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Enterococcus faecalis BM4518 is resistant to vancomycin by synthesis of peptidoglycan precursors ending in D-alanyl-D-serine . In the chromosomal vanG locus , transcription of the resistance genes from the PYG resistance promoter is inducible and , upstream from these genes , there is an unusual three-component regulat...	Various modes of gene regulation coexist in cells . One corresponds to the “switch on/ off” mechanism in which the regulator induces the promoter to a defined level . In another mechanism , the regulator activates the promoter to various levels according to the intensity or the nature of an input signal . In this study...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Competition between VanUG Repressor and VanRG Activator Leads to Rheostatic Control of vanG Vancomycin Resistance Operon Expression
Although invasive cytomegalovirus ( CMV ) disease is uncommon in the era of antiretroviral therapy ( ART ) , asymptomatic CMV coinfection is nearly ubiquitous in HIV infected individuals . While microbial translocation and gut epithelial barrier dysfunction may promote persistent immune activation in treated HIV infect...	Intestinal epithelial barrier dysfunction is a well-known consequence of HIV infection that persists in spite of ART . The underlying mechanisms by which HIV perturbs intestinal epithelial junctions remain unclear , and the impact of opportunistic viral pathogens in the gut has not been fully appreciated . HIV-infected...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "cell", "physiology", "hiv", "infections", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "biopsy", "antiviral", "therapy", "pathogens", "immunology", "junctional", "complexes", "microbiology", "surgical", "and", "invasive", "medi...	2017	Replication of CMV in the gut of HIV-infected individuals and epithelial barrier dysfunction
Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid phase separation ( LLPS ) . However , many proteins involved in this phase separation are at least partially disordered . The molecular mechanism and the sequen...	Liquid liquid phase separation ( LLPS ) of low-complexity protein sequences has emerged as an important research topic due to its relevance to membraneless organelles and intracellular compartmentalization . However a molecular level understanding of LLPS cannot be easily obtained by experimental methods due to difficu...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "sequencing", "techniques", "protein", "interactions", "enzymes", "electricity", "enzymology", "simulation", "and", "modeling", "electrostatics", "phase", "diagrams", "molecular", "biology", "techniques", "intrinsically", "disordered", "proteins", "research", "and", "analys...	2018	Sequence determinants of protein phase behavior from a coarse-grained model
The Kaposi sarcoma associated herpesvirus ( KSHV ) genome encodes more than 85 open reading frames ( ORFs ) . Serological evaluation of KSHV infection now generally relies on reactivity to just one latent and/or one lytic protein ( commonly ORF73 and K8 . 1 ) . Most of the other polypeptides encoded by the virus have u...	Kaposi sarcoma-associated herpesvirus ( KSHV ) is the cause of Kaposi sarcoma , primary effusion lymphoma and a form of multicentric Castleman's disease , affecting mainly persons with HIV , other immunosuppressed patients and elderly men . Such diseases are most common where KSHV prevalence is high , in sub-Saharan Af...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunodeficiency", "viruses", "infectious", "diseases", "medicine", "and", "health", "sciences", "diagnostic", "medicine", "pathology", "and", "laboratory", "medicine", "immunity", "medical", "microbiology", "hiv", "viral", "pathogens", "virology", "microbial", "pathogen...	2014	Heterogeneity and Breadth of Host Antibody Response to KSHV Infection Demonstrated by Systematic Analysis of the KSHV Proteome
Modelling ionic channels represents a fundamental step towards developing biologically detailed neuron models . Until recently , the voltage-gated ion channels have been mainly modelled according to the formalism introduced by the seminal works of Hodgkin and Huxley ( HH ) . However , following the continuing achieveme...	A unifying novel kinetic model of human voltage-gated sodium channels is proposed , which is able to reproduce in detail the macroscopic currents of all the ion-channel isomers , from NaV1 . 1 to NaV1 . 9 . Its topology consists of six states ( two closed , two open , two inactivated ) and twelve transitions , and it i...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "action", "potentials", "chemical", "compounds", "markov", "models", "membrane", "potential", "electrophysiology", "neuroscience", "isomerism", "ion", "channels", "mathematics", "sodium", "channels", "isomers", "animal", "cells", ...	2017	A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms
Methods to determine blood-meal sources of hematophagous Triatominae bugs ( Chagas disease vectors ) are serological or based on PCR employing species-specific primers or heteroduplex analysis , but these are expensive , inaccurate , or problematic when the insect has fed on more than one species . To solve those probl...	Chagas disease is one of the most important tropical diseases in America . This disease is caused by the parasite Trypanosoma cruzi and transmitted through the feces of blood-sucking insects known as triatomines . Different species of insects have different habits and food sources that confer variable degrees of epidem...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "neglected", "tropical", "diseases" ]	2012	High-Resolution Melting (HRM) of the Cytochrome B Gene: A Powerful Approach to Identify Blood-Meal Sources in Chagas Disease Vectors
Proteases have been implicated in a variety of developmental processes during the malaria parasite lifecycle . In particular , invasion and egress of the parasite from the infected hepatocyte and erythrocyte , critically depend on protease activity . Although falcipain-1 was the first cysteine protease to be characteri...	Malaria affects hundreds of millions of people and is the cause of hundreds of thousands of deaths each year . Infection begins with the inoculation of sporozoites into the skin during the bite of an infected mosquito . Sporozoites subsequently travel to the liver , where they invade and replicate in hepatocytes , even...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "medicine", "and", "health", "sciences", "parasite", "groups", "body", "fluids", "cloning", "parasitic", "diseases", "parasitic", "protozoans", "parasitology", "parasitemia", "apicomplexa", "protozoans", "red", "blood", "cells", "molecular", "biology",...	2017	Deletion of the rodent malaria ortholog for falcipain-1 highlights differences between hepatic and blood stage merozoites
Mirtrons are microRNA ( miRNA ) substrates that utilize the splicing machinery to bypass the necessity of Drosha cleavage for their biogenesis . Expanding our recent efforts for mammalian mirtron annotation , we use meta-analysis of aggregate datasets to identify ~500 novel mouse and human introns that confidently gene...	Bulk miRNAs in most animal cells derive from cleavage of hairpin precursor transcripts by the Drosha and Dicer RNase III enzymes . A variety of non-canonical miRNA biogenesis strategies are known , including "mirtrons" for which splicing substitutes for Drosha . However , as non-canonical miRNAs usually account for a m...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Analysis of Nearly One Thousand Mammalian Mirtrons Reveals Novel Features of Dicer Substrates
Persistent infection of basal keratinocytes with high-risk human papillomavirus ( hrHPV ) may cause cancer . Keratinocytes are equipped with different pattern recognition receptors ( PRRs ) but hrHPV has developed ways to dampen their signals resulting in minimal inflammation and evasion of host immunity for sustained ...	A persistent infection with high-risk human papillomavirus ( hrHPV ) may cause cancer . Whereas keratinocytes – the cells infected by hrHPV – are equipped with different receptors allowing them to recognize invading pathogens and to activate the immune system , hrHPV has developed ways to evade the host's immune respon...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "signal", "transduction", "viral", "immune", "evasion", "immunity", "viral", "persistence", "and", "latency", "virology", "innate", "immunity", "gene", "expression", "immunology", "immune", "suppression", "biology", "microbiology", "molecular", "cell", "biology", "immun...	2013	Human Papillomavirus (HPV) Upregulates the Cellular Deubiquitinase UCHL1 to Suppress the Keratinocyte's Innate Immune Response
Cox regression is commonly used to predict the outcome by the time to an event of interest and in addition , identify relevant features for survival analysis in cancer genomics . Due to the high-dimensionality of high-throughput genomic data , existing Cox models trained on any particular dataset usually generalize poo...	Network-based computational models are attracting increasing attention in studying cancer genomics because molecular networks provide valuable information on the functional organizations of molecules in cells . Survival analysis mostly with the Cox proportional hazard model is widely used to predict or correlate gene e...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microarrays", "systems", "biology", "genomics", "functional", "genomics", "mathematics", "statistics", "biology", "computational", "biology", "statistical", "methods" ]	2013	Network-based Survival Analysis Reveals Subnetwork Signatures for Predicting Outcomes of Ovarian Cancer Treatment
It is well established that the variability of the neural activity across trials , as measured by the Fano factor , is elevated . This fact poses limits on information encoding by the neural activity . However , a series of recent neurophysiological experiments have changed this traditional view . Single cell recording...	To understand how neurons encode information , neuroscientists record their firing activity while the animal executes a given task for many trials . Surprisingly , it has been found that the neural response is highly variable , which a priori limits the encoding of information by these neurons . However , recent experi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology", "neuroscience" ]	2012	Neural Network Mechanisms Underlying Stimulus Driven Variability Reduction
The matrix ( M ) proteins of rhabdoviruses are multifunctional proteins essential for virus maturation and budding that also regulate the expression of viral and host proteins . We have solved the structures of M from the vesicular stomatitis virus serotype New Jersey ( genus: Vesiculovirus ) and from Lagos bat virus (...	Rhabdoviruses are of considerable socioeconomic importance . For example , rabies virus causes lethal encephalitis resulting in approximately 50 , 000 human deaths per year . Rhabdoviruses infect cells and propagate despite having small genomes that encode only five multifunctional proteins . One of these , the matrix ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "virology/virion", "structure,", "assembly,", "and", "egress", "infectious", "diseases/neglected", "tropical", "diseases", "biophysics/macromolecular", "assemblies", "and", "machines" ]	2008	Rhabdovirus Matrix Protein Structures Reveal a Novel Mode of Self-Association
