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The nature of the optical cycle of photoactive yellow protein ( PYP ) makes its elucidation challenging for both experiment and theory . The long transition times render conventional simulation methods ineffective , and yet the short signaling-state lifetime makes experimental data difficult to obtain and interpret . H...	Many protein systems of biological interest undergo dynamical changes on a time scale too long to be modeled using standard computational methods . One example is photoactive yellow protein ( PYP ) , found in several bacterial species . Blue light , potentially harmful for DNA , triggers several structural changes in P...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "physics", "biology", "and", "life", "sciences", "physical", "sciences", "biophysics", "biophysical", "simulations" ]	2014	Multiscale Approach to the Determination of the Photoactive Yellow Protein Signaling State Ensemble
Lymphatic filariasis is widely endemic in Myanmar . Despite the establishment of an elimination program in 2000 , knowledge of the remaining burden of disease relies predominantly on programmatic information . To assist the program , we conducted an independent cross-sectional household cluster survey to determine the ...	Lymphatic filariasis ( LF ) is a mosquito-transmitted worm infection that causes chronic and progressive swelling of the limbs ( lymphoedema ) and testis ( hydrocoele ) . Over time this swelling results in significant disfigurement and disability for sufferers . In 2000 , Myanmar commenced a National Program to Elimina...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "tropical", "diseases", "parasitic", "diseases", "health", "care", "filariasis", "signs", "and", "symptoms", "pharmaceutics", "myanmar", "drug", "administ...	2018	The prevalence of lymphatic filariasis infection and disease following six rounds of mass drug administration in Mandalay Region, Myanmar
Since we still know very little about stem cells in their natural environment , it is useful to explore their dynamics through modelling and simulation , as well as experimentally . Most models of stem cell systems are based on deterministic differential equations that ignore the natural heterogeneity of stem cell popu...	Stem cells portend great potential for advances in medicine . However , these advances require detailed understanding of the dynamics of stem cells . In vitro studies are now routine and challenge our preconceptions about stem cell biology , but the dynamics of stem cells in vivo remain poorly understood . Thus , there...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "systems", "biology", "developmental", "biology", "computer", "and", "information", "sciences", "computer", "modeling", "mathematics", "stem", "cells", "animal", "cells", "cell", "biology", "theoretical", "biology", "applied", "mathematics", "biology", "and", "life", ...	2014	Stochastic Dynamics of Interacting Haematopoietic Stem Cell Niche Lineages
The development of new diagnostics is an important tool in the fight against disease . Latent Class Analysis ( LCA ) is used to estimate the sensitivity and specificity of tests in the absence of a gold standard . The main field diagnostic for Schistosoma mansoni infection , Kato-Katz ( KK ) , is not very sensitive at ...	Schistosomiasis is a debilitating disease affecting over 200 million people worldwide , mainly in developing countries . Treatment for schistosomiasis is straightforward and involves treating all school-age children , and sometimes also adults , in areas where schistosomiasis is known to occur . However , detecting int...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "schistosoma", "invertebrates", "schistosoma", "mansoni", "medicine", "and", "health", "sciences", "body", "fluids", "education", "helminths", "sociology", "geographical", "locations", "tropical", "diseases", "uganda", "social", "sciences", "parasitic", "diseases", "anima...	2017	Interpreting ambiguous ‘trace’ results in Schistosoma mansoni CCA Tests: Estimating sensitivity and specificity of ambiguous results with no gold standard
We investigated the roles played by the cysteine proteases cathepsin B and cathepsin L ( brucipain ) in the pathogenesis of Trypansoma brucei brucei in both an in vivo mouse model and an in vitro model of the blood–brain barrier . Doxycycline induction of RNAi targeting cathepsin B led to parasite clearance from the bl...	African trypanosomiasis , or sleeping sickness , is caused by the single-cell parasite Trypanosoma brucei ( T . brucei ) . Two parasite-derived enzyme proteins have been hypothesized to play an important role in the viability of the parasite or its ability to produce disease in the human host . Utilizing RNA interferen...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "infectious", "diseases/neglected", "tropical", "diseases" ]	2008	RNA Interference of Trypanosoma brucei Cathepsin B and L Affects Disease Progression in a Mouse Model
In human leishmaniasis Th1/Th2 dichotomy similar to murine model is not clearly defined and surrogate marker ( s ) of protection is not yet known . In this study , Th1/Th2 cytokines ( IL-5 , IL-10 , IL-13 and IFN-γ ) profile induced by purified CD4+/CD8+ T cells in response to Leishmania antigens were assessed at trans...	Cutaneous leishmaniasis ( CL ) is usually a self-healing skin lesion caused by different species of Leishmania parasite . Resistance and susceptibility of mice to Leishmania major infection is associated with two types of CD4+ T lymphocytes development: Th1 type response with production of cytokine IFN-γ is associated ...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology/immune", "response" ]	2010	CD8+ T Cells as a Source of IFN-γ Production in Human Cutaneous Leishmaniasis
Embryonic stem ( ES ) cells are pluripotent cells derived from the inner cell mass of the mammalian blastocyst . Cellular differentiation entails loss of pluripotency and gain of lineage-specific characteristics . However , the molecular controls that govern the differentiation process remain poorly understood . We hav...	The discovery of the first microRNA ( lin-4 ) in C . elegans in 1993 and the increasing realization that small RNAs are at the heart of many biological processes have led to a revolution in our thinking about development and disease . In animals , several hundred microRNAs ( miRNAs ) have been identified that regulate ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/cell", "differentiation", "developmental", "biology/germ", "cells", "developmental", "biology/stem", "cells", "genetics", "and", "genomics/bioinformatics" ]	2009	Highly Dynamic and Sex-Specific Expression of microRNAs During Early ES Cell Differentiation
The human T-cell leukemia virus type 1 ( HTLV-1 ) Tax protein hijacks the host ubiquitin machinery to activate IκB kinases ( IKKs ) and NF-κB and promote cell survival; however , the key ubiquitinated factors downstream of Tax involved in cell transformation are unknown . Using mass spectrometry , we undertook an unbia...	HTLV-1 infection is etiologically linked to the development of the neuroinflammatory disorder HTLV-1 associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) and adult T-cell leukemia ( ATL ) , an aggressive CD4+CD25+ malignancy . The HTLV-1 regulatory protein Tax constitutively activates the IκB kinases ( IKKs )...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "medicine", "and", "health", "sciences" ]	2014	HTLV-1 Tax Stabilizes MCL-1 via TRAF6-Dependent K63-Linked Polyubiquitination to Promote Cell Survival and Transformation
The innate immune response constitutes the first line of defense against infections . Pattern recognition receptors recognize pathogen structures and trigger intracellular signaling pathways leading to cytokine and chemokine expression . Reactive oxygen species ( ROS ) are emerging as an important regulator of some of ...	Herpes simplex virus ( HSV ) type 1 and 2 are important human pathogens , which can give rise to severe diseases during both primary and recurrent infections . In addition to activating “classical” innate and adaptive immune responses , many infections stimulate other cellular activities such as and production of react...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "immunology", "biology", "microbiology" ]	2011	HSV Infection Induces Production of ROS, which Potentiate Signaling from Pattern Recognition Receptors: Role for S-glutathionylation of TRAF3 and 6
Entamoeba nuttalli is an intestinal protozoan with pathogenic potential that can cause amebic liver abscess . It is highly prevalent in wild and captive macaques . Recently , cysts were detected in a caretaker of nonhuman primates in a zoo , indicating that E . nuttalli may be a zoonotic pathogen . Therefore , it is im...	Entamoeba nuttalli is the phylogenetically closest protozoan to Entamoeba histolytica and is highly prevalent in macaques . Previous studies have indicated that E . nuttalli is virulent in a hamster model . In this study , we compared the immunopathological basis of formation of liver abscess in hamsters between E . nu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "trophozoites", "parasite", "groups", "medicine", "and", "health", "sciences", "innate", "immune", "system", "immune", "cells", "immune", "physiology", "pathology", "and", "laboratory", "medicine", "cytokines", "pathogens", "immunology", "vertebrates",...	2018	Characteristics of inflammatory reactions during development of liver abscess in hamsters inoculated with Entamoeba nuttalli
Infection of the developing fetus with human cytomegalovirus ( HCMV ) is a major cause of central nervous system disease in infants and children; however , mechanism ( s ) of disease associated with this intrauterine infection remain poorly understood . Utilizing a mouse model of HCMV infection of the developing CNS , ...	Intrauterine infection with human cytomegalovirus ( HCMV ) is a leading cause of developmental brain damage . In the U . S . , an estimated 2 , 000 infants a year develop brain damage as a result of intrauterine infection with HCMV . In this study , we examined the contribution of host immune responses induced by CMV i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "neurogenesis", "immunologic", "subspecialties", "immunology", "microbiology", "host-pathogen", "interaction", "cytomegalovirus", "infection", "neuroscience", "cell", "differentiation", "developmental", "biology", "stem", "cells", "emerging", "infectious", "diseases...	2013	Glucocortiocoid Treatment of MCMV Infected Newborn Mice Attenuates CNS Inflammation and Limits Deficits in Cerebellar Development
Natural progression of HIV-1 infection depends on genetic variation in the human major histocompatibility complex ( MHC ) class I locus , and the CD8+ T cell response is thought to be a primary mechanism of this effect . However , polymorphism within the MHC may also alter innate immune activity against human immunodef...	Leukocyte immunoglobulin-like receptors B1 and B2 ( LILRB1 and LILRB2 ) bind HLA class I allotypes with variable affinities . Here , we show that the binding strength of LILRB2 to HLA class I positively associates with level of viremia in a large cohort of untreated HIV-1-infected patients . This effect appears to be d...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "hiv", "retrovirology", "and", "hiv", "immunopathogenesis", "viral", "diseases" ]	2014	LILRB2 Interaction with HLA Class I Correlates with Control of HIV-1 Infection
Locomotor activity rhythms are controlled by a network of ~150 circadian neurons within the adult Drosophila brain . They are subdivided based on their anatomical locations and properties . We profiled transcripts “around the clock” from three key groups of circadian neurons with different functions . We also profiled ...	Organisms ranging from bacteria to humans contain circadian clocks . They keep internal time and also integrate environmental cues such as light to provide external time information for entrainment . In the fruit fly Drosophila melanogaster , ~150 brain neurons contain the circadian machinery and are critical for contr...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "invertebrates", "neurochemistry", "messenger", "rna", "neuroscience", "animals", "circadian", "oscillators", "hormones", "animal", "models", "drosophila", "melanogaster", "model", "organisms", "experimental", "organism", "systems", "chronobiology", "neuropeptides", "drosophi...	2017	RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides
