "biology", "molecular", "biology", ...	2012	Igf1r Signaling Is Indispensable for Preimplantation Development and Is Activated via a Novel Function of E-cadherin
Could some vaccines drive the evolution of more virulent pathogens ? Conventional wisdom is that natural selection will remove highly lethal pathogens if host death greatly reduces transmission . Vaccines that keep hosts alive but still allow transmission could thus allow very virulent strains to circulate in a populat...	There is a theoretical expectation that some types of vaccines could prompt the evolution of more virulent ( “hotter” ) pathogens . This idea follows from the notion that natural selection removes pathogen strains that are so “hot” that they kill their hosts and , therefore , themselves . Vaccines that let the hosts su...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Imperfect Vaccination Can Enhance the Transmission of Highly Virulent Pathogens
Dengue is the most widespread vector-borne viral disease caused by dengue virus ( DENV ) for which there are no safe , effective drugs approved for clinical use . Here , by using sequential antigen panning of a yeast antibody library derived from healthy donors against the DENV envelop protein domain III ( DIII ) combi...	Dengue virus infects 50–100 million people each year . Infection is initiated by entry of the virus into cells mediated by the viral envelope glycoproteins . There are four closely related DENV serotypes , but they all are antigenically distinct , with each comprising several genotypes that exhibit differences in their...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "dengue", "virus", "medicine", "and", "health", "sciences", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "pathogens", "animal", "models", "of", "disease", "immunology", "microbiology", "viruses", "animal", "models", "vaccines", "preventive", "...	2019	A broadly neutralizing germline-like human monoclonal antibody against dengue virus envelope domain III
TNF expression of macrophages is under stringent translational control that depends on the p38 MAPK/MK2 pathway and the AU–rich element ( ARE ) in the TNF mRNA . Here , we elucidate the molecular mechanism of phosphorylation-regulated translation of TNF . We demonstrate that translation of the TNF-precursor at the ER r...	For immediate response and better control of gene expression , eukaryotic cells have developed means to specifically regulate the stability and translation of pre-formed mRNA transcripts . This post-transcriptional regulation of gene expression is realized by a variety of mRNA-binding proteins , which target specific m...	[ "Abstract", "Introduction", "Results", "Discussion", "Experimental", "Procedures" ]	[ "signal", "transduction", "inflammation", "molecular", "cell", "biology", "immunity", "protein", "translation", "gene", "expression", "molecular", "biology", "immunology", "biology", "mapk", "signaling", "cascades", "rna", "stability", "signaling", "cascades" ]	2012	The p38/MK2-Driven Exchange between Tristetraprolin and HuR Regulates AU–Rich Element–Dependent Translation
Sporulation in the bacterium Bacillus subtilis is a developmental program in which a progenitor cell differentiates into two different cell types , the smaller of which eventually becomes a dormant cell called a spore . The process begins with an asymmetric cell division event , followed by the activation of a transcri...	A central feature of developmental programs is the establishment of asymmetry and the production of genetically identical daughter cells that display different cell fates . Sporulation in the bacterium Bacillus subtilis is a simple developmental program in which the cell divides asymmetrically to produce two daughter c...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "cell", "biology", "biology", "and", "life", "sciences", "developmental", "biology", "microbiology" ]	2014	Asymmetric Division and Differential Gene Expression during a Bacterial Developmental Program Requires DivIVA
We most often consider muscle as a motor generating force in the direction of shortening , but less often consider its roles as a spring or a brake . Here we develop a fully three-dimensional spatially explicit model of muscle to isolate the locations of forces and energies that are difficult to separate experimentally...	Locomotion requires energy . Very fast locomotion requires a larger amount of energy than muscle can produce in such a short time period , thus muscle must use energy that it previously produced and stored as elastic deformation . Cyclical or repeated movements can be directly powered by muscle , but energy may be cons...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "musculoskeletal", "system", "biophysic", "al", "simulations", "physiology", "muscle", "functions", "biology", "anatomy", "and", "physiology", "computational", "biology", "biophysics", "biomechanics", "muscle" ]	2012	Elastic Energy Storage and Radial Forces in the Myofilament Lattice Depend on Sarcomere Length

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