The human pathogen Haemophilus influenzae has the ability to quickly adapt to different host environments through phase variation of multiple structures on its lipooligosaccharide ( LPS ) , including phosphorylcholine ( ChoP ) . During colonization with H . influenzae , there is a selection for ChoP+ phase variants . I...	The bacterial pathogen Haemophilus influenzae evades immune responses during colonization in its human host . Decoration of the bacterial surface with different structures is one way that Haemophilus avoids host recognition . In this study , we show that the attachment of the small molecule phosphorylcholine , or ChoP ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "immunity", "immunology", "biology", "microbiology", "bacterial", "pathogens" ]	2012	Phosphorylcholine Allows for Evasion of Bactericidal Antibody by Haemophilus influenzae
One of the major challenges that developing organs face is scaling , that is , the adjustment of physical proportions during the massive increase in size . Although organ scaling is fundamental for development and function , little is known about the mechanisms that regulate it . Bone superstructures are projections th...	One of the major challenges that developing organs face is scaling , that is , the adjustment of physical proportions during the massive increase in size . Bone superstructures are projections that typically serve for tendon and ligament insertion or articulation . Therefore , superstructure position along the bone is ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Isometric Scaling in Developing Long Bones Is Achieved by an Optimal Epiphyseal Growth Balance
The Human T-Lymphotropic Virus type 1c subtype ( HTLV-1c ) is highly endemic to central Australia where the most frequent complication of HTLV-1 infection in Indigenous Australians is bronchiectasis . We carried out a prospective study to quantify the prognosis of HTLV-1c infection and chronic lung disease and the risk...	The Human T-Lymphotropic Virus type 1 ( HTLV-1 ) infects up to 20 million people worldwide who predominantly reside in resource-limited areas . The virus is associated with a haematological malignancy ( adult T-cell leukaemia/lymphoma , ATL ) , and inflammatory diseases involving organ systems including the spinal cord...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "death", "rates", "blood", "cells", "inflammatory", "diseases", "medicine", "and", "health", "sciences", "body", "fluids", "immune", "cells", "pathology", "and", "laboratory", "medicine", "respiratory", "infections", "pathogens", "immunology", "microbiology", "diet", ...	2018	Human T-Lymphotropic Virus type 1c subtype proviral loads, chronic lung disease and survival in a prospective cohort of Indigenous Australians
INT6/eIF3e is a highly conserved component of the translation initiation complex that interacts with both the 26S proteasome and the COP9 signalosome , two complexes implicated in ubiquitin-mediated protein degradation . The INT6 gene was originally identified as the insertion site of the mouse mammary tumor virus ( MM...	INT6 is an evolutionarily conserved gene originally identified as the insertion site of the mouse mammary tumor virus that causes tumors in mice . INT6 is downregulated in many human cancers , suggesting that it acts as tumor suppressor gene . The INT6 protein is involved in several biological processes , including tra...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "invertebrates", "rna", "interference", "classical", "mechanics", "anaphase", "chromosome", "structure", "and", "function", "metaphase", "centromeres", "cell", "cycle", "and", "cell", "division", "cell", "processes", "animals", "animal", "models", "drosophila", "melanog...	2017	The Drosophila orthologue of the INT6 onco-protein regulates mitotic microtubule growth and kinetochore structure
There are limited data describing the functional characteristics of HIV-1 specific antibodies in breast milk ( BM ) and their role in breastfeeding transmission . The ability of BM antibodies to bind HIV-1 envelope , neutralize heterologous and autologous viruses and direct antibody-dependent cell cytotoxicity ( ADCC )...	In the absence of intervention , only about one third of infants born to HIV-1 infected mothers who are continuously exposed to maternal breast milk over prolonged periods get infected . This observation raises the possibility that immune factors in infected women play a role in limiting HIV-1 transmission . Identifyin...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "immunology", "biology", "microbiology" ]	2012	HIV-Specific Antibodies Capable of ADCC Are Common in Breastmilk and Are Associated with Reduced Risk of Transmission in Women with High Viral Loads
Plants have evolved a considerable number of intrinsic tolerance strategies to acclimate to ambient temperature increase . However , their molecular mechanisms remain largely obscure . Here we report a DEAD-box RNA helicase , TOGR1 ( Thermotolerant Growth Required1 ) , prerequisite for rice growth themotolerance . Regu...	Global warming is increasingly posing negative impacts on crop productivity . In this study , we report a nucleolar-located RNA helicase TOGR1 for thermotolerant growth in rice . TOGR1 maintains pre-rRNA homeostasis under high temperature by securing a proper pre-rRNA structure via elevating its helicase activity . Its...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "small", "nucleolar", "rnas", "plant", "anatomy", "panicles", "enzymes", "gene", "regulation", "enzymology", "cereal", "crops", "plant", "science", "rice", "model", "organisms", "rna", "helicases", "crops", "seedlings", "cell", "nucleus", "inflorescences", "plants", ...	2016	Nucleolar DEAD-Box RNA Helicase TOGR1 Regulates Thermotolerant Growth as a Pre-rRNA Chaperone in Rice
CD4+ T cells orchestrate the adaptive immune response in vertebrates . While both experimental and modeling work has been conducted to understand the molecular genetic mechanisms involved in CD4+ T cell responses and fate attainment , the dynamic role of intrinsic ( produced by CD4+ T lymphocytes ) versus extrinsic ( p...	CD4+ T cells orchestrate adaptive immune responses in vertebrates . These cells differentiate into several types depending on environmental signals and immunological challenges . Once these cells are committed to a particular fate , they can switch to different cell types , thus exhibiting plasticity that enables the i...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	A Minimal Regulatory Network of Extrinsic and Intrinsic Factors Recovers Observed Patterns of CD4+ T Cell Differentiation and Plasticity
Invasion by infectious pathogens can elicit a range of cytokine responses from host cells . These cytokines provide the initial host defense mechanism . In this report , we demonstrate that TNF-α , a pro-inflammatory cytokine , can be induced by hepatitis C virus ( HCV ) in its host cells in a biphasic manner . The ini...	Hepatitis C virus ( HCV ) patients have increased levels of circulating tumor necrosis factor-α ( TNF-α ) . In this report , we demonstrate that HCV can directly induce the expression of TNF-α in hepatocytes in a biphasic manner via NF-κB . The induction of TNF-α by HCV in the first phase is prompt , requires no HCV ge...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	TNF-α Induced by Hepatitis C Virus via TLR7 and TLR8 in Hepatocytes Supports Interferon Signaling via an Autocrine Mechanism
The wide range of time scales involved in neural excitability and synaptic transmission might lead to ongoing change in the temporal structure of responses to recurring stimulus presentations on a trial-to-trial basis . This is probably the most severe biophysical constraint on putative time-based primitives of stimulu...	The idea that sensory objects are represented by the order in which neurons are recruited in response to stimulus presentation was put forward over a decade ago , largely based on computational biology considerations . While intensively analyzed in simulation studies , the general biological applicability of this highl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "neuroscience/theoretical", "neuroscience", "neuroscience/sensory", "systems" ]	2008	Order-Based Representation in Random Networks of Cortical Neurons
Numerical models for simulating outbreaks of infectious diseases are powerful tools for informing surveillance and control strategy decisions . However , large-scale spatially explicit models can be limited by the amount of computational resources they require , which poses a problem when multiple scenarios need to be ...	Numerical models for simulating the outbreak of infectious disease are powerful tools that can be used to inform policy decisions by simulating outbreaks and control actions . However , they rely on considerable computational power to explore all outcomes and scenarios of interest . Focusing on model types commonly use...	[ "Abstract", "Introduction", "Method", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "ruminants", "applied", "mathematics", "tropical", "diseases", "vertebrates", "parasitic", "diseases", "animals", "mammals", "simulation", "and", "modeling", "algorithms", "kernel", "functions", "farms", "mathematics", "neglected",...	2018	Need for speed: An optimized gridding approach for spatially explicit disease simulations
The signal transduction protein SmTK4 from Schistosoma mansoni belongs to the family of Syk kinases . In vertebrates , Syk kinases are known to play specialized roles in signaling pathways in cells of the hematopoietic system . Although Syk kinases were identified in some invertebrates , their role in this group of ani...	Parasitic blood flukes of the genus Schistosoma cause schistosomiasis , one of the most important infectious diseases for humans and animals worldwide . Besides their medical importance , schistosomes possess unique biological features . Among these is the sexual maturation of the female , which requires a constant pai...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "genetics", "and", "genomics/gene", "discovery", "cell", "biology/cell", "signaling", "developmental", "biology/cell", "differentiation", "infectious", "diseases/helminth", "infections", "genetics", "and", "genomics/gene", "function", ...	2010	The Syk Kinase SmTK4 of Schistosoma mansoni Is Involved in the Regulation of Spermatogenesis and Oogenesis
Frameworks such as BioNetGen , Kappa and Simmune use “reaction rules” to specify biochemical interactions compactly , where each rule specifies a mechanism such as binding or phosphorylation and its structural requirements . Current rule-based models of signaling pathways have tens to hundreds of rules , and these numb...	Signaling in living cells is mediated through a complex network of chemical interactions . Current predictive models of signal pathways have hundreds of reaction rules that specify chemical interactions , and a comprehensive model of a stem cell or cancer cell would be expected to have many more . Visualizations of rul...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "phosphorylation", "linguistics", "enzymes", "enzymology", "social", "sciences", "signaling", "networks", "reactants", "network", "analysis", "computer", "and", "information", "sciences", "syntax", "network", "motifs", "proteins", "chemistry", "grammar", "physics", "bioch...	2017	Automated visualization of rule-based models