Envenoming by viper snakes constitutes an important public health problem in Brazil and other developing countries . Local hemorrhage is an important symptom of these accidents and is correlated with the action of snake venom metalloproteinases ( SVMPs ) . The degradation of vascular basement membrane has been proposed...	Snakebite accidents by vipers cause a massive disturbance in hemostasis and tissue damage at the snakebite area . The systemic effects are often prevented by antivenom therapy . However , the local symptoms are not neutralized by antivenoms and are related to the temporary or permanent disability observed in many patie...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "biology/extra-cellular", "matrix", "cell", "biology/cell", "adhesion", "biochemistry/protein", "chemistry" ]	2010	Mechanisms of Vascular Damage by Hemorrhagic Snake Venom Metalloproteinases: Tissue Distribution and In Situ Hydrolysis
Reciprocal interactions between neurons and oligodendrocytes are not only crucial for myelination , but also for long-term survival of axons . Degeneration of axons occurs in several human myelin diseases , however the molecular mechanisms of axon-glia communication maintaining axon integrity are poorly understood . He...	Brain function largely depends on the communication between electrically excitable neurons and surrounding glial cells . Myelinating oligodendrocytes are a type of brain cell that insulate major neuronal processes ( axons ) and help to sustainably maintain axonal health , which is poorly understood in molecular terms ....	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunocytochemistry", "medicine", "cellular", "structures", "subcellular", "organelles", "molecular", "neuroscience", "neurochemistry", "multiple", "sclerosis", "macromolecular", "assemblies", "neuroscience", "demyelinating", "disorders", "biological", "transport", "neurotransmi...	2013	Neurotransmitter-Triggered Transfer of Exosomes Mediates Oligodendrocyte–Neuron Communication
Protein domains shallowly inserting into the membrane matrix are ubiquitous in peripheral membrane proteins involved in various processes of intracellular membrane shaping and remodeling . It has been suggested that these domains sense membrane curvature through their preferable binding to strongly curved membranes , t...	Selective targeting of soluble proteins to cellular membranes relies on different mechanisms such as receptor-mediated recruitment or direct binding to specific lipids . A new paradigm has been recently proposed , according to which membrane binding of some proteins is driven by the geometrical and physical properties ...	[ "Abstract", "Introduction", "Model", "Results", "Discussion" ]	[ "physics", "biology", "and", "life", "sciences", "physical", "sciences" ]	2014	Sensing Membrane Stresses by Protein Insertions
Sleeping sickness ( human African trypanosomiasis [HAT] ) is a neglected tropical disease with limited treatment options that currently require parenteral administration . In previous studies , orally administered pafuramidine was well tolerated in healthy patients ( for up to 21 days ) and stage 1 HAT patients ( for u...	Sleeping sickness , or human African trypanosomiasis ( HAT ) , is a neglected tropical disease . Because only 2 treatment options are available to treat persons with stage 1 disease , and both require parenteral administration , oral drugs would be of great benefit to the affected population . In this Phase 3 , multi-c...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "body", "fluids", "clinical", "research", "design", "maternal", "health", "obstetrics", "and", "gynecology", "african", "trypanosomiasis", "nervous", "system", "tropical", "diseases", "parasitic", "diseases", "parasitology", "res...	2016	Efficacy and Safety of Pafuramidine versus Pentamidine Maleate for Treatment of First Stage Sleeping Sickness in a Randomized, Comparator-Controlled, International Phase 3 Clinical Trial
Among mammals , only eutherians and marsupials are viviparous and have genomic imprinting that leads to parent-of-origin-specific differential gene expression . We used comparative analysis to investigate the origin of genomic imprinting in mammals . PEG10 ( paternally expressed 10 ) is a retrotransposon-derived imprin...	Genomic imprinting is a gene regulatory mechanism controlling parent-of-origin-dependent expression of genes . In eutherians , imprinting is essential for fetal and placental development and defects in this mechanism are the cause of several genetic disorders . In eutherian mammals , genomic imprinting is controlled by...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods", "Supporting", "Information" ]	[ "evolutionary", "biology", "molecular", "biology", "developmental", "biology", "mammals" ]	2007	Retrotransposon Silencing by DNA Methylation Can Drive Mammalian Genomic Imprinting
We often perform movements and actions on the basis of internal motivations and without any explicit instructions or cues . One common example of such behaviors is our ability to initiate movements solely on the basis of an internally generated sense of the passage of time . In order to isolate the neuronal signals res...	One advantage of studying sensory systems is that external stimuli can be readily controlled and quantified . Our internal perception of time , however , is not as easily approachable . To address this challenge , we developed a task that leverages our knowledge of the neuronal circuits underlying eye movements . Monke...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "social", "and", "behavioral", "sciences", "decision", "making", "neuropsychology", "neuroscience", "motor", "systems", "cognitive", "neuroscience", "cognition", "computational", "neuroscience", "coding", "mechanisms", "circuit", "models", "biology", "psychology", "central"...	2012	Temporal Production Signals in Parietal Cortex
Host-directed therapies ( HDTs ) constitute promising alternatives to traditional therapy that directly targets the pathogen but is often hampered by pathogen resistance . HDT could represent a new treatment strategy for leishmaniasis , a neglected tropical disease caused by the obligate intracellular parasite Leishman...	Leishmaniasis is a poverty-related disease threatening 350 million people throughout the world . It is caused by the protozoan parasite Leishmania , a digenetic organism that switches from an extracellular stage in the sand fly vector to an intracellular stage in phagocytes of the vertebrate host . Drugs currently avai...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "intracellular", "pathogens", "viral", "transmission", "and", "infection", "pathogens", "immunology", "microbiology", "parasitic", "diseases", "pr...	2016	Naloxonazine, an Amastigote-Specific Compound, Affects Leishmania Parasites through Modulation of Host-Encoded Functions
PhyloGibbs , our recent Gibbs-sampling motif-finder , takes phylogeny into account in detecting binding sites for transcription factors in DNA and assigns posterior probabilities to its predictions obtained by sampling the entire configuration space . Here , in an extension called PhyloGibbs-MP , we widen the scope of ...	Proteins in a living cell are not expressed all the time: instead , genes are turned on or off on demand . Indeed , though nearly every cell in a multicellular organism has a complete copy of the genome , each cell expresses only a fraction of the encoded proteins . Regulation of gene expression occurs in various ways ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/transcriptional", "regulation" ]	2008	PhyloGibbs-MP: Module Prediction and Discriminative Motif-Finding by Gibbs Sampling
Pathogens have evolved diverse strategies to maximize their transmission fitness . Here we investigate these strategies for directly transmitted pathogens using mathematical models of disease pathogenesis and transmission , modeling fitness as a function of within- and between-host pathogen dynamics . The within-host m...	Infectious diseases vary widely in how they affect those who get infected and how they are transmitted . As an example , the duration of a single infection can range from days to years , while transmission can occur via the respiratory route , water or sexual contact . Measles and HIV are contrasting examples—both are ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/evolutionary", "modeling", "public", "health", "and", "epidemiology/infectious", "diseases", "infectious", "diseases", "public", "health", "and", "epidemiology/epidemiology" ]	2009	Antigenic Diversity, Transmission Mechanisms, and the Evolution of Pathogens
The intracellular protozoan parasite Leishmania donovani causes human visceral leishmaniasis . Intracellular L . donovani that proliferate inside macrophage phagolysosomes compete with the host for arginine , creating a situation that endangers parasite survival . Parasites have a sensor that upon arginine deficiency a...	Leishmania donovani , the causative agent of visceral leishmaniasis , leads a digenetic life cycle as a flagellated promastigote in the vector sandfly and aflagellated amastigote within phagolysosomes of infected macrophages . Arginine is an essential amino acid for Leishmania which possesses a high specificity arginin...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "chemical", "compounds", "immunology", "microbiology", "parasitic", "protozoans", "organic", "compounds", "protozoan", "life", "cycles", "developmental", "biology", "protozoans", "leishmania", ...	2019	The arginine sensing and transport binding sites are distinct in the human pathogen Leishmania
RNA viruses such as poliovirus have high mutation rates , and a diverse viral population is likely required for full virulence . We previously identified limitations on poliovirus spread after peripheral injection of mice expressing the human poliovirus receptor ( PVR ) , and we hypothesized that the host interferon re...	RNA viruses are highly error prone , and can use their replication infidelity to adapt to complex environments within an infected host . However , viral populations may experience bottlenecks , which limit their diversity and potentially reduce their virulence . We hypothesized that natural barriers may limit the sprea...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virus", "evolution", "and", "symbiosis", "gastroenterology", "and", "hepatology/gastrointestinal", "infections", "virology/animal", "models", "of", "infection", "virology", "virology/mechanisms", "of", "resistance", "and", "susceptibility,", "including", "host", "ge...	2008	Multiple Host Barriers Restrict Poliovirus Trafficking in Mice
Nonenveloped viruses undergo conformational changes that enable them to bind to , disrupt , and penetrate a biological membrane leading to successful infection . We assessed whether cytosolic factors play any role in the endoplasmic reticulum ( ER ) membrane penetration of the nonenveloped SV40 . We find the cytosolic ...	The nonenveloped simian virus 40 ( SV40 ) is a model member of the Polyomaviridae family of viruses containing several related species that cause diseases in immunocompromised individuals . As with other nonenveloped viruses , the membrane penetration step during SV40 entry is mechanistically obscure . Productive SV40 ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "and", "life", "sciences", "microbiology", "virology" ]	2014	A Cytosolic Chaperone Complexes with Dynamic Membrane J-Proteins and Mobilizes a Nonenveloped Virus out of the Endoplasmic Reticulum