Human T-Lymphotropic Virus Type 1 ( HTLV-1 ) infection causes lethal adult T-cell leukemia ( ATL ) and severely debilitating HTLV-associated myelopathy/tropical spastic paraparesis ( HAM/TSP ) in up to 5% of infected adults . HTLV-1 is endemic in parts of Africa and the highest prevalence in West Africa ( 5% ) has been...	Human T-Lymphotropic Virus type 1 ( HTLV-1 ) affects millions of people worldwide . It is very similar to Simian T-Lymphotropic Virus , a virus that circulates in monkeys . HTLV-1 causes a lethal form of leukemia ( Adult T-cell Leukemia ) and a debilitating neurological syndrome ( HTLV-associated myelopathy/tropical sp...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "zoonoses", "global", "health", "neglected", "tropical", "diseases", "viral", "diseases" ]	2012	Molecular Epidemiology of Endemic Human T-Lymphotropic Virus Type 1 in a Rural Community in Guinea-Bissau
Hepatitis C virus ( HCV ) is a major cause of chronic liver disease affecting around 130 million people worldwide . While great progress has been made to define the principle steps of the viral life cycle , detailed knowledge how HCV interacts with its host cells is still limited . To overcome this limitation we conduc...	As obligate intracellular parasites with limited gene coding capacity viruses exploit host cell machineries for the sake of efficient replication and spread . Thus , identification of these cellular machineries and factors is necessary to understand how a given virus achieves efficient replication and eventually causes...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "cell", "biology", "gastroenterology", "and", "hepatology", "biology", "and", "life", "sciences", "molecular", "biology" ]	2015	Identification of HNRNPK as Regulator of Hepatitis C Virus Particle Production
FSD-1 , a designed small ultrafast folder with a ββα fold , has been actively studied in the last few years as a model system for studying protein folding mechanisms and for testing of the accuracy of computational models . The suitability of this protein to describe the folding of naturally occurring α/β proteins has ...	The protein folding process , in which a linear chain of amino acids reaches its biologically active three-dimensional shape , is fundamental to life . Small “ultrafast” folders , proteins that fold in microseconds , have received considerable attention , because these proteins serve as model systems for the folding of...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysics/protein", "folding", "biophysics/experimental", "biophysical", "methods", "biophysics/theory", "and", "simulation" ]	2010	On the Origins of the Weak Folding Cooperativity of a Designed ββα Ultrafast Protein FSD-1
Clonorchiasis is a neglected tropical disease caused by Chinese liver fluke , Clonorchis sinensis infection . C . sinensis is a biological carcinogen causing cholangiocarcinoma in humans . In the mammalian host , C . sinensis newly excysted juveniles ( CsNEJs ) migrate from the duodenum into the bile duct . Bile drives...	We previously reported that Clonorchis sinensis newly excysted juveniles ( CsNEJs ) were chemotactically attracted to bile . However , there is still a paucity of information regarding which components and what concentration of bile induce the chemotactic behavior . Here , we show , among various bile components tested...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "biliary", "system", "invertebrates", "cell", "motility", "medicine", "and", "health", "sciences", "liver", "body", "fluids", "helminths", "gallbladder", "bile", "social", "sciences", "animals", "trematodes", "clonorchis", "sinensis", "chemotaxis", "assay", "animal", ...	2018	Bile acids drive chemotaxis of Clonorchis sinensis juveniles to the bile duct
Drosophila melanogaster Piwi functions within the germline stem cells ( GSCs ) and the somatic niche to regulate GSC self-renewal and differentiation . How Piwi influences GSCs is largely unknown . We uncovered a genetic interaction between Piwi and c-Fos in the somatic niche that influences GSCs . c-Fos is a proto-onc...	The Drosophila melanogaster ovary is consisted of germ cells differentiated from GSCs and ovarian somatic cells that provide structural support to the organ . Piwi is a ribonucleoprotein required for GSC maintenance and differentiation in the Drosophila ovary . Piwi does so by influencing GSC-autonomous mechanisms or t...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "invertebrates", "medicine", "and", "health", "sciences", "reproductive", "system", "3'", "utr", "messenger", "rna", "animals", "cell", "differentiation", "germ", "cells", "animal", "models", "developmental", "biology", "drosophila", "melanogaster", "model", "organisms"...	2016	c-Fos Repression by Piwi Regulates Drosophila Ovarian Germline Formation and Tissue Morphogenesis
Dengue is the commonest arboviral disease of humans . An early and accurate diagnosis of dengue can support clinical management , surveillance and disease control and is central to achieving the World Health Organisation target of a 50% reduction in dengue case mortality by 2020 . 5729 children with fever of <72hrs dur...	Dengue is a very common acute infectious disease in the tropical world . Health care professionals are able to better care for dengue patients if they can make an early diagnosis and make a plan for case management . This current study investigated fever in 5729 children in Vietnam with 3 days or less of fever and iden...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[]	2015	Sensitivity and Specificity of a Novel Classifier for the Early Diagnosis of Dengue
N6-methyladenosine ( m6A ) is the most abundant methylation , existing in >25% of human mRNAs . Exciting recent discoveries indicate the close involvement of m6A in regulating many different aspects of mRNA metabolism and diseases like cancer . However , our current knowledge about how m6A levels are controlled and whe...	The goal of this work is to identify functional significant m6A-regulated genes and m6A-associated diseases from analyzing an extensive collection of MeRIP-seq data . To achieve this , we first developed Deep-m6A , a CNN model for single-base m6A prediction . To our knowledge , this is the first condition-specific sing...	[ "Abstract", "Introduction", "Result", "Discussion", "Methods", "and", "materials" ]	[ "genetic", "networks", "rna", "sequences", "gene", "regulation", "protein", "interaction", "networks", "methylation", "network", "analysis", "sequence", "motif", "analysis", "research", "and", "analysis", "methods", "sequence", "analysis", "computer", "and", "informatio...	2019	Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods
The liver plays a key role in removing harmful chemicals from the body and is therefore often the first tissue to suffer potentially adverse consequences . To protect public health it is necessary to quantitatively estimate the risk of long-term low dose exposure to environmental pollutants . Animal testing is the prim...	Virtual tissues are emerging as a powerful tool for computational biology . By encoding known biology into a simulation of tissue function , gaps in knowledge can be identified . As a simulation of tissue function , in silico experiments can be performed inexpensively and rapidly . There are over 6000 chemicals produce...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "oncology", "computer", "science/applications", "computational", "biology/synthetic", "biology", "gastroenterology", "and", "hepatology/hepatology", "biophysics/theory", "and", "simulation", "pathology/histopathology", "pharmacology/drug", "development", "physiology/gastroenterology", ...	2010	Simulating Microdosimetry in a Virtual Hepatic Lobule
A SARS-CoV lacking the full-length E gene ( SARS-CoV-∆E ) was attenuated and an effective vaccine . Here , we show that this mutant virus regained fitness after serial passages in cell culture or in vivo , resulting in the partial duplication of the membrane gene or in the insertion of a new sequence in gene 8a , respe...	Zoonotic coronaviruses , including SARS-CoV , Middle East respiratory syndrome ( MERS-CoV ) , porcine epidemic diarrhea virus ( PEDV ) and swine delta coronavirus ( SDCoV ) have recently emerged causing high morbidity and mortality in human or piglets . No fully protective therapy is still available for these CoVs . Th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Identification of the Mechanisms Causing Reversion to Virulence in an Attenuated SARS-CoV for the Design of a Genetically Stable Vaccine
Dengue is an emerging health problem in several coastlines along the Red Sea . The objective of the present work is to elucidate spatial and temporal patterns of dengue transmission in Port Sudan . A longitudinal study with three cross-sectional surveys was carried out in upper , middle and lower class neighborhoods , ...	Dengue is a tropical infectious disease that is of emerging global importance . As a dengue vaccine is still a distant prospect , descriptive epidemiological studies are a vital tool for developing a surveillance system capable of preventing dengue outbreaks . In the current work , the investigators describe epidemiolo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "infectious", "diseases", "public", "health", "and", "epidemiology", "survey", "methods", "entomology", "epidemiology", "infectious", "disease", "epidemiology", "dengue", "fever", "neglected", "tropical", "diseases", "biology", "zoology" ]	2012	Spatial and Temporal Patterns of Dengue Transmission along a Red Sea Coastline: A Longitudinal Entomological and Serological Survey in Port Sudan City
Suppressor of cytokine signalling 3 ( SOCS3 ) negatively regulates STAT3 activation in response to several cytokines such as those in the gp130-containing IL-6 receptor family . Thus , SOCS3 may play a major role in immune responses to pathogens . In the present study , the role of SOCS3 in M . tuberculosis infection w...	Tuberculosis is a severe disease caused by infection with the intracellular bacteria Mycobacterium tuberculosis . The protein “suppressor of cytokine signalling 3” ( SOCS3 ) inhibits the responses of cells to several cytokines and growth factors that signal via the STAT3 transcription factor . Since STAT3 is a major co...	[ "Abstract", "Introduction", "Results", "Discussion", "Material", "and", "Methods" ]	[ "immunity", "immunity", "to", "infections", "immune", "defense", "immunology", "biology", "immunomodulation" ]	2013	Critical and Independent Role for SOCS3 in Either Myeloid or T Cells in Resistance to Mycobacterium tuberculosis
Array-based comparative genomic hybridization ( Array-CGH ) is an important technology in molecular biology for the detection of DNA copy number polymorphisms between closely related genomes . Hidden Markov Models ( HMMs ) are popular tools for the analysis of Array-CGH data , but current methods are only based on firs...	Array-based comparative genomics is a standard approach for the identification of DNA copy number polymorphisms between closely related genomes . The huge amounts of data produced by these experiments require efficient and accurate bioinformatics tools for the identification of copy number polymorphisms . Hidden Markov...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results/Discussion" ]	[ "algorithms", "computer", "science", "model", "organisms", "plant", "and", "algal", "models", "plant", "biology", "biology", "computational", "biology" ]	2012	Parsimonious Higher-Order Hidden Markov Models for Improved Array-CGH Analysis with Applications to Arabidopsis thaliana