Leishmania ( Viannia ) parasites present particular challenges , as human and murine immune responses to infection are distinct from other Leishmania species , indicating a unique interaction with the host . Further , vaccination studies utilizing small animal models indicate that modalities and antigens that prevent i...	Leishmania ( Viannia ) are the predominant agents of leishmaniasis in Latin America . Given the fact that leishmaniasis is a zoonosis , eradication is unlikely; a vaccine could provide effective prevention of disease . However , these parasites present a challenge and we do not fully understand what elements of the hos...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunity", "biology", "microbiology", "parasitology", "pathogenesis" ]	2011	TLR1/2 Activation during Heterologous Prime-Boost Vaccination (DNA-MVA) Enhances CD8+ T Cell Responses Providing Protection against Leishmania (Viannia)
Leptospirosis is a bacterial zoonotic disease of worldwide importance , though relatively neglected in many African countries including sub Saharan Africa that is among areas with high burden of this disease . The disease is often mistaken for other febrile illnesses such as dengue , malaria , rickettsioses and enteric...	Leptospirosis is caused by a spirochete bacterium of the genus Leptospira . The disease is worldwide distributed , although highly neglected in some parts of the developing world . This study investigated the prevalence of antibodies against Leptospira in sugarcane plantation workers , a fishing community and rodents a...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "leptospira", "pathology", "and", "laboratory", "medicine", "shrews", "pathogens", "sociology", "tropical", "diseases", "microbiology", "vertebrates", "social", "sciences", "geographical", "locations", "animals", "mammals", "social...	2019	Leptospirosis in sugarcane plantation and fishing communities in Kagera northwestern Tanzania
Nutation is an oscillatory movement that plants display during their development . Despite its ubiquity among plants movements , the relation between the observed movement and the underlying biological mechanisms remains unclear . Here we show that the kinematics of the full organ in 3D give a simple picture of plant n...	In his writings , Darwin considered nutation , the revolving movement of the apical tip of plants , as the most widespread plant movement . In spite of its ubiquity , plant nutation has not received as much attention as other plant movements , and its underlying mechanism remains unclear . A better understanding of thi...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ellipses", "classical", "mechanics", "plant", "growth", "and", "development", "phototropism", "social", "sciences", "plant", "physiology", "geometry", "neuroscience", "circadian", "oscillators", "developmental", "biology", "plant"...	2016	The Kinematics of Plant Nutation Reveals a Simple Relation between Curvature and the Orientation of Differential Growth
Substrate permissiveness has long been regarded as the raw materials for the evolution of new enzymatic functions . In land plants , hydroxycinnamoyltransferase ( HCT ) is an essential enzyme of the phenylpropanoid metabolism . Although essential enzymes are normally associated with high substrate specificity , HCT can...	Examples abound of enzymes that can process substrates other than their native ones . However , the structural and dynamic basis of this promiscuity remains to be fully understood . In this work , we examine HCT , an intrinsically promiscuous acyltransferase with conserved function in all land plants . We uncover the s...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "crystal", "structure", "chemical", "compounds", "molecular", "dynamics", "enzymes", "condensed", "matter", "physics", "enzymology", "organic", "compounds", "enzyme", "metabolism", "basic", "amino", "acids", "amino", "acids", "crystallography", "enzyme", "chemistry", "c...	2018	Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT)
Bacteria move towards favourable and away from toxic environments by changing their swimming pattern . This response is regulated by the chemotaxis signalling pathway , which has an important feature: it uses feedback to ‘reset’ ( adapt ) the bacterial sensing ability , which allows the bacteria to sense a range of bac...	Bacteria move towards favourable environments by changing their swimming pattern . An important feature of this response , which is called bacterial chemotaxis , is that their sensing ability remains independent of the background environment in which they find themselves . This feature has been studied extensively in t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods", "Measuring", "chemotactic", "performance", "Parametric", "sensitivity", "analysis", "Linear", "systems", "analysis", "techniques", "Model", "parameters", "Response", "to", "noisy", "ligand...	[ "microbiology/microbial", "physiology", "and", "metabolism", "biochemistry/cell", "signaling", "and", "trafficking", "structures", "computational", "biology/systems", "biology", "computational", "biology/signaling", "networks" ]	2011	Feedback Control Architecture and the Bacterial Chemotaxis Network
It is widely assumed that active RNA polymerases track along their templates to produce a transcript . We test this using chromosome conformation capture and human genes switched on rapidly and synchronously by tumour necrosis factor alpha ( TNFα ) ; one is 221 kbp SAMD4A , which a polymerase takes more than 1 h to tra...	We were all taught that an RNA polymerase becomes active by diffusing to a promoter , initiating transcription , and then tracking like a locomotive down the DNA template . We test this using tumour necrosis factor alpha ( TNFα ) to switch on transcription of two human genes which lie far apart on the genetic map and t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "cell", "biology/nuclear", "structure", "and", "function", "genetics", "and", "genomics/nuclear", "structure", "and", "function", "molecular", "biology...	2010	Active RNA Polymerases: Mobile or Immobile Molecular Machines?
Information is encoded in neural circuits using both graded and action potentials , converting between them within single neurons and successive processing layers . This conversion is accompanied by information loss and a drop in energy efficiency . We investigate the biophysical causes of this loss of information and ...	As in electronics , many of the brain's neural circuits convert continuous time signals into a discrete-time binary code . Although some neurons use only graded voltage signals , most convert these signals into discrete-time action potentials . Yet the costs and benefits associated with such a switch in signalling mech...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience", "biology", "computational", "neuroscience" ]	2014	Consequences of Converting Graded to Action Potentials upon Neural Information Coding and Energy Efficiency
Cognition can reveal itself in the pupil , as latent cognitive processes map onto specific pupil responses . For instance , the pupil dilates when we make decisions and these pupil size fluctuations reflect decision-making computations during and after a choice . Surprisingly little is known , however , about how pupil...	It has long been known that the pupil dilates when we decide . These pupil dilations have predominantly been linked to arousal . However , reward-related processes may trigger pupil dilations as well , as dilations have been linked to activity in the dopaminergic midbrain , a region important for reward processing and ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "learning", "medicine", "and", "health", "sciences", "neurochemistry", "chemical", "compounds", "decision", "making", "social", "sciences", "neuroscience", "learning", "and", "memory", "organic", "compounds", "hormones", "cognitive", "psychology", "mathematics", "cognitio...	2018	How pupil responses track value-based decision-making during and after reinforcement learning
This study was undertaken in five onchocerciasis/lymphatic filariasis ( LF ) co-endemic local government areas ( LGAs ) in Plateau and Nasarawa , Nigeria . Annual MDA with ivermectin had been given for 17 years , 8 of which were in combination with albendazole . In 2008 , assessments indicated that LF transmission was ...	Both lymphatic filariasis and onchocerciasis are treated with ivermectin-based mass drug administration ( MDA ) regimens in Africa . Where the infections are co-endemic , ivermectin treatments cannot be stopped until both infection transmission cycles are broken . This report follows a previous determination that the L...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "helminth", "infections", "infectious", "diseases", "medicine", "and", "health", "sciences", "plant", "science", "filariasis", "infectious", "disease", "epidemiology", "epidemiology", "global", "health", "plant", "pathology", "...	2014	Status of Onchocerciasis Transmission after More Than a Decade of Mass Drug Administration for Onchocerciasis and Lymphatic Filariasis Elimination in Central Nigeria: Challenges in Coordinating the Stop MDA Decision
Nucleotide Excision Repair ( NER ) , which removes a variety of helix-distorting lesions from DNA , is initiated by two distinct DNA damage-sensing mechanisms . Transcription Coupled Repair ( TCR ) removes damage from the active strand of transcribed genes and depends on the SWI/SNF family protein CSB . Global Genome R...	Nucleotide Excision Repair ( NER ) removes many forms of helix-distorting DNA damage which interfere with transcription and replication , including those induced by UV irradiation . NER is initiated when damage is sensed during transcription , i . e . Transcription-Coupled Repair ( TCR ) , or when damage is sensed in n...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/gene", "discovery", "developmental", "biology", "molecular", "biology/dna", "repair", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2010	Involvement of Global Genome Repair, Transcription Coupled Repair, and Chromatin Remodeling in UV DNA Damage Response Changes during Development
Here we describe a chemical biology strategy performed in Staphylococcus aureus and Staphylococcus epidermidis to identify MnaA , a 2-epimerase that we demonstrate interconverts UDP-GlcNAc and UDP-ManNAc to modulate substrate levels of TarO and TarA wall teichoic acid ( WTA ) biosynthesis enzymes . Genetic inactivation...	Staphylococcus aureus and Staphylococcus epidermidis cause life-threatening infections that are commonly acquired in hospitals as well as the community and remain difficult to treat with current antibiotics . In part , this is due to the emergence of methicillin-resistant S . aureus and S . epidermidis ( MRSA and MRSE ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biofilms", "bacteriology", "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "microbiology", "staphylococcus", "aureus", "methicillin-resistant", "staphylococcus", "aureus", "antibiotics", "pharmaco...	2016	Chemical Genetic Analysis and Functional Characterization of Staphylococcal Wall Teichoic Acid 2-Epimerases Reveals Unconventional Antibiotic Drug Targets
Large-scale sequencing efforts have captured a rapidly growing catalogue of genetic variations . However , the accurate establishment of gene variant pathogenicity remains a central challenge in translating personal genomics information to clinical decisions . Interferon Regulatory Factor 6 ( IRF6 ) gene variants are s...	Advances in sequencing technologies have led to rapid increases in personalized genetics information . Millions of differences exist when comparing the genomes of two individuals , accounting for the diversity of humans and occasionally disease pathogenicity . Accurate determination of the functional consequences of th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "biotechnology", "genome", "engineering", "fish", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "microinjection", "engineering", "and", "technology", "synthetic", "biology", "messenger", "rna", "vertebrates", "animals", "synthetic"...	2017	Rapid functional analysis of computationally complex rare human IRF6 gene variants using a novel zebrafish model