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics , but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes . Many felid species exhibit polymorphism for melanism b...	Color polymorphism in closely related animal species provides an opportunity to study how the balance between natural selection and genetic drift shapes the evolution of appearance and form . The cat family , Felidae , is especially interesting; 13 of 37 extant species exhibit polymorphism for melanism , but evidence f...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Recurrent Evolution of Melanism in South American Felids
Taenia solium , a pork-borne parasitic zoonosis , is the cause of taeniasis and cysticercosis in humans . In Vietnam , poor sanitation , the practice of outdoor defecation and consumption of raw/undercooked pork have been associated with infection/exposure to T . solium in both humans and pigs . The broad-scale geograp...	Taenia solium is a pork-bone zoonotic parasite . Humans acquire taeniasis from consumption of raw/undercooked pork contaminated with T . solium cysticerci . Pigs and humans acquire cysticercosis following consumption of food contaminated with eggs shed from the feces of humans with T . solium taeniasis . In Vietnam , t...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "cross-sectional", "studies", "population", "dynamics", "tropical", "diseases", "geographical", "locations", "vertebrates", "diet", "parasitic", "diseases", "animals", "mammals", "animal", "products", "research", "design", "nutriti...	2018	Spatial distribution of Taenia solium exposure in humans and pigs in the Central Highlands of Vietnam
The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates . However , it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution . We generated genome-wide mRNA and accessible chromatin data from...	The epithelium lining the intestine is an ancient animal tissue that serves as a primary site of nutrient absorption and interaction with microbiota . Its formation and function require complex patterns of gene transcription that vary along the intestine and in specialized intestinal epithelial cell ( IEC ) subtypes . ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "gene", "regulation", "vertebrates", "animals", "animal", "models", "osteichthyes", "model", "organisms", "experimental", "organism", "systems", "sequence", "motif", "analysis", "epigenetics", "mammalian", "genomics", "chromatin", ...	2017	Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells
Extracellular signaling is a mechanism that higher eukaryotes have evolved to facilitate organismal homeostasis . Recent years have seen an emerging interest in the role of secreted microvesicles , termed extracellular vesicles ( EV ) or exosomes in this signaling network . EV contents can be modified by the cell in re...	The role of extracellular vesicles ( EV ) has received considerable attention in recent years . The contents of these cell-derived vesicles have been shown to be modulated upon challenge by a virus or neoplastic transformation , and can influence the behavior of recipient cells . Here we demonstrate that purified EV fr...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "flow", "cytometry", "phosphorylation", "cell", "motility", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "natural", "antisense", "transcripts", "gene", "regulati...	2019	Extracellular vesicles from Kaposi Sarcoma-associated herpesvirus lymphoma induce long-term endothelial cell reprogramming
The goal of training is to produce learning for a range of activities that are typically more general than the training task itself . Despite a century of research , predicting the scope of learning from the content of training has proven extremely difficult , with the same task producing narrowly focused learning stra...	Predicting what humans will learn from a training task , in particular , whether learning will generalize beyond the specifics of the given experience , is of both significant practical and theoretical interest . However , a principled understanding of the relationship between training conditions and learning generaliz...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "experimental", "psychology", "learning", "psychology", "social", "and", "behavioral", "sciences", "cognitive", "psychology", "psychophysics", "sensory", "perception" ]	2014	Task-Specific Response Strategy Selection on the Basis of Recent Training Experience
Multiple Acyl-CoA Dehydrogenase Deficiency ( MADD ) is a severe mitochondrial disorder featuring multi-organ dysfunction . Mutations in either the ETFA , ETFB , and ETFDH genes can cause MADD but very little is known about disease specific mechanisms due to a paucity of animal models . We report a novel zebrafish mutan...	Mitochondrial disorders have multiple genetic causes and are usually associated with severe , multi-organ disease . We report a novel zebrafish model of mitochondrial disease by inactivating the etfa gene . Loss of this gene in humans causes multiple acyl-Co dehydrogenase deficiency ( MADD ) that manifests with brain ,...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "metabolic", "disorders", "biology", "medicine" ]	2013	Multi-organ Abnormalities and mTORC1 Activation in Zebrafish Model of Multiple Acyl-CoA Dehydrogenase Deficiency
In mammals , the synaptonemal complex is a structure required to complete crossover recombination . Although suggested by cytological work , in vivo links between the structural proteins of the synaptonemal complex and the proteins of the recombination process have not previously been made . The central element of the ...	Production of sperm and eggs , also known as gametes , requires a reduction in the number of copies of the genome , from the two found in most cells of the body to the single copy found in gametes . This is a complex process , made even more complex because it is coupled with recombination , a process that is an import...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology/germ", "cells", "cell", "biology", "genetics", "and", "genomics/chromosome", "biology" ]	2009	Mutation of the Mouse Syce1 Gene Disrupts Synapsis and Suggests a Link between Synaptonemal Complex Structural Components and DNA Repair
Ebola virus emerged in West Africa in December 2013 . The high population mobility and poor public health infrastructure in this region led to the development of the largest Ebola virus disease ( EVD ) outbreak to date . On September 26 , 2014 , China dispatched a Mobile Biosafety Level-3 Laboratory ( MBSL-3 Lab ) and ...	A Mobile Biosafety Level-3 Laboratory ( MBSL-3 Lab ) and a well-trained diagnostic team were dispatched to Sierra Leone to assist in Ebola virus disease ( EVD ) diagnosis when the largest outbreak of EVD to date emerged in West Africa in 2014 . This setup allowed for the diagnosis of suspected EVD cases in less than 4 ...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "laboratory", "equipment", "engineering", "and", "technology", "pathogens", "rna", "extraction", "microbiology", "disinfection", "health", "care", "viruses", "preventive", "medicine", ...	2017	Rapid deployment of a mobile biosafety level-3 laboratory in Sierra Leone during the 2014 Ebola virus epidemic
Paramutations represent heritable epigenetic alterations that cause departures from Mendelian inheritance . While the mechanism responsible is largely unknown , recent results in both mouse and maize suggest paramutations are correlated with RNA molecules capable of affecting changes in gene expression patterns . In ma...	Genetics is founded on the principle that heritable changes in genes are caused by mutations and that the regulatory state of gene pairs ( alleles ) is passed on to progeny unchanged . An exception to this rule , paramutations—which reflect the outcome of interactions between alleles—produce changes in gene control tha...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology", "molecular", "biology", "genetics", "and", "genomics" ]	2007	A Novel Snf2 Protein Maintains trans-Generational Regulatory States Established by Paramutation in Maize
Atherosclerosis is the main cause of coronary heart disease and stroke , the two major causes of death in developed society . There is emerging evidence of excess risk of cardiovascular disease at low radiation doses in various occupationally exposed groups receiving small daily radiation doses . Assuming that they are...	Atherosclerosis is the main cause of coronary heart disease and stroke , the two major causes of death in developed society . There is emerging evidence of excess risk of cardiovascular disease in various occupationally exposed groups , exposed to fractionated radiation doses with small doses/fraction . The mechanisms ...	[ "Abstract", "Introduction", "Models", "Results", "Discussion" ]	[ "public", "health", "and", "epidemiology/occupational", "and", "industrial", "medicine", "cardiovascular", "disorders/vascular", "biology", "mathematics", "public", "health", "and", "epidemiology/epidemiology", "cardiovascular", "disorders/coronary", "artery", "disease", "cardi...	2009	A Model of Cardiovascular Disease Giving a Plausible Mechanism for the Effect of Fractionated Low-Dose Ionizing Radiation Exposure
Type I chaperonins are large , double-ring complexes present in bacteria ( GroEL ) , mitochondria ( Hsp60 ) , and chloroplasts ( Cpn60 ) , which are involved in mediating the folding of newly synthesized , translocated , or stress-denatured proteins . In Escherichia coli , GroEL comprises 14 identical subunits and has ...	Chaperonins assist the folding of some nascent and denatured proteins to their native , functional forms . Each chaperonin consists of a pair of protein complexes resembling two stacked toroids; folding occurs inside the toroid cavity . Chaperonins are ubiquitous in both bacteria and more complex nucleated cells , as w...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2011	A Chaperonin Subunit with Unique Structures Is Essential for Folding of a Specific Substrate
Epstein-Barr virus ( EBV ) is a human herpesvirus associated with B-cell and epithelial cell malignancies . EBV lytically infects normal differentiated oral epithelial cells , where it causes a tongue lesion known as oral hairy leukoplakia ( OHL ) in immunosuppressed patients . However , the cellular mechanism ( s ) th...	Lytic EBV infection of differentiated oral epithelial cells results in the release of infectious viral particles and is required for efficient transmission of EBV from host to host . Lytic infection also causes a tongue lesion known as oral hairy leukoplakia ( OHL ) . However , surprisingly little is known in regard to...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Differentiation-Dependent KLF4 Expression Promotes Lytic Epstein-Barr Virus Infection in Epithelial Cells
HTLV-1 orf-I is linked to immune evasion , viral replication and persistence . Examining the orf-I sequence of 160 HTLV-1-infected individuals; we found polymorphism of orf-I that alters the relative amounts of p12 and its cleavage product p8 . Three groups were identified on the basis of p12 and p8 expression: predomi...	HTLV-1 persists despite a vigorous host immune response . We found that polymorphism of HTLV-1 orf-I alter the relative amounts of the p12 precursor and its cleavage product p8 , and is associated with differences in blood virus levels in humans , a correlate of disease risk . Reverse genetics in 160 HTLV-1 infected in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "biology", "and", "life", "sciences", "immunology", "medicine", "and", "health", "sciences" ]	2014	Co-dependence of HTLV-1 p12 and p8 Functions in Virus Persistence
Olfactory receptors ( ORs ) , which are involved in odorant recognition , form the largest mammalian protein superfamily . The genomic content of OR genes is considerably reduced in humans , as reflected by the relatively small repertoire size and the high fraction ( ∼55% ) of human pseudogenes . Since several recent l...	Copy-number variants ( CNVs ) are deletions and duplications of DNA segments , responsible for most of the genome variation in mammals . To help elucidate the impact of CNVs on evolution and function , we provide a high-resolution CNV map of the largest gene superfamily in humans , i . e . , the olfactory receptor ( OR...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics", "computational", "biology" ]	2008	High-Resolution Copy-Number Variation Map Reflects Human Olfactory Receptor Diversity and Evolution
Buruli ulcer disease ( BUD ) , caused by Mycobacterium ( M . ) ulcerans , is the third most common mycobacterial disease after tuberculosis and leprosy . BUD causes necrotic skin lesions and is a significant problem for health care in the affected countries . As for other mycobacterial infections , T cell mediated immu...	Buruli ulcer disease ( BUD ) is a devastating skin disease characterised by nodules , plaque or oedema at early stages , which progress to a characteristic form of ulcer . Without treatment the disease can cause broader tissue destruction , affect bones and cause permanent disabilities . BUD is treated with a combinati...	[ "Abstract", "Introduction", "Materials", "and", "methods", "Results", "Discussion" ]	[ "blood", "cells", "antimicrobials", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "body", "fluids", "drugs", "immunology", "microbiology", "p...	2017	Analysis of Mycobacterium ulcerans-specific T-cell cytokines for diagnosis of Buruli ulcer disease and as potential indicator for disease progression
We report a genome-wide assessment of single nucleotide polymorphisms ( SNPs ) and copy number variants ( CNVs ) in schizophrenia . We investigated SNPs using 871 patients and 863 controls , following up the top hits in four independent cohorts comprising 1 , 460 patients and 12 , 995 controls , all of European origin ...	Schizophrenia is a highly heritable disease . While the drugs commonly used to treat schizophrenia offer important relief from some symptoms , other symptoms are not well treated , and the drugs cause serious adverse effects in many individuals . This has fueled intense interest over the years in identifying genetic co...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "genetics", "and", "genomics/genetics", "of", "disease", "genetics", "and", "genomics/complex", "traits", "genetics", "and", "genomics/medical", "genetics" ]	2009	A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia
Trachoma has been endemic in The Gambia for decades . National trachoma control activities have been in place since the mid-1980's , but with no mass antibiotic treatment campaign . We aimed to assess the prevalence of active trachoma and of actual ocular Chlamydia trachomatis infection as measured by polymerase chain ...	Trachoma is the leading infectious cause of blindness worldwide , and is mainly found in tropical and poor countries . It is caused by infection of the eyes with the bacterium Chlamydia trachomatis . However , sometimes the clinical signs of disease can be present without infection being detected . Control efforts invo...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "ophthalmology/eye", "infections", "public", "health", "and", "epidemiology", "infectious", "diseases/neglected", "tropical", "diseases", "public", "health", "and", "epidemiology/epidemiology", "public", "health", "and", "epidemiology/infectious", "d...	2009	Active Trachoma and Ocular Chlamydia trachomatis Infection in Two Gambian Regions: On Course for Elimination by 2020?
The mucosal surface of the intestinal tract represents a major entry route for many microbes . Despite recent progress in the understanding of the IL-21/IL-21R signaling axis in the generation of germinal center B cells , the roles played by this signaling pathway in the context of enteric microbial infections is not w...	Diarrheal diseases still remain the second leading cause of mortality in children younger than 5 years old worldwide , leading to 1 . 3 million deaths per annum . The diarrheagenic Escherichia coli ( DEC ) pathotypes are considered NIAID Biodefense Category B agents . Human infections with enteropathogenic and enterohe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "blood", "cells", "innate", "immune", "system", "medicine", "and", "health", "sciences", "immune", "cells", "immune", "physiology", "cytokines", "pathology", "and", "laboratory", "medicine", "immunology", "animal", "models", "developmental", "biology", "model", "organ...	2019	Interleukin 21 collaborates with interferon-γ for the optimal expression of interferon-stimulated genes and enhances protection against enteric microbial infection
The SUPPRESSOR OF rps4-RLD1 ( SRFR1 ) gene was identified based on enhanced AvrRps4-triggered resistance in the naturally susceptible Arabidopsis accession RLD . No other phenotypic effects were recorded , and the extent of SRFR1 involvement in regulating effector-triggered immunity was unknown . Here we show that muta...	Plants , like humans , have an immune system to defend against disease . This immune system seeks out the presence of disease-causing microbes and other invaders by detecting non-plant molecules and proteins . Plants rely on this surveillance to activate an antimicrobial response of appropriate strength at the right ti...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant-biotic", "interactions", "genetics", "and", "genomics/gene", "discovery", "plant", "biology/plant", "genetics", "and", "gene", "expression" ]	2010	The Arabidopsis Resistance-Like Gene SNC1 Is Activated by Mutations in SRFR1 and Contributes to Resistance to the Bacterial Effector AvrRps4
Rabies has been eliminated from domestic dog populations in Western Europe and North America , but continues to kill many thousands of people throughout Africa and Asia every year . A quantitative understanding of transmission dynamics in domestic dog populations provides critical information to assess whether global e...	Canine rabies has been successfully eliminated from Western Europe and North America , but in the developing world , someone dies every ten minutes from this horrific disease , which is primarily spread by domestic dogs . A quantitative understanding of rabies transmission dynamics in domestic dog populations is crucia...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "infectious", "diseases", "public", "health", "and", "epidemiology", "ecology" ]	2009	Transmission Dynamics and Prospects for the Elimination of Canine Rabies
The malaria agent Plasmodium falciparum is predicted to export a “secretome” of several hundred proteins to remodel the host erythrocyte . Prediction of protein export is based on the presence of an ER-type signal sequence and a downstream Host-Targeting ( HT ) motif ( which is similar to , but distinct from , the clos...	The parasite Plasmodium falciparum causes malaria by replicating inside red blood cells of infected individuals . By exporting many different proteins into the host cell , the parasite changes many of its properties . Knowledge of the identity and function of all the exported proteins will both increase our understandi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genetics", "and", "genomics/genomics", "cell", "biology/membranes", "and", "sorting", "microbiology/parasitology", "infectious", "diseases/protozoal", "infections", "infectious", "diseases/tropical", "and", "travel-associated", "diseases" ]	2008	The Malaria Secretome: From Algorithms to Essential Function in Blood Stage Infection
In Germany , rabies in bats is a notifiable zoonotic disease , which is caused by European bat lyssaviruses type 1 and 2 ( EBLV-1 and 2 ) , and the recently discovered new lyssavirus species Bokeloh bat lyssavirus ( BBLV ) . As the understanding of bat rabies in insectivorous bat species is limited , in addition to rou...	According to the World Health Organization rabies is considered both a neglected zoonotic and a tropical disease . The causative agents are lyssaviruses which have their primary reservoir in bats . Although bat rabies is notifiable in Germany , the number of submitted bats during routine surveillance is rarely represen...	[ "Abstract", "Introduction", "Material", "and", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases", "rabies", "veterinary", "diseases", "zoonoses", "medicine", "and", "health", "sciences", "infectious", "diseases", "of", "the", "nervous", "system", "emerging", "infectious", "diseases", "veterinary", "microbiology", "virology", "emerging", "vi...	2014	Enhanced Passive Bat Rabies Surveillance in Indigenous Bat Species from Germany - A Retrospective Study
Scrub typhus is a mite-borne febrile disease caused by O . tsutsugamushi infection . Recently , emergence of scrub typhus has attracted considerable attention in several endemic countries in Asia and the western Pacific . In addition , the antigenic diversity of the intracellular pathogen has been a serious obstacle fo...	Scrub typhus , caused by Orientia tsutsugamushi infection , is a mite-borne febrile illness endemic in the Asia-Pacific region . Recent emergence and continuous local outbreaks in many of the endemic countries make it a serious public health issue . In addition , the antigenic diversity of the tsa56 gene , encoding a m...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "biogeography", "invertebrates", "typhus", "medicine", "and", "health", "sciences", "ecology", "and", "environmental", "sciences", "pathology", "and", "laboratory", "medicine", "pathogens", "population", "genetics", "geographical", "locations", "microbiology", "animals", ...	2017	Diversification of Orientia tsutsugamushi genotypes by intragenic recombination and their potential expansion in endemic areas
Schlemm's canal ( SC ) plays central roles in ocular physiology . These roles depend on the molecular phenotypes of SC endothelial cells ( SECs ) . Both the specific phenotype of SECs and development of SC remain poorly defined . To allow a modern and extensive analysis of SC and its origins , we developed a new whole-...	Schlemm's canal serves as a drainage tube for fluid from the anterior chamber of the eye and is directly relevant to glaucoma , a disease that causes vision loss in over 70 million people . Aqueous humor enters the canal and then drains into connected veins . Molecular understanding of the development of Schlemm's cana...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "medicine", "and", "health", "sciences", "cell", "biology", "physiology", "ophthalmology", "biology", "and", "life", "sciences" ]	2014	Schlemm's Canal Is a Unique Vessel with a Combination of Blood Vascular and Lymphatic Phenotypes that Forms by a Novel Developmental Process