Complex diseases result from molecular changes induced by multiple genetic factors and the environment . To derive a systems view of how genetic loci interact in the context of tissue-specific molecular networks , we constructed an F2 intercross comprised of >500 mice from diabetes-resistant ( B6 ) and diabetes-suscept...	Alzheimer's disease and type 2 diabetes are two common aging-related diseases . Numerous studies have shown that the two diseases are associated . However , the mechanisms of such connection are not clear . Both diseases are complex diseases that are induced by multiple genetic factors and the environment . To understa...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "systems", "biology", "genetics", "of", "disease", "genomics", "computational", "neuroscience", "gene", "expression", "genetics", "regulatory", "networks", "molecular", "genetics", "biology", "computational", "biology", "gene", "networks", "genetics", "and"...	2012	Integrative Analysis of a Cross-Loci Regulation Network Identifies App as a Gene Regulating Insulin Secretion from Pancreatic Islets
Microorganisms are capable of communication and cooperation to perform social activities . Cooperation can be enforced using kind discrimination mechanisms in which individuals preferentially help or punish others , depending on genetic relatedness only at certain loci . In the filamentous fungus Neurospora crassa , ge...	Microorganisms undergo social activities that benefit the species , but for social microbes , the ability to discriminate between genetically similar and genetically dissimilar individuals is instrumental in preventing cheaters from taking advantage of altruistic behavior . While kin recognition is important in animals...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "sequencing", "techniques", "cell", "physiology", "fungal", "genetics", "fungi", "model", "organisms", "molecular", "biology", "techniques", "research", "and", "analysis", "methods", "sequence", "analysis", "mycology", "sequence", "alignment", "cell", "communication", "...	2016	Characterization of Greenbeard Genes Involved in Long-Distance Kind Discrimination in a Microbial Eukaryote
Cell size is thought to play an important role in choosing between temporal and spatial sensing in chemotaxis . Large cells are thought to use spatial sensing due to large chemical difference at its ends whereas small cells are incapable of spatial sensing due to rapid homogenization of proteins within the cell . Howev...	Unicellular organisms and other single cells often have to migrate towards food sources or away from predators by sensing chemicals present in the environment . There are two ways for a cell to sense these external chemicals: temporal sensing , where the cell senses the external chemical at two different time points af...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "blood", "cells", "cell", "motility", "medicine", "and", "health", "sciences", "immune", "cells", "engineering", "and", "technology", "signal", "processing", "immunology", "germ", "cells", "protozoans", "network", "analysis", "cellular", "structures", "and", "organell...	2018	A computational model for how cells choose temporal or spatial sensing during chemotaxis
Wolbachia pipientis is an endosymbiotic bacterium estimated to chronically infect between 40–75% of all arthropod species . Aedes aegypti , the principle mosquito vector of dengue virus ( DENV ) , is not a natural host of Wolbachia . The transinfection of Wolbachia strains such as wAlbB , wMel and wMelPop-CLA into Ae ....	Dengue fever is a viral disease transmitted by Aedes aegypti mosquitoes and more than 30% of the world’s population is at risk . The control of dengue virus ( DENV ) transmission has been problematic as no vaccines or drugs are effective against the four serotypes . Vector control of mosquitoes during epidemics is cons...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "body", "fluids", "abdomen", "microbiology", "saliva", "animals", "wolbachia", "insect", "vectors", "bacteria", "digestive", "system", "infectious", "diseases", "epidemiology", "exocrine", "glands", "superinfection...	2016	Establishment of a Wolbachia Superinfection in Aedes aegypti Mosquitoes as a Potential Approach for Future Resistance Management
The YbeB ( DUF143 ) family of uncharacterized proteins is encoded by almost all bacterial and eukaryotic genomes but not archaea . While they have been shown to be associated with ribosomes , their molecular function remains unclear . Here we show that YbeB is a ribosomal silencing factor ( RsfA ) in the stationary gro...	The YbeB/DUF143 family of proteins is one of the most widely conserved proteins with homologues present in almost all bacteria and eukaryotic organelles such as mitochondria and chloroplasts ( but not archaea ) . While it has been shown that these proteins associate with ribosomes , their molecular function remained my...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "bacteriology", "cellular", "structures", "subcellular", "organelles", "functional", "genomics", "protein", "interactions", "macromolecular", "assemblies", "microbiology", "bacterial", "biochemistry", "gene", "function", "protein", "synthesis", "protein", "structure", "molecu...	2012	RsfA (YbeB) Proteins Are Conserved Ribosomal Silencing Factors
Identifying the genetic determinants of phenotypes that impact disease severity is of fundamental importance for the design of new interventions against malaria . Here we present a rapid genome-wide approach capable of identifying multiple genetic drivers of medically relevant phenotypes within malaria parasites via a ...	Developing a greater understanding of malaria genetics is a key step in combating the threat posed by the disease . Here we use a novel approach to study two important properties of the parasite; the rate at which parasites grow within a single host , and the means by which parasites are affected by the host immune sys...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "plasmodium", "yoelii", "tropical", "diseases", "cloning", "parasitic", "diseases", "alleles", "parasitic", "protozoans", "protozoans", "molecular", "biology", "techniques", "mammalian", "genomics", "research", "and", "analysis", ...	2017	Rapid identification of genes controlling virulence and immunity in malaria parasites
Since 2001 , outbreaks of Nipah virus have occurred almost every year in Bangladesh with high case-fatality rates . Epidemiological data suggest that in Bangladesh , Nipah virus is transmitted from the natural reservoir , fruit bats , to humans via consumption of date palm sap contaminated by bats , with subsequent hum...	In Bangladesh , outbreaks of Nipah virus occur almost every year , resulting in respiratory and neurological disease with high case-fatality rates . Based on epidemiological data Nipah virus is thought to be transmitted from fruit bats to humans via drinking of date palm sap contaminated by bats that drink from the sap...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "viral", "transmission", "and", "infection", "emerging", "viral", "diseases", "nipah", "fever", "microbiology", "animal", "models", "model", "organisms", "viral", "pneumonia", "emerging", "infectious", "diseases", "neglected", "tropical", "diseases", "infect...	2014	Foodborne Transmission of Nipah Virus in Syrian Hamsters
Human genome-wide association studies ( GWASs ) are revealing the genetic architecture of anthropomorphic and biomedical traits , i . e . , the frequencies and effect sizes of variants that contribute to heritable variation in a trait . To interpret these findings , we need to understand how genetic architecture is sha...	One of the central goals of evolutionary genetics is to understand the processes that give rise to phenotypic variation in humans and other taxa . Genome-wide association studies ( GWASs ) in humans provide an unprecedented opportunity in that regard , revealing the genetic basis of variation in numerous traits . Howev...	[ "Abstract", "Introduction", "The", "model", "Results", "Discussion" ]	[ "genome-wide", "association", "studies", "genomics", "genetic", "polymorphism", "phenotypes", "natural", "selection", "genome", "analysis", "heredity", "genetics", "biology", "and", "life", "sciences", "population", "genetics", "population", "biology", "computational", "b...	2018	A population genetic interpretation of GWAS findings for human quantitative traits
Identifying effective therapeutic drug combinations that modulate complex signaling pathways in platelets is central to the advancement of effective anti-thrombotic therapies . However , there is no systems model of the platelet that predicts responses to different inhibitor combinations . We developed an approach whic...	Drugs are often used in combinations , but establishing the best combinations is a considerable challenge for basic and clinical research . Anti-platelet therapies reduce thrombosis and heart attacks by lowering the activation of platelet cells . We wanted to find good drug combinations , but a full systems model of th...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Discovering Anti-platelet Drug Combinations with an Integrated Model of Activator-Inhibitor Relationships, Activator-Activator Synergies and Inhibitor-Inhibitor Synergies
HTLV-1 is the causative agent of a severe form of adult T cell leukemia/Lymphoma ( ATL ) , and of a chronic progressive neuromyelopathy designated HTLV-1 associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) . Two important HTLV-1-encoded proteins , Tax-1 and HBZ , play crucial roles in the generation and main...	Currently , more than 10 million people worldwide are infected with HTLV-1 , the first discovered human oncogenic retrovirus . Up to 7% of infected individuals experience during their life a severe form of T cell malignancy or a chronic progressive inflammatory disease of the nervous system designated HTLV-1-associated...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "immune", "cells", "pathology", "and", "laboratory", "medicine", "pathogens", "immunology", "microbiology", "light", "microscopy", "cloning", "retroviruses", "viruses", "cytoplasmic", "staining", "rna", "viruses...	2017	Cytoplasmic Localization of HTLV-1 HBZ Protein: A Biomarker of HTLV-1-Associated Myelopathy/Tropical Spastic Paraparesis (HAM/TSP)
The p400 E1A-associated protein , which mediates H2A . Z incorporation at specific promoters , plays a major role in cell fate decisions: it promotes cell cycle progression and inhibits induction of apoptosis or senescence . Here , we show that p400 expression is required for the correct control of ROS metabolism . Dep...	External or internal causes can lead to the generation of oxidative stress in mammalian cells . This oxidative stress is detrimental to cell life since it can induce protein damages or , even worse , DNA damages . Thus , cells have to control strictly oxidative stress levels . In this manuscript , we show that the p400...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "cell", "biology/gene", "expression", "cell", "biology/cellular", "death", "and", "stress", "responses" ]	2010	The E1A-Associated p400 Protein Modulates Cell Fate Decisions by the Regulation of ROS Homeostasis
Prion diseases are fatal , neurodegenerative disorders in humans and animals and are characterized by the accumulation of an abnormally folded isoform of the cellular prion protein ( PrPC ) , denoted PrPSc , which represents the major component of infectious scrapie prions . Characterization of the mechanism of convers...	The misfolded form ( PrPSc or prion ) of the naturally occuring prion protein ( PrPC or cellular PrP ) is responsible for neurodegenerative diseases such as Creutzfeldt-Jakob disease ( CJD ) , bovine spongiform encephalopathy ( BSE ) ( also known as ‘mad cow disease’ ) and a new variant of CJD ( vCJD ) , which is thoug...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cell", "biology/membranes", "and", "sorting", "infectious", "diseases/prion", "diseases" ]	2009	Identification of an Intracellular Site of Prion Conversion