The glyoxylate bypass allows Escherichia coli to grow on carbon sources with only two carbons by bypassing the loss of carbons as CO2 in the tricarboxylic acid cycle . The flux toward this bypass is regulated by the phosphorylation of the enzyme isocitrate dehydrogenase ( IDH ) by a bifunctional kinase–phosphatase call...	To grow well , the cell needs to produce a balanced set of building blocks by means of its metabolic network . Regulatory circuits are used to maintain appropriate fluxes as metabolites flow through the branching pathways in the network . Here , we asked how such regulatory circuits can work precisely , despite the fac...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "computational", "biology/systems", "biology", "physics/interdisciplinary", "physics" ]	2009	Robustness in Glyoxylate Bypass Regulation
The molecular details of Chlamydia trachomatis binding , entry , and spread are incompletely understood , but heparan sulfate proteoglycans ( HSPGs ) play a role in the initial binding steps . As cell surface HSPGs facilitate the interactions of many growth factors with their receptors , we investigated the role of HSP...	Chlamydia trachomatis is an obligate intracellular bacterium that is an important cause of human disease , including sexually transmitted diseases and acquired blindness in developing countries . The inability to carry out conventional genetic manipulations limits our understanding of the mechanisms of C . trachomatis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "microbial", "pathogens", "biology", "microbiology", "host-pathogen", "interaction", "bacterial", "pathogens", "pathogenesis" ]	2011	Chlamydia trachomatis Co-opts the FGF2 Signaling Pathway to Enhance Infection
Nutritional immunity – the withholding of nutrients by the host – has long been recognised as an important factor that shapes bacterial-host interactions . However , the dynamics of nutrient availability within local host niches during fungal infection are poorly defined . We have combined laser ablation-inductively co...	Microbial pathogens must assimilate essential micronutrients to establish infections . During bacterial infection , mammals limit the availability of micronutrients to inhibit the growth of the pathogen – a phenomenon termed ‘nutrient immunity . ’ Nutrient immunity has not been examined during disseminated candidiasis ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	Fungal Iron Availability during Deep Seated Candidiasis Is Defined by a Complex Interplay Involving Systemic and Local Events
Hydatidosis is a zoonotic disease of worldwide distribution caused by Echinococcus granulosus . Our study aimed to determine the prevalence of human and canine echinococcosis as well as the associated risk factors in a rural area of the Limarí province in northern Chile . A cross-sectional study was conducted between A...	Hydatidosis is a hyperendemic zoonotic disease in Chile caused by the dog tapeworm , Echinococcus granulosus . In Chile as in many other countries in South America , this disease has been largely neglected with few exceptions . Chile's growing economy and the interest of health authorities has lead to an increase in th...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "public", "and", "occupational", "health", "medicine", "and", "health", "sciences", "epidemiology", "parasitology", "biology", "and", "life", "sciences", "tropical", "diseases", "parasitic", "diseases", "veterinary", "science" ]	2014	Prevalence and Risk Factors for Echinococcal Infection in a Rural Area of Northern Chile: A Household-Based Cross-Sectional Study
Polyploidy , a state in which the chromosome complement has undergone an increase , is a major force in evolution . Understanding the consequences of polyploidy has received much attention , and allopolyploids , which result from the union of two different parental genomes , are of particular interest because they must...	Organisms are complex biological systems that must continue to function even as their genomes evolve . While evolution is usually gradual , the formation of new species by the hybridization of different parents—allopolyploidization—occurs nearly instantaneously . A key question is what happens to expression of the two ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome", "expression", "analysis", "mycology", "fungi", "gene", "expression", "genetics", "gene", "regulation", "molecular", "genetics", "biology", "genomics", "evolutionary", "biology", "genomic", "evolution", "microbiology", "computational", "biology", "dna", "transcri...	2014	An Interspecific Fungal Hybrid Reveals Cross-Kingdom Rules for Allopolyploid Gene Expression Patterns
Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria , blurring the boundary between a virus and a cell . Structural studies of Mimivirus have been difficult because of its size and long surface fibers . Here we report the use of enzymatic digestions to remove the su...	Mimiviruses are larger than any other known virus , yet despite their size , the capsid has been shown to be a regular icosahedron . Using cryo-electron microscopy and atomic force microscopy , we show that the icosahedral symmetry is only approximate , in part because one of the 5-fold vertices has a unique “starfish-...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biophysics/macromolecular", "assemblies", "and", "machines", "virology/virion", "structure,", "assembly,", "and", "egress", "virology", "biophysics" ]	2009	Structural Studies of the Giant Mimivirus
The early steps of retrovirus replication leading up to provirus establishment are highly dependent on cellular processes and represent a time when the virus is particularly vulnerable to antivirals and host defense mechanisms . However , the roles played by cellular factors are only partially understood . To identify ...	A genetic screen was used to identify host cell functions important for the replication of retroviruses , including human immunodeficiency viruses . These studies have uncovered a heretofore unexpected role for the cellular sulfonation pathway in an intracellular step of retroviral replication . Through the addition of...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "virology/immunodeficiency", "viruses", "virology", "cell", "biology/cell", "signaling" ]	2008	The Host Cell Sulfonation Pathway Contributes to Retroviral Infection at a Step Coincident with Provirus Establishment
Establishing the general and promoter-specific mechanistic features of gene transcription initiation requires improved understanding of the sequence-dependent structural/dynamic features of promoter DNA . Experimental data suggest that a spontaneous dsDNA strand separation at the transcriptional start site is likely to...	Accessing the information encoded in DNA requires that RNA polymerases recognize the core promoter , a sequence that marks the start of a gene . Statistical analysis of known promoter sequences has failed to reveal a simple code for identifying promoters , leading to the suggestion that promoter DNA is distinguished by...	[ "Abstract", "Introduction", "Methods", "Results/Discussion" ]	[ "computational", "biology/transcriptional", "regulation" ]	2009	Toward a Detailed Description of the Thermally Induced Dynamics of the Core Promoter
Mutualistic cooperation often requires multiple individuals to behave in a coordinated fashion . Hence , while the evolutionary stability of mutualistic cooperation poses no particular theoretical difficulty , its evolutionary emergence faces a chicken and egg problem: an individual cannot benefit from cooperating unle...	Mutualistic behaviours wherein several individuals act together for a common benefit , such as a collective hunt , are often deemed of minor interest by theoreticians in evolutionary biology . These behaviours benefit all the individuals involved , and therefore , so the argument goes , their evolution is straightforwa...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "ecology", "and", "environmental", "sciences", "engineering", "and", "technology", "predator-prey", "dynamics", "applied", "mathematics", "population", "dynamics", "robotic", "behavior", "simulation", "and", "modeling", "algorithms", "evolutionary", "computation", "mathemat...	2016	To Cooperate or Not to Cooperate: Why Behavioural Mechanisms Matter
Most genomes of bacteria contain toxin–antitoxin ( TA ) systems . These gene systems encode a toxic protein and its cognate antitoxin . Upon antitoxin degradation , the toxin induces cell stasis or death . TA systems have been linked with numerous functions , including growth modulation , genome maintenance , and stres...	Most bacteria harbor toxin–antitoxin ( TA ) systems , in which a bacterial toxin is rendered inactive under resting conditions by its antitoxin counterpart . Under conditions of stress , however , the antitoxin is degraded , freeing the toxin to attack its host bacterium . One such TA system , PezAT , has been difficul...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biomacromolecule-ligand", "interactions", "microbial", "metabolism", "streptococci", "small", "molecules", "enzymes", "microbiology", "proteoglycans", "bacterial", "pathogens", "enzyme", "classes", "transferases", "biology", "drug", "discovery", "biochemistry", "glycobiology" ...	2011	A Novel Mechanism of Programmed Cell Death in Bacteria by Toxin–Antitoxin Systems Corrupts Peptidoglycan Synthesis
In yeast , the G1 cyclin Cln3 promotes cell cycle entry by activating the transcription factor SBF . In mammals , there is a parallel system for cell cycle entry in which cyclin dependent kinase ( CDK ) activates transcription factor E2F/Dp . Here we show that Cln3 regulates SBF by at least two different pathways , one...	Cells seem to divide only after they have grown “big enough . ” Entry into the cell cycle , at a point called Start in budding yeast , is triggered by activation of the Cln3 cyclin-dependent kinase ( CDK ) , which in turn activates downstream transcription . We find that the Cln3-CDK acts through a histone deacetylase ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/histone", "modification", "molecular", "biology/transcription", "initiation", "and", "activation", "genetics", "and", "genomics/gene", "expression", "cell", "biology/cell", "growth", "and", "division", "genetics", "and", "genomics/gene", "function", "b...	2009	Recruitment of Cln3 Cyclin to Promoters Controls Cell Cycle Entry via Histone Deacetylase and Other Targets
The prevalence of type 2 diabetes in the United States is projected to double or triple by 2050 . We reasoned that the genes that modulate insulin production might be new targets for diabetes therapeutics . Therefore , we developed an siRNA screening system to identify genes important for the activity of the insulin pr...	Pancreatic beta cells are the only physiologic source of insulin . When these cells are destroyed in type 1 diabetics , there is uncontrolled hyperglycemia from complete insulin deficiency . In type 2 diabetes , these same cells fail to increase insulin secretion to compensate for peripheral insulin resistance leading ...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "diabetic", "endocrinology", "endocrinology", "endocrine", "system", "physiology", "biology", "anatomy", "and", "physiology", "diabetes", "and", "endocrinology", "endocrine", "physiology" ]	2012	An siRNA Screen in Pancreatic Beta Cells Reveals a Role for Gpr27 in Insulin Production