Adult Clonorchis sinensis live in the bile duct and cause clonorchiasis . It is known that the C . sinensis metacercariae excyst in the duodenum and migrate up to the bile duct through the common bile duct . However , no direct evidence is available on the in vivo migration of newly excysted C . sinensis juveniles ( Cs...	Clonorchis sinensis adults habituating in the bile duct cause clonorchiasis endemic in East Asian countries , in which about 15–20 million people are supposedly infected . It has previously been reported that C . sinensis metacercariae excyst in the duodenum and that the juvenile flukes migrate to the bile duct through...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biology", "microbiology", "parasitology" ]	2011	Tracing of the Bile-Chemotactic Migration of Juvenile Clonorchis sinensis in Rabbits by PET-CT
Human T-lymphotropic virus type 1 ( HTLV-1 ) and type 2 ( HTLV-2 ) both cause lifelong persistent infections , but differ in their clinical outcomes . HTLV-1 infection causes a chronic or acute T-lymphocytic malignancy in up to 5% of infected individuals whereas HTLV-2 has not been unequivocally linked to a T-cell mali...	The two human retroviruses HTLV-1 and HTLV-2 are similar in their structure , replication cycle and the manner through which they spread between and within individuals . They differ in their preferred host T-cell type and in their possible clinical outcomes . HTLV-2 has not been linked with a specific disease , whereas...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "virology", "biology", "microbiology" ]	2014	Clonality of HTLV-2 in Natural Infection
The regulatory roles of sphingolipids in diverse cell functions have been characterized extensively . However , the dynamics and interactions among the different sphingolipid species are difficult to assess , because de novo biosynthesis , metabolic inter-conversions , and the retrieval of sphingolipids from membranes ...	Sphingolipids play dual roles by serving as components of membrane rafts and by regulating numerous key cell functions . Although sphingolipids have been studied extensively , the details of their functioning are difficult to understand , because their synthesis , pathways of inter-conversion , and utilization constitu...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "complex", "systems", "systems", "biology", "biochemistry", "cellular", "stress", "responses", "mathematics", "theoretical", "biology", "biochemistry", "simulations", "metabolic", "pathways", "applied", "mathematics", "biology", "molecular", "cell", "biology", "metabolism",...	2013	Coordination of Rapid Sphingolipid Responses to Heat Stress in Yeast
Sporotrichosis is a subcutaneous mycosis caused by pathogenic species of the Sporothrix genus . A new emerging species , Sporothrix brasiliensis , is related to cat-transmitted sporotrichosis and has severe clinical manifestations . The cell wall of pathogenic fungi is a unique structure and impacts directly on the hos...	Sporotrichosis was for many years attributed to a single etiological agent , Sporothrix schenckii . However , more recently , a new emerging pathogenic species , Sporothrix brasiliensis , has been shown to cause severe cases in humans and is associated with cat-transmitted sporotrichosis . In contrast , S . schenckii i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "cell", "walls", "chitin", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "microbiology", "fungal", "structure", "fungi", "materials", "science", "sporothrix", "schenckii", "cellular", "structures", "and", "organelles...	2018	Cell walls of the dimorphic fungal pathogens Sporothrix schenckii and Sporothrix brasiliensis exhibit bilaminate structures and sloughing of extensive and intact layers
Immunity to malaria is widely believed to wane in the absence of reinfection , but direct evidence for the presence or absence of durable immunological memory to malaria is limited . Here , we analysed malaria-specific CD4+ T cell responses of individuals living in an area of low malaria transmission in northern Thaila...	Despite some recent successes in reducing the burden of malaria in several African countries , malaria still causes up to 500 million cases of acute illness every year , killing over a million people . The widespread availability of a safe and effective vaccine would greatly increase our chances of controlling this dis...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/protozoal", "infections", "immunology/immunity", "to", "infections" ]	2011	Short-Lived IFN-γ Effector Responses, but Long-Lived IL-10 Memory Responses, to Malaria in an Area of Low Malaria Endemicity
The brain can learn and detect mixed input signals masked by various types of noise , and spike-timing-dependent plasticity ( STDP ) is the candidate synaptic level mechanism . Because sensory inputs typically have spike correlation , and local circuits have dense feedback connections , input spikes cause the propagati...	In natural environments , although sensory inputs are often highly mixed with one another and obscured by noise , animals can detect and learn discrete signals from this mixture . For example , humans easily detect the mention of their names from across a noisy room , a phenomenon known as the cocktail party effect . S...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[]	2015	Mixed Signal Learning by Spike Correlation Propagation in Feedback Inhibitory Circuits
Pythium guiyangense , an oomycete from a genus of mostly plant pathogens , is an effective biological control agent that has wide potential to manage diverse mosquitoes . However , its mosquito-killing mechanisms are almost unknown . In this study , we observed that P . guiyangense could utilize cuticle penetration and...	Utilization of biocontrol agents has emerged as a promising mosquito control strategy , and Pythium guiyangense has wide potential to manage diverse mosquitoes with high efficiency . However , the molecular mechanisms underlying pathological processes remain almost unknown . We observed that P . guiyangense invades mos...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "taxonomy", "oomycetes", "enzymes", "computational", "biology", "microbiology", "enzymology", "invertebrate", "genomics", "fungal", "structure", "developmental", "biology", "fungi", "plant", "science", "mycelium", "phylogenetics", "data", "management", "phylogenetic", "anal...	2019	Infection mechanisms and putative effector repertoire of the mosquito pathogenic oomycete Pythium guiyangense uncovered by genomic analysis
Malaria transmission remains high in Sub-Saharan Africa despite large-scale implementation of malaria control interventions . A comprehensive understanding of the transmissibility of infections to mosquitoes may guide the design of more effective transmission reducing strategies . The impact of P . falciparum sexual st...	Submicroscopic gametocyte infections are efficiently transmitted from humans to mosquitoes in settings with efficient malaria vectors and may pose challenges for malaria control and elimination efforts . Our understanding of what mechanisms contribute to submicroscopic gametocytes infectiousness remains limited . Here ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "parasite", "groups", "immune", "physiology", "enzyme-linked", "immunoassays", "oocysts", "gametocytes", "immunology", "tropical", "diseases", "parasitic", "diseases", "animals", "parasitology", "germ", "cells", "a...	2018	Modeling the impact of Plasmodium falciparum sexual stage immunity on the composition and dynamics of the human infectious reservoir for malaria in natural settings
Influenza viruses present major challenges to public health , evident by the 2009 influenza pandemic . Highly pathogenic influenza virus infections generally coincide with early , high levels of inflammatory cytokines that some studies have suggested may be regulated in a strain-dependent manner . However , a comprehen...	Vaccines suffice for protecting public health against seasonal influenza viruses , but when unexpected strains appear against which the vaccine does not confer protection , alternative treatments are necessary . In this work , we used gene expression and virus growth data from influenza-infected mice to determine how m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation
Automatic responses enable us to react quickly and effortlessly , but they often need to be inhibited so that an alternative , voluntary action can take place . To investigate the brain mechanism of controlled behavior , we investigated a biologically-based network model of spiking neurons for inhibitory control . In c...	We propose a novel neural circuit mechanism and construct a spiking neural network model for resolving conflict between an automatic response and a volitional one . In this mechanism the two types of responses compete against each other under the modulation of top-down control via multiple neural pathways . The model i...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "neural", "networks", "decision", "making", "reaction", "time", "nervous", "system", "brain", "social", "sciences", "neuroscience", "cognitive", "neuroscience", "cognition", "vision", "sensory", "physiology", "computer", "and", ...	2016	Conflict Resolution as Near-Threshold Decision-Making: A Spiking Neural Circuit Model with Two-Stage Competition for Antisaccadic Task
Pyridoxal 5′-phosphate ( PLP ) , the active form of vitamin B6 , has been implicated in preventing human pathologies , such as diabetes and cancer . However , the mechanisms underlying the beneficial effects of PLP are still unclear . Using Drosophila as a model system , we show that PLP deficiency , caused either by m...	We show that the active form of vitamin B6 ( Pyridoxal 5′-phosphate , PLP ) plays an important role in the maintenance of genome integrity . We found , using Drosophila as a model system , that PLP deficiency results in chromosome breaks and rearrangements ( collectively dubbed chromosome aberrations , abbreviated with...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "of", "disease", "cancer", "genetics", "genetic", "mutation", "genetics", "biology", "cytogenetics" ]	2014	Sugar and Chromosome Stability: Clastogenic Effects of Sugars in Vitamin B6-Deficient Cells
Schistosomiasis is an important neglected tropical disease caused by digenean helminth parasites of the genus Schistosoma . Schistosomes are unusual in that they are dioecious and the adult worms live in the blood system . MicroRNAs play crucial roles during gene regulation and are likely to be important in sex differe...	Schistosomiasis is the second most common disease caused by a parasite , affecting over 200 million people . The parasites involved are flatworms of the genus Schistosoma . Unlike most non-parasitic flatworms , Schistosoma species have separate sexes , and the emergence of sex has been associated with the development o...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Sex-Biased Expression of MicroRNAs in Schistosoma mansoni
Aedes albopictus is one of the most invasive human disease vectors . Its control has been largely based on insecticides , such as the larvicide temephos . Temephos resistance has been associated with the up-regulation , through gene amplification , of two carboxylesterase ( CCE ) genes closely linked on the genome , ca...	Control of mosquito borne diseases is being seriously challenged by the ongoing development of insecticide resistance . Resistance of Aedes albopictus , a major arbovirus vector , to the organophosphate larvicide temephos was recently associated with the up-regulation , through gene amplification , of two carboxylester...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "taxonomy", "invertebrates", "united", "states", "medicine", "and", "health", "sciences", "enzymes", "geographical", "locations", "enzymology", "animals", "genetic", "mapping", "north", "america", "phylogenetics", "data", "management", "phylogenetic", "analysis", "molecul...	2017	Carboxylesterase gene amplifications associated with insecticide resistance in Aedes albopictus: Geographical distribution and evolutionary origin
During replication , mismatch repair proteins recognize and repair mispaired bases that escape the proofreading activity of DNA polymerase . In this work , we tested the model that the eukaryotic mismatch recognition complex tracks with the advancing replisome . Using yeast , we examined the dynamics during replication...	During replication , errors that escape the replication machinery are identified and repaired by DNA mismatch repair proteins . A mismatch in the helix is recognized by MutS homologs and subsequent events include excision of the error-containing strand followed by re-synthesis . A critical step in this process is direc...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	The Eukaryotic Mismatch Recognition Complexes Track with the Replisome during DNA Synthesis
The retinoblastoma ( Rb ) tumor suppressor acts with a number of chromatin cofactors in a wide range of species to suppress cell proliferation . The Caenorhabditis elegans retinoblastoma gene and many of these cofactors , called synMuv B genes , were identified in genetic screens for cell lineage defects caused by grow...	In metazoans , soma and germline have specialized functions that require differential tissue-specific gene expression . In C . elegans , explicit chromatin marks deposited by the MES-4 histone methyltransferase and the MRG-1 chromodomain protein allow germline expression of particular suites of target genes . Conversel...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2012	Repression of Germline RNAi Pathways in Somatic Cells by Retinoblastoma Pathway Chromatin Complexes
Respiratory syncytial virus ( RSV ) infection can result in severe disease partially due to its ability to interfere with the initiation of Th1 responses targeting the production of type I interferons ( IFN ) and promoting a Th2 immune environment . Epigenetic modulation of gene transcription has been shown to be impor...	Respiratory syncytial virus ( RSV ) is a significant public health concern . Nearly all children are infected by two years of age , and severe infection often results in hospitalization . There is no vaccine for RSV , and previous attempts have resulted in increased disease severity in immunized children once they were...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	RSV-Induced H3K4 Demethylase KDM5B Leads to Regulation of Dendritic Cell-Derived Innate Cytokines and Exacerbates Pathogenesis In Vivo
Hepatitis A virus ( HAV ) , an enigmatic and ancient pathogen , is a major causative agent of acute viral hepatitis worldwide . Although there are effective vaccines , antivirals against HAV infection are still required , especially during fulminant hepatitis outbreaks . A more in-depth understanding of the antigenic c...	Hepatitis A virus ( HAV ) is a unique , hepatotropic human picornavirus that infects approximately 1 . 5 million people annually and continues to cause mortality despite a successful vaccine . There are no licensed therapeutic drugs to date . Better knowledge of HAV antigenic features and neutralizing mechanisms will f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "immune", "physiology", "enzyme-linked", "immunoassays", "pathology", "and", "laboratory", "medicine", "pathogens", "drugs", "immunology", "microbiology", "electron", "cryo-microscopy", "viruses", "microscopy", "pha...	2019	Structural basis for neutralization of hepatitis A virus informs a rational design of highly potent inhibitors
The complete connectional map ( connectome ) of a neural circuit is essential for understanding its structure and function . Such maps have only been obtained in Caenorhabditis elegans . As an attempt at solving mammalian circuits , we reconstructed the connectomes of six interscutularis muscles from adult transgenic m...	Conventionally , the organization of a neural circuit is studied by sparsely labeling its constituent neurons and pooling data from multiple samples . If significant variation exists among circuits , this approach may not answer how each neuron integrates into the circuit's functional organization . An alternative is t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience" ]	2009	The Interscutularis Muscle Connectome
A 26 year-old female patient presented to the Tropical Medicine outpatient unit of the Ludwig Maximilians-University in Munich with febrile illness after returning from Southern Africa , where she contracted a bite by a large mite-like arthropod , most likely a soft-tick . Spirochetes were detected in Giemsa stained bl...	A patient reported an arthropod bite on her dorsal metatarsal region 2/3 of her anterior foot during a trip to the Kalahari Desert in Southern Africa . Eventually , a rash developed at the site of the bite and high-grade fever started 8 days later . Spirochetes were detected in the blood smear and the patient was treat...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "borrelia", "infection", "invertebrates", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "tropical", "diseases", "microbiology", "animals", "relapsing", "fever", "bacterial", "diseases", "phy...	2016	"Candidatus Borrelia kalaharica" Detected from a Febrile Traveller Returning to Germany from Vacation in Southern Africa
Resequencing is an emerging tool for identification of rare disease-associated mutations . Rare mutations are difficult to tag with SNP genotyping , as genotyping studies are designed to detect common variants . However , studies have shown that genetic heterogeneity is a probable scenario for common diseases , in whic...	Resequencing is an emerging tool for the identification of rare disease-associated mutations . Recent studies have shown that groups of multiple rare mutations together can explain a large proportion of the genetic basis for some diseases . Therefore , we propose a new statistical method for analysing a group of mutati...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "genetics", "and", "genomics/disease", "models", "genetics", "and", "genomics/genetics", "of", "disease", "public", "health", "and", "epidemiology/epidemiology", "mathematics/statistics", "genetics", "and", "genomics/medical", "genetics" ]	2009	A Groupwise Association Test for Rare Mutations Using a Weighted Sum Statistic
The role of sensory systems is to provide an organism with information about its environment . Because sensory information is noisy and insufficient to uniquely determine the environment , natural perceptual systems have to cope with systematic uncertainty . The extent of that uncertainty is often crucial to the organi...	Most work in vision science focuses on the question of why we perceive what we do , and we now have many models explaining what physical properties of a stimulus make us see depth , colour , etc . Here we ask instead what makes us feel confident in our visual perception: in the context of a visual task , what are the p...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "neuroscience/psychology", "neuroscience/natural", "and", "synthetic", "vision" ]	2009	Evaluation of Objective Uncertainty in the Visual System
Enterotoxigenic Escherichia coli ( ETEC ) are common causes of diarrheal morbidity and mortality in developing countries for which there is currently no vaccine . Heterogeneity in classical ETEC antigens known as colonization factors ( CFs ) and poor efficacy of toxoid-based approaches to date have impeded development ...	Infectious diarrhea is one of the leading causes of death among young children in developing countries , and a major cause of morbidity in all age groups . The enterotoxigenic Escherichia coli contribute substantially to this burden of diarrheal illness , and have been a focus of vaccine development efforts for more th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Conservation and Immunogenicity of Novel Antigens in Diverse Isolates of Enterotoxigenic Escherichia coli
With the recent success of genome-wide association studies ( GWAS ) , a wealth of association data has been accomplished for more than 200 complex diseases/traits , proposing a strong demand for data integration and interpretation . A combinatory analysis of multiple GWAS datasets , or an integrative analysis of GWAS d...	The recent success of genome-wide association studies ( GWAS ) has generated a wealth of genotyping data critical to studies of genetic architectures of many complex diseases . In contrast to traditional single marker analysis , an integrative analysis of multiple genes and the assessment of their joint effects have be...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "of", "disease", "genome", "analysis", "tools", "genomics", "genetic", "networks", "genetic", "association", "studies", "genetics", "biology", "computational", "biology", "gene", "networks", "genetics", "and", "genomics", "human", "genetics" ]	2012	Network-Assisted Investigation of Combined Causal Signals from Genome-Wide Association Studies in Schizophrenia
Apicomplexan parasites rely on a novel form of actin-based motility called gliding , which depends on parasite actin polymerization , to migrate through their hosts and invade cells . However , parasite actins are divergent both in sequence and function and only form short , unstable filaments in contrast to the stabil...	Cellular movement is key to life and in the case of intracellular parasites , provides a vital mechanism to gain access to the protected niche they require . The parasite Toxoplasma gondii is a model for a group of parasites called apicomplexans , which move by an actin-dependent process referred to as gliding motility...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "genetics", "biology", "microbiology", "evolutionary", "biology", "biophysics", "genetics", "and", "genomics" ]	2011	Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites
We consider the statistical analysis of population structure using genetic data . We show how the two most widely used approaches to modeling population structure , admixture-based models and principal components analysis ( PCA ) , can be viewed within a single unifying framework of matrix factorization . Specifically ...	Two different approaches have become widely used in the analysis of population structure: admixture-based models and principal components analysis ( PCA ) . In admixture-based models each individual is assumed to have inherited some proportion of its ancestry from one of several distinct populations . PCA projects the ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/population", "genetics", "mathematics/statistics", "genetics", "and", "genomics/population", "genetics" ]	2010	Analysis of Population Structure: A Unifying Framework and Novel Methods Based on Sparse Factor Analysis
Yersinia delivers Yops into numerous types of cultured cells , but predominantly into professional phagocytes and B cells during animal infection . The basis for this cellular tropism during animal infection is not understood . This work demonstrates that efficient and specific Yop translocation into phagocytes by Yers...	Many bacterial pathogens use a needle-like structure to deliver proteins into host cells to cause disease . Yersinia species use one such structure , called a type III secretion system , to deliver a set of 6–7 proteins , called Yops , into host cells . These Yops act to dismantle host defenses and establish infection ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "genetics", "immunology", "biology", "microbiology" ]	2013	Adhesins and Host Serum Factors Drive Yop Translocation by Yersinia into Professional Phagocytes during Animal Infection