Domestic dog breeds exhibit remarkable morphological variations that result from centuries of artificial selection and breeding . Identifying the genetic changes that contribute to these variations could provide critical insights into the molecular basis of tissue and organismal morphogenesis . Bulldogs , French Bulldo...	Some dog breeds are characterized by extreme morphological differences from their ancestor , the wolf . One group of three breeds ( Bulldog , French Bulldog and Boston Terrier ) is characterized by a wide head , short muzzle , widely spaced eyes , small size and abnormalities of the vertebral bones of the back and tail...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "phosphorylation", "animal", "types", "medicine", "and", "health", "sciences", "spine", "vertebrates", "pets", "and", "companion", "animals", "animals", "mammals", "dogs", "mutation", "vertebrae", "animal", "anatomy", "skeleton", "mammalian", "genomics", "frameshift", ...	2018	Whole genome variant association across 100 dogs identifies a frame shift mutation in DISHEVELLED 2 which contributes to Robinow-like syndrome in Bulldogs and related screw tail dog breeds
Endogenous retroviruses ( ERVs ) arise from retroviruses chromosomally integrated in the host germline . ERVs are common in vertebrate genomes and provide a valuable fossil record of past retroviral infections to investigate the biology and evolution of retroviruses over a deep time scale , including cross-species tran...	The cross-species transmission of viruses poses a continuous threat to public health . Bats are increasingly recognized as a major reservoir for zoonotic RNA viruses , including rabies , Ebola , and possibly MERS , but little is known about their capacity to harbor and transmit retroviruses . Here we investigated past ...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[]	2015	Cross-Species Transmission and Differential Fate of an Endogenous Retrovirus in Three Mammal Lineages
The digenetic trematode Schistosoma mansoni is a human parasite that uses the mollusc Biomphalaria glabrata as intermediate host . Specific S . mansoni strains can infect efficiently only certain B . glabrata strains ( compatible strain ) while others are incompatible . Strain-specific differences in transcription of a...	Schistosoma mansoni is a parasitic worm and agent of a disease that causes a considerable economic burden in African and South American countries . The propagation of the parasite requires passage through a freshwater snail of Biomphalaria genus . In the field , actually very few snails are infected . This is due to th...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "biology" ]	2013	Schistosoma mansoni Mucin Gene (SmPoMuc) Expression: Epigenetic Control to Shape Adaptation to a New Host
During a dengue outbreak on the Caribbean island Aruba , highly elevated levels of ferritin were detected in dengue virus infected patients . Ferritin is an acute-phase reactant and hyperferritinaemia is a hallmark of diseases caused by extensive immune activation , such as haemophagocytic lymphohistiocytosis . The aim...	Ferritin is an acute-phase reactant and produced by reticulo-endothelial cells in response to inflammation and infection . In general , ferritin levels are increased in inflammatory conditions , but in this study we found that ferritin levels were much higher in dengue virus infected patients than in patients with othe...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "biochemistry", "infectious", "diseases", "medicine", "and", "health", "sciences", "protein", "complexes", "human", "ferritin", "proteins", "dengue", "fever", "ferritin", "biology", "and", "life", "sciences", "viral", "diseases" ]	2014	Hyperferritinaemia in Dengue Virus Infected Patients Is Associated with Immune Activation and Coagulation Disturbances
In this paper we report a quantitative laser Biospeckle method using VDRL plates to monitor the activity of Trypanosoma cruzi and the calibration conditions including three image processing algorithms and three programs ( ImageJ and two programs designed in this work ) . Benznidazole was used as a test drug . Variable ...	Biospeckle refers to a pattern that occurs when a laser beam illuminates a dynamic surface , such as a liquid that contains microorganisms . The movement or the roughness of its surface causes the wave fronts to interfere and produce a pattern of moving dots that resemble boiling water . This research describes the app...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion", "Conclusions" ]	[ "medicine", "and", "health", "sciences", "engineering", "and", "technology", "signal", "processing", "applied", "mathematics", "lasers", "microbiology", "parasitic", "diseases", "protozoan", "life", "cycles", "parasitic", "protozoans", "drug", "screening", "simulation", ...	2016	Quantitative Laser Biospeckle Method for the Evaluation of the Activity of Trypanosoma cruzi Using VDRL Plates and Digital Analysis
In sub-Saharan Africa , non-typhoidal Salmonella ( NTS ) are emerging as a prominent cause of invasive disease ( bacteremia and focal infections such as meningitis ) in infants and young children . Importantly , including data from Mali , three serovars , Salmonella enterica serovar Typhimurium , Salmonella Enteritidis...	The genus Salmonella has more than 2500 serological variants ( serovars ) , such as Salmonella enterica serovar Typhi and Salmonella Paratyphi A and B , that cause , respectively , typhoid and paratyphoid fevers ( enteric fevers ) , and a large number of non-typhoidal Salmonella ( NTS ) serovars that cause gastroenteri...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "infectious", "diseases/bacterial", "infections", "infectious", "diseases/neglected", "tropical", "diseases", "infectious", "diseases", "infectious", "diseases/epidemiology", "and", "control", "of", "infectious", "diseases" ]	2010	Identification by PCR of Non-typhoidal Salmonella enterica Serovars Associated with Invasive Infections among Febrile Patients in Mali
The corn smut fungus Ustilago maydis requires the unfolded protein response ( UPR ) to maintain homeostasis of the endoplasmic reticulum ( ER ) during the biotrophic interaction with its host plant Zea mays ( maize ) . Crosstalk between the UPR and pathways controlling pathogenic development is mediated by protein-prot...	Biotrophic pathogens establish compatible interactions with their host to cause disease . A critical step in this process is the suppression of plant defense responses by secreted effector proteins . In the maize infecting fungus Ustilago maydis expression of effector encoding genes is coordinately upregulated at defin...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "medicine", "and", "health", "sciences", "ustilago", "maydis", "pathology", "and", "laboratory", "medicine", "fungal", "genetics", "pathogens", "plant", "physiology", "fungi", "plant", "science", "model", "organisms", "experimental", "organism", "systems", "plant", "p...	2019	Signal peptide peptidase activity connects the unfolded protein response to plant defense suppression by Ustilago maydis
Transposable elements represent a large proportion of the eukaryotic genomes . Long Terminal Repeat ( LTR ) retrotransposons are very abundant and constitute the predominant family of transposable elements in plants . Recent studies have identified chromoviruses to be a widely distributed lineage of Gypsy elements . Th...	In contrast to animals , where germline differentiation initiates early in embryogenesis , germline differentiation in plants starts in the adult phase during reproductive development . Transpositions of transposable elements in both somatic and gametic cells can be transmitted to the next generation . As a result , pl...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "plant", "biology/plant", "genomes", "and", "evolution", "genetics", "and", "genomics/plant", "genomes", "and", "evolution", "genetics", "and", "genomics/epigenetics", "plant", "biology/plant", "genetics", "and", "gene", "expression", "genetics", "and", "genomics/plant", ...	2010	Derepression of the Plant Chromovirus LORE1 Induces Germline Transposition in Regenerated Plants
The majority of the heritability of coronary artery disease ( CAD ) remains unexplained , despite recent successes of genome-wide association studies ( GWAS ) in identifying novel susceptibility loci . Integrating functional genomic data from a variety of sources with a large-scale meta-analysis of CAD GWAS may facilit...	Sudden death due to heart attack ranks among the top causes of death in the world , and family studies have shown that genetics has a substantial effect on heart disease risk . Recent studies suggest that multiple genetic factors each with modest effects are necessary for the development of CAD , but the genes and mole...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "systems", "biology", "genomics", "gene", "regulatory", "networks", "genome", "analysis", "genetics", "biology", "and", "life", "sciences", "computational", "biology", "genetics", "of", "disease", "human", "genetics" ]	2014	Integrative Genomics Reveals Novel Molecular Pathways and Gene Networks for Coronary Artery Disease
TRIM proteins play important roles in the innate immune defense against retroviral infection , including human immunodeficiency virus type-1 ( HIV-1 ) . Rhesus macaque TRIM5α ( TRIM5αrh ) targets the HIV-1 capsid and blocks infection at an early post-entry stage , prior to reverse transcription . Studies have shown tha...	The cellular protein TRIM5α is a host cell restriction factor that blocks HIV-1 infection in Rhesus macaque cells by targeting the viral capsid . Here , we show that direct binding of a TRIM5α protein , consisting of the coiled-coil and B30 . 2/SPRY domains , to the viral capsid results in disruption of the surface lat...	[ "Abstract", "Introduction", "Results", "and", "Discussion", "Materials", "and", "Methods" ]	[ "immunodeficiency", "viruses", "biochemistry", "protein", "interactions", "viral", "core", "proteins", "virology", "macromolecular", "assemblies", "biology", "microbiology", "viral", "structure", "biophysics" ]	2011	Rhesus TRIM5α Disrupts the HIV-1 Capsid at the InterHexamer Interfaces
Infectious complications are a common cause of morbidity and mortality in cancer patients undergoing chemotherapy due to increased risk of oral and gastrointestinal candidiasis , candidemia and septicemia . Interactions between C . albicans and endogenous mucosal bacteria are important in understanding the mechanisms o...	In cancer patients receiving high dose chemotherapy mucosal candidiasis is common and can lead to invasive , systemic fungal infection with mortality ranging 25–30% . We showed that in chemotherapy-immunosuppressed mice C . albicans induces a dysbiotic switch that favors growth of enterococci on mucosal surfaces , part...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "antimicrobials", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "enterococcus", "infections", "pathogens", "drugs", "microbiology", "animal", "models", "bacterial", "diseases", "fungi", "model", "organisms", "tongue", "antibiotics"...	2019	Candida albicans induces mucosal bacterial dysbiosis that promotes invasive infection