To subvert host defenses , Mycobacterium tuberculosis ( Mtb ) avoids being delivered to degradative phagolysosomes in macrophages by arresting the normal host process of phagosome maturation . Phagosome maturation arrest by Mtb involves multiple effectors and much remains unknown about this important aspect of Mtb path...	Mycobacterium tuberculosis ( Mtb ) is the infectious agent of the disease tuberculosis . Inside the host , Mtb replicates primarily within the phagosome of macrophages . To replicate within macrophages , Mtb modifies the phagosome by inhibiting the normal host process of phagosomes maturing into acidified degradative p...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "vesicles", "immune", "cells", "immunofluorescence", "staining", "enzymes", "immunology", "enzymology", "phosphatases", "physiological", "processes", "phagosomes", "immunologic", "techniques", "cellular", "structure...	2018	The SecA2 pathway of Mycobacterium tuberculosis exports effectors that work in concert to arrest phagosome and autophagosome maturation
Bacteria , yeast and human cancer cells possess mechanisms of mutagenesis upregulated by stress responses . Stress-inducible mutagenesis potentially accelerates adaptation , and may provide important models for mutagenesis that drives cancers , host pathogen interactions , antibiotic resistance and possibly much of evo...	Mutagenesis mechanisms upregulated by stress responses promote de novo antibiotic resistance and cross resistance in bacteria , anti-fungal-drug resistance in yeasts , and genome instability in cancer cells under hypoxic stress . Stress-induced mutagenesis is implicated as the main source of spontaneous mutagenesis tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "cellular", "stress", "responses", "ultraviolet", "radiation", "cell", "processes", "dna-binding", "proteins", "light", "electromagnetic", "radiation", "dna", "damage", "polymerases", "dna", "replication", "dna", "proteins", "physics", "mutagenesis", "biochemistry", "dna"...	2017	Persistent damaged bases in DNA allow mutagenic break repair in Escherichia coli
Mitogen-activated protein kinase ( MAP ) cascades are important in antiviral immunity through their regulation of interferon ( IFN ) production as well as virus replication . Although the serine-threonine MAP kinase tumor progression locus 2 ( Tpl2/MAP3K8 ) has been implicated as a key regulator of Type I ( IFNα/β ) an...	Influenza viruses infect millions of people annually causing significant morbidity , mortality and socio-economic burdens . Host immune responses against influenza virus are initiated upon virus recognition by specific intracellular receptors . Signals relayed from these receptors trigger various signaling cascades , w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Tumor Progression Locus 2 Promotes Induction of IFNλ, Interferon Stimulated Genes and Antigen-Specific CD8+ T Cell Responses and Protects against Influenza Virus
Antibodies are thought to play an essential role in naturally acquired immunity to malaria . Prospective cohort studies have frequently shown how continuous exposure to the malaria parasite Plasmodium falciparum cause an accumulation of specific responses against various antigens that correlate with a decreased risk of...	Understanding naturally acquired immunity against P . falciparum malaria is of fundamental importance for malaria control and elimination efforts . The identification of parasite antigens that could potentially be considered as vaccine targets often relies on prospective cohort studies where observed infection rates ar...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "immune", "physiology", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "protozoans", "forecasting", "mathematics", "statistics", "(mathematics)", "artificial", "intelligence", "antibodies", ...	2017	Identification of immune signatures predictive of clinical protection from malaria
Ribosomes are the highly complex macromolecular assemblies dedicated to the synthesis of all cellular proteins from mRNA templates . The main principles underlying the making of ribosomes are conserved across eukaryotic organisms and this process has been studied in most detail in the yeast Saccharomyces cerevisiae . Y...	Ribosomes are the molecular machines that generate proteins from mRNA templates . The biogenesis of eukaryotic ribosomes is an outstandingly complex process , in which around 80 ribosomal proteins and four ribosomal RNAs are accurately pieced together . Actively growing yeast cells must produce more than 160’000 riboso...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site
Kaposi's sarcoma ( KS ) is a mesenchymal tumour , which is caused by Kaposi's sarcoma herpesvirus ( KSHV ) and develops under inflammatory conditions . KSHV-infected endothelial spindle cells , the neoplastic cells in KS , show increased invasiveness , attributed to the elevated expression of metalloproteinases ( MMPs ...	Kaposi's sarcoma ( KS ) is a tumour caused by Kaposi's sarcoma herpesvirus ( KSHV ) and dysregulated inflammation . Both factors contribute to the high angiogenicity and invasiveness of KS . Various cellular kinases have been reported to regulate the KSHV latent-lytic switch and thereby virus pathogenicity . In this st...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The Inflammatory Kinase MAP4K4 Promotes Reactivation of Kaposi's Sarcoma Herpesvirus and Enhances the Invasiveness of Infected Endothelial Cells
Recent results indicate that genome-wide association studies ( GWAS ) have the potential to explain much of the heritability of common complex phenotypes , but methods are lacking to reliably identify the remaining associated single nucleotide polymorphisms ( SNPs ) . We applied stratified False Discovery Rate ( sFDR )...	Modern genome-wide association studies ( GWAS ) have failed to identify large portions of the genetic basis of common , complex traits . Recent work suggested this could be because many genetic variants , each with individually small effects , compose their genetic architecture , limiting the power of GWAS . Moreover ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "genome", "analysis", "tools", "functional", "genomics", "mathematics", "genome", "scans", "genetic", "association", "studies", "statistics", "genetics", "statistical", "methods", "biology", "genomics", "biostatistics", "computationa...	2013	All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs
Cerebrovascular dysfunction plays a key role in the pathogenesis of cerebral malaria . In experimental cerebral malaria ( ECM ) induced by Plasmodium berghei ANKA , cerebrovascular dysfunction characterized by vascular constriction , occlusion and damage results in impaired perfusion and reduced cerebral blood flow and...	Cerebrovascular dysfunction plays a key role in the pathogenesis of murine cerebral malaria ( CM ) . Low nitric oxide ( NO ) bioavailability has been attributed as a cause of the dysfunction . However , it is unclear if the NO deficit could be inflicted by decreased NO production from its enzymatic sources ( NO synthas...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "infectious", "diseases", "cerebrovascular", "diseases", "tropical", "diseases", "(non-neglected)", "neurology", "neurodegenerative", "diseases", "malaria", "parasitic", "diseases" ]	2013	Nitric Oxide Synthase Dysfunction Contributes to Impaired Cerebroarteriolar Reactivity in Experimental Cerebral Malaria
The regulated secretion of peptide hormones , neural peptides and many growth factors depends on their sorting into large dense core vesicles ( LDCVs ) capable of regulated exocytosis . LDCVs form at the trans-Golgi network , but the mechanisms that sort proteins to this regulated secretory pathway and the cytosolic ma...	The physiological action of peptide hormones and neural peptides depends on their sorting to vesicles capable of regulated exocytosis in response to stimulation . Despite the diversity and importance of signals released by this pathway , surprisingly little is understood about the molecular mechanisms involved in sorti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Widespread Dysregulation of Peptide Hormone Release in Mice Lacking Adaptor Protein AP-3
GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals . XylE , an Escherichia coli homolog of GLUT1 , utilizes proton gradient as an energy source to drive uphill D-xylose transport . Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue ( Asp27...	We seek to address one intriguing question , the mechanistic distinction between active proton-coupled symporters and passive uniporters that are related in evolution . Proton-coupled symporters harness the transmembrane proton gradient to drive the substrate transport , while uniporters can only facilitate the passive...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "protons", "crystal", "structure", "condensed", "matter", "physics", "network", "analysis", "crystallography", "thermodynamics", "computer", "and", "information", "sciences", "solid", "state", "physics", "proteins", "pegylation", "biophysics", "nucleons", "free", "energy"...	2017	Molecular determinants for the thermodynamic and functional divergence of uniporter GLUT1 and proton symporter XylE
Martinotti cells are the most prominent distal dendrite–targeting interneurons in the cortex , but their role in controlling pyramidal cell ( PC ) activity is largely unknown . Here , we show that the nicotinic acetylcholine receptor α2 subunit ( Chrna2 ) specifically marks layer 5 ( L5 ) Martinotti cells projecting to...	Cognitive functions and information processing are linked to the coordination of neuronal events and activities . This coordination is achieved through the synchronization of neuronal signals within subnetworks . Local networks contain different types of nerve cells , each of them playing distinct roles in the synchron...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "carbachol", "action", "potentials", "medicine", "and", "health", "sciences", "drugs", "membrane", "potential", "electrophysiology", "light", "neuroscience", "electromagnetic", "radiation", "interneurons", "pharmacology", "neuronal", "dendrites", "nicotinic", "acetylcholine",...	2017	Chrna2-Martinotti Cells Synchronize Layer 5 Type A Pyramidal Cells via Rebound Excitation
Acquisition of cis-regulatory elements is a major driving force of evolution , and there are several examples of developmental enhancers derived from transposable elements ( TEs ) . However , it remains unclear whether one enhancer element could have been produced via cooperation among multiple , yet distinct , TEs dur...	Acquisition of cis-regulatory elements is a major driving force of evolution , but its whole evolutionary significance is poorly understood . Here , we found an unprecedented case in that three TEs cooperatively and synergistically act as a distal enhancer for wnt5a expression in mammalian frontonasal region , being in...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "sequencing", "techniques", "medicine", "and", "health", "sciences", "vertebrates", "animals", "mammals", "palate", "developmental", "biology", "sequence", "motif", "analysis", "mammalian", "genomics", "molecular", "biology", "techniques", "embryos", "digestive", "system"...	2016	Coordinately Co-opted Multiple Transposable Elements Constitute an Enhancer for wnt5a Expression in the Mammalian Secondary Palate
Bartonella spp . are globally distributed bacteria that cause endocarditis in humans and domestic animals . Recent work has suggested bats as zoonotic reservoirs of some human Bartonella infections; however , the ecological and spatiotemporal patterns of infection in bats remain largely unknown . Here we studied the ge...	Bartonella are globally distributed bacteria that can cause endocarditis in humans and domestic animals . Bats have been implicated as a likely reservoir host for these bacteria , but little is known about how prevalence varies over time , routes of transmission , and the genetic diversity of Bartonella in bats . We pr...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biogeography", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "body", "fluids", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "genetics", "vector-borne", "diseases", "microbiology", "vertebrates", "saliv...	2018	Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats
Depletion of synaptic neurotransmitter vesicles induces a form of short term depression in synapses throughout the nervous system . This plasticity affects how synapses filter presynaptic spike trains . The filtering properties of short term depression are often studied using a deterministic synapse model that predicts...	Neurons communicate through electro-chemical connections called synapses . Action potentials in a presynaptic neuron cause neurotransmitter vesicles to release their contents which then bind to nearby receptors on a postsynaptic neuron's membrane , transiently altering its conductance . After it is released , the repla...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "synapses", "computational", "neuroscience", "single", "neuron", "function", "biology", "neuroscience", "neurophysiology", "coding", "mechanisms" ]	2012	Short Term Synaptic Depression Imposes a Frequency Dependent Filter on Synaptic Information Transfer
Chagas disease , caused by the protozoan Trypanosoma cruzi , is the leading cause of heart failure in Latin America . The clinical treatment of Chagas disease is limited to two 60 year-old drugs , nifurtimox and benznidazole , that have variable efficacy against different strains of the parasite and may lead to severe ...	Chagas disease is a parasitic disease caused by the Trypanosoma cruzi . The infection may result in gastrointestinal manifestations and cardiomyopathy . Benznidazole , the current treatment , has limited efficacy and often leads to serious side effects . Aiming to develop new treatments , our group has identified new i...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "cardiovascular", "anatomy", "immunology", "tropical", "diseases", "parasitic", "diseases", "parasitic", "protozoans", "electromagnetic", "radiation", "parasitology", "animal", "models", ...	2017	4-aminopyridyl-based lead compounds targeting CYP51 prevent spontaneous parasite relapse in a chronic model and improve cardiac pathology in an acute model of Trypanosoma cruzi infection
An extensive proteostatic network comprised of molecular chaperones and protein clearance mechanisms functions collectively to preserve the integrity and resiliency of the proteome . The efficacy of this network deteriorates during aging , coinciding with many clinical manifestations , including protein aggregation dis...	Aging is the gradual and progressive decline of vitality . A hallmark of aging is the decay of protective mechanisms that normally preserve the robustness and resiliency of cells and tissues . Proteostasis is the term that applies specifically to those mechanisms that promote stability of the proteome , the collection ...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "cell", "death", "invertebrates", "autophagic", "cell", "death", "rna", "interference", "classical", "mechanics", "caenorhabditis", "gene", "regulation", "regulatory", "proteins", "cell", "processes", "dna-binding", "proteins", "mechanical", "stress", "neuroscience", "ani...	2017	The homeodomain-interacting protein kinase HPK-1 preserves protein homeostasis and longevity through master regulatory control of the HSF-1 chaperone network and TORC1-restricted autophagy in Caenorhabditis elegans
Computational methods attempting to identify instances of cis-regulatory modules ( CRMs ) in the genome face a challenging problem of searching for potentially interacting transcription factor binding sites while knowledge of the specific interactions involved remains limited . Without a comprehensive comparison of the...	Transcriptional regulation involves multiple transcription factors binding to DNA sequences . A limited repertoire of transcription factors performs this complex regulatory step through various spatial and temporal interactions between themselves and their binding sites . These transcription factor binding interactions...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computational", "biology/sequence", "motif", "analysis", "computational", "biology/transcriptional", "regulation", "computational", "biology/comparative", "sequence", "analysis", "computational", "biology/evolutionary", "modeling", "evolutionary", "biology/bioinformatics" ]	2010	Assessing Computational Methods of Cis-Regulatory Module Prediction
Microbial diversity is typically characterized by clustering ribosomal RNA ( SSU-rRNA ) sequences into operational taxonomic units ( OTUs ) . Targeted sequencing of environmental SSU-rRNA markers via PCR may fail to detect OTUs due to biases in priming and amplification . Analysis of shotgun sequenced environmental DNA...	Microorganisms comprise the majority of the biodiversity on the planet . Because the overwhelming majority of microbes are not readily cultured in the laboratory , researchers often rely on PCR-based investigations of genomic sequence to characterize microbial diversity . These analyses have dramatically expanded our u...	[ "Abstract", "Introduction", "Results", "Discussion" ]	[ "microbiology/environmental", "microbiology", "genetics", "and", "genomics/microbial", "evolution", "and", "genomics", "evolutionary", "biology/microbial", "evolution", "and", "genomics", "ecology/marine", "and", "freshwater", "ecology", "computer", "science/applications", "mar...	2011	PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data
Cellular differentiation entails reprogramming of the transcriptome from a pluripotent to a unipotent fate . This process was suggested to coincide with a global increase of repressive heterochromatin , which results in a reduction of transcriptional plasticity and potential . Here we report the dynamics of the transcr...	Epigenetic modifications of DNA and bound histones are major determinants of cell type–specific gene expression patterns . A prevalent model in stem cell biology suggests that the loss of pluripotency entails global increase in heterochromatin and coinciding shutdown of lineage unrelated genes . We performed analysis o...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "developmental", "biology", "cell", "fate", "determination", "stem", "cells", "embryonic", "stem", "cells", "gene", "expression", "genetics", "epigenetics", "biology", "chromatin", "genetics", "and", "genomics", "cell", "differentiation", "dna", "transcription", "histon...	2011	Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells
Erythema nodosum leprosum ( ENL ) is a debilitating multisystem disorder which complicates leprosy . It is characterised by fever , malaise and painful erythematous cutaneous nodules . ENL is often recurrent or chronic in nature and frequently severe . Patients often require prolonged treatment with high doses of oral ...	Erythema nodosum leprosum ( ENL ) is an immunologically mediated complication of leprosy . It is a painful debilitating multi-system condition which can occur before , during or after completion of treatment of the multi-drug therapy for leprosy . ENL is often a chronic condition requiring long-term treatment often wit...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine" ]	2014	The Mortality Associated with Erythema Nodosum Leprosum in Ethiopia: A Retrospective Hospital-Based Study
Deacetylases of the Sir2 family regulate lifespan and response to stress . We have examined the evolutionary history of Sir2 and Hst1 , which arose by gene duplication in budding yeast and which participate in distinct mechanisms of gene repression . In Saccharomyces cerevisiae , Sir2 interacts with the SIR complex to ...	Sir2 deacetylases are found in organisms ranging from bacteria to mammals . Sir2 from the yeast Saccharomyces cerevisiae deacetylates histones and is part of the SIR complex that spreads across chromatin to repress gene expression . A related histone deacetylase , Hst1 , interacts with a DNA–binding protein , Sum1 , to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/molecular", "evolution", "molecular", "biology/chromatin", "structure" ]	2009	The Sir2-Sum1 Complex Represses Transcription Using Both Promoter-Specific and Long-Range Mechanisms to Regulate Cell Identity and Sexual Cycle in the Yeast Kluyveromyces lactis
The family Flaviviridae includes viruses that have different virion structures and morphogenesis mechanisms . Most cellular and molecular studies have been so far performed with viruses of the Hepacivirus and Flavivirus genera . Here , we studied bovine viral diarrhea virus ( BVDV ) , a member of the Pestivirus genus ....	Bovine viral diarrhea virus ( BVDV ) is the etiologic agent of mucosal disease and bovine viral diarrhea , two economically important diseases of the livestock . BVDV is a member of the Pestivirus genus in the Flaviviridae family , which also includes Hepacivirus and Flavivirus genera . Members of this family share sim...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "and", "health", "sciences", "vesicles", "pathology", "and", "laboratory", "medicine", "hepacivirus", "pathogens", "microbiology", "viral", "structure", "electron", "cryo-microscopy", "viruses", "rna", "viruses", "microscopy", "cellular", "structures", "and", ...	2016	Morphology and Molecular Composition of Purified Bovine Viral Diarrhea Virus Envelope
Recent whole genome polymerase binding assays in the Drosophila embryo have shown that a substantial proportion of uninduced genes have pre-assembled RNA polymerase-II transcription initiation complex ( PIC ) bound to their promoters . These constitute a subset of promoter proximally paused genes for which mRNA elongat...	Gene activation is an inherently random process because numerous diffusing proteins and DNA must first interact by random association before transcription can begin . For many genes the necessary protein–DNA associations only begin after activation , but it has recently been noted that a large class of genes in multice...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "computational", "biology/transcriptional", "regulation", "genetics", "and", "genomics/gene", "expression", "biophysics/theory", "and", "simulation", "biochemistry/theory", "and", "simulation", "biochemistry/transcription", "and", "translation", "mathematics/statistics", "biophysic...	2011	Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability
Peroxisomes are subcellular organelles involved in lipid metabolic processes , including those of very-long-chain fatty acids and branched-chain fatty acids , among others . Peroxisome matrix proteins are synthesized in the cytoplasm . Targeting signals ( PTS or peroxisomal targeting signal ) at the C-terminus ( PTS1 )...	Peroxisomes are subcellular organelles that are present in almost all eukaryotic cells . The syllables “per-oxi” reflect the oxidative functions of these single-membrane-bound organelles in various metabolic processes , including those of very-long-chain fatty acids and branched-chain fatty acids . In an earlier study ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "medicine", "urology", "medicinal", "chemistry", "anatomy", "and", "physiology", "chemical", "biology", "histology", "model", "organisms", "chemistry", "biology", "chromatography", "metabolic", "disorders", "biochemistry", "physiology", "genetics", "molecular", "cell", "b...	2013	Tysnd1 Deficiency in Mice Interferes with the Peroxisomal Localization of PTS2 Enzymes, Causing Lipid Metabolic Abnormalities and Male Infertility
Epstein-Barr virus ( EBV ) , a lymphomagenic human herpesvirus , colonises the host through polyclonal B cell-growth-transforming infections yet establishes persistence only in IgD+ CD27+ non-switched memory ( NSM ) and IgD− CD27+ switched memory ( SM ) B cells , not in IgD+ CD27− naïve ( N ) cells . How this selectivi...	Epstein-Barr virus ( EBV ) , a growth-transforming virus linked to several B cell lymphomas in man , is usually carried as an asymptomatic latent infection in B lymphocytes . Such virus carriage selectively involves memory , but not naive , B cells . How this selectivity is achieved is poorly understood since we find t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology", "immunology", "biology", "microbiology" ]	2012	Epstein-Barr Virus Infection of Naïve B Cells In Vitro Frequently Selects Clones with Mutated Immunoglobulin Genotypes: Implications for Virus Biology

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