Cutaneous leishmaniasis ( CL ) is the most frequent form of leishmaniasis , with 0 . 7 to 1 . 2 million cases per year globally . However , the burden of CL is poorly documented in some regions . We carried out this review to synthesize knowledge on the epidemiological burden of CL in sub-Saharan Africa . We systematic...	Cutaneous leishmaniasis ( CL ) is the most common form of this group of parasitic diseases , transmitted by sandflies . In sub-Saharan Africa , its extent of the problem is unknown , while elsewhere its disfigurement and stigma may cause a severe impact . This study systematically searched the literature to find eviden...	[ "Abstract", "Introduction", "Methods", "Data", "extraction", "and", "synthesis", "Results", "Discussion" ]	[ "dermatology", "medicine", "and", "health", "sciences", "pathology", "and", "laboratory", "medicine", "geographical", "locations", "tropical", "diseases", "sudan", "parasitic", "diseases", "signs", "and", "symptoms", "global", "health", "neglected", "tropical", "disease...	2018	Uncharted territory of the epidemiological burden of cutaneous leishmaniasis in sub-Saharan Africa—A systematic review
DNA double-strand breaks ( DSBs ) represent one of the most deleterious forms of DNA damage to a cell . In cancer therapy , induction of cell death by DNA DSBs by ionizing radiation ( IR ) and certain chemotherapies is thought to mediate the successful elimination of cancer cells . However , cancer cells often evolve t...	Radiation therapy and most chemotherapies elicit cancer cell death through the induction of excessive DNA damage . However , cancer cells can harbor genetic defects that confer resistance to these therapies . To identify cellular components whose targeted therapeutic inactivation could potentially enhance the sensitivi...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "developmental", "biology", "model", "organisms", "genetics", "biology", "molecular", "cell", "biology", "genetics", "and", "genomics", "radiobiology" ]	2012	Ccdc94 Protects Cells from Ionizing Radiation by Inhibiting the Expression of p53
In vivo , antibiotics are often much less efficient than ex vivo and relapses can occur . The reasons for poor in vivo activity are still not completely understood . We have studied the fluoroquinolone antibiotic ciprofloxacin in an animal model for complicated Salmonellosis . High-dose ciprofloxacin treatment efficien...	Antibiotics that are known to kill bacteria in vitro can be less efficacious in vivo . The reasons for this have remained poorly understood . Using a mouse model for Salmonella diarrhea , we found that bacterial persistence occurs in the presence of the antibiotic ciprofloxacin because Salmonella can exist in two diffe...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "computer", "science", "computer", "modeling", "immunology", "population", "biology", "biology", "microbiology" ]	2014	Cecum Lymph Node Dendritic Cells Harbor Slow-Growing Bacteria Phenotypically Tolerant to Antibiotic Treatment
The biophysical nature of the interaction between a transcription factor and its target sequences in vitro is sufficiently well understood to allow for the effects of DNA sequence alterations on affinity to be predicted . But even in relatively simple in vivo systems , the complexities of promoter organization and acti...	A major challenge in molecular genetics has been to understand how cis-regulatory information is integrated to determine the amount of transcript generated . The difficulty has been that there are a large number of variables ( known and unknown ) that combine through an extensive array of possible mechanisms . Differen...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "molecular", "biology/transcription", "initiation", "and", "activation", "computational", "biology/genomics", "computational", "biology/transcriptional", "regulation" ]	2010	The Fitness Landscapes of cis-Acting Binding Sites in Different Promoter and Environmental Contexts
Catalytic loop motions facilitate substrate recognition and binding in many enzymes . While these motions appear to be highly flexible , their functional significance suggests that structure-encoded preferences may play a role in selecting particular mechanisms of motions . We performed an extensive study on a set of e...	Protein loops have critical roles in ligand binding and catalysis . An unresolved issue in this context is the extent to which the intrinsic dynamics of proteins predispose loops to perform their molecular function . In this work , we ( i ) critically examine the structural changes undergone by functional/catalytic loo...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biophysic", "al", "simulations", "biology", "computational", "biology" ]	2012	Coupling between Catalytic Loop Motions and Enzyme Global Dynamics
Candida albicans is a common commensal in the human gut but in predisposed patients it can become an important human fungal pathogen . As a commensal , C . albicans adapts to low-oxygen conditions and represses its hyphal development by the transcription factor Efg1 , which under normoxia activates filamentation . The ...	Candida albicans is an important cause of human disease that occurs if the fungus proliferates strongly on skin surfaces or in several internal organs causing superficial and systemic mycosis . Remarkably , at low cell numbers , C . albicans is also a normal inhabitant of mucosal surfaces and the gut and it is believed...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Hypoxia and Temperature Regulated Morphogenesis in Candida albicans
Despite large vaccination campaigns , measles virus ( MeV ) and canine distemper virus ( CDV ) cause major morbidity and mortality in humans and animals , respectively . The MeV and CDV cell entry system relies on two interacting envelope glycoproteins: the attachment protein ( H ) , consisting of stalk and head domain...	With the ultimate aim to develop pan-morbillivirus fusion inhibitors , we here characterized a potent neutralizing monoclonal antibody . The antibody recognizes the ectodomain of the membrane-bound tetrameric attachment ( H ) protein , which together with the fusion protein and a host cell receptor executes plasma memb...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2015	Sequential Conformational Changes in the Morbillivirus Attachment Protein Initiate the Membrane Fusion Process
Sepsis is characterized by a dysregulated host-pathogen response , leading to high cytokine levels , excessive coagulation and failure to eradicate invasive bacteria . Novel therapeutic strategies that address crucial pathogenetic steps during infection are urgently needed . Here , we describe novel bioactive roles and...	Bacterial infections , especially sepsis , are worldwide a major cause of morbidity and mortality . Sepsis is characterized by an excessive and uncontrolled immune and coagulation response caused by bacteria and bacterial products , which eventually leads to multiple organ failure . Despite supportive treatments and ad...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[]	2013	The TFPI-2 Derived Peptide EDC34 Improves Outcome of Gram-Negative Sepsis
Stochastic channel gating is the major source of intrinsic neuronal noise whose functional consequences at the microcircuit- and network-levels have been only partly explored . A systematic study of this channel noise in large ensembles of biophysically detailed model neurons calls for the availability of fast numerica...	A possible approach to understanding the neuronal bases of the computational properties of the nervous system consists of modelling its basic building blocks , neurons and synapses , and then simulating their collective activity emerging in large networks . In developing such models , a satisfactory description level m...	[ "Abstract", "Introduction", "Materials", "and", "Methods", "Results", "Discussion" ]	[ "neuroscience/theoretical", "neuroscience", "computational", "biology/computational", "neuroscience" ]	2011	Accurate and Fast Simulation of Channel Noise in Conductance-Based Model Neurons by Diffusion Approximation
Mother-to-infant transmission ( MTIT ) of HIV is a serious global health concern , with over 300 , 000 children newly infected in 2011 . SIV infection of rhesus macaques ( RMs ) results in similar rates of MTIT to that of HIV in humans . In contrast , SIV infection of sooty mangabeys ( SMs ) rarely results in MTIT . Th...	Currently 2 . 5 million children are infected with HIV , largely as a result of mother-to-child transmission , and there is no effective vaccine or cure . Studies of Simian Immunodeficiency Virus ( SIV ) infection of nonhuman primate species termed “natural hosts” have shown that mother-to-infant transmission of SIV in...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "medicine", "immune", "cells", "viral", "transmission", "and", "infection", "retrovirology", "and", "hiv", "immunopathogenesis", "immunology", "host-pathogen", "interaction", "microbiology", "animal", "models", "immunodeficiency", "viruses", "mechanisms", "of", "resistance"...	2014	Target Cell Availability, Rather than Breast Milk Factors, Dictates Mother-to-Infant Transmission of SIV in Sooty Mangabeys and Rhesus Macaques
Alternative transcriptional initiation ( ATI ) refers to the frequent observation that one gene has multiple transcription start sites ( TSSs ) . Although this phenomenon is thought to be adaptive , the specific advantage is rarely known . Here , we propose that each gene has one optimal TSS and that ATI arises primari...	Multiple surveys of transcriptional initiation showed that mammalian genes typically have multiple transcription start sites such that transcription is initiated from any one of these sites . Many researchers believe that this phenomenon is adaptive because it allows production of multiple transcripts , from the same g...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "methods" ]	[ "sequencing", "techniques", "ecology", "and", "environmental", "sciences", "gene", "regulation", "dna", "transcription", "gene", "sequencing", "molecular", "biology", "techniques", "rna", "sequencing", "simpson", "index", "research", "and", "analysis", "methods", "ecolo...	2019	Evidence that alternative transcriptional initiation is largely nonadaptive
The ascomycete fungus Tolypocladium inflatum , a pathogen of beetle larvae , is best known as the producer of the immunosuppressant drug cyclosporin . The draft genome of T . inflatum strain NRRL 8044 ( ATCC 34921 ) , the isolate from which cyclosporin was first isolated , is presented along with comparative analyses o...	Tolypocladium inflatum , the fungus from which the immunosuppressant drug cyclosporin was isolated , is a prolific producer of secondary metabolites with potential applications in medicine and agriculture . We have sequenced the first draft reference genome of T . inflatum , which also represents the first genome of a ...	[ "Abstract", "Introduction", "Results/Discussion", "Materials", "and", "Methods" ]	[ "medicine", "biochemistry", "genomics", "drugs", "and", "devices", "chemical", "biology", "chemistry", "microbiology", "biology", "evolutionary", "biology" ]	2013	The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster
Trachoma is widely considered a disease of poverty . Although there are many epidemiological studies linking trachoma to factors normally associated with poverty , formal quantitative data linking trachoma to household economic poverty within endemic communities is very limited . Two hundred people with trachomatous tr...	Trachoma has long been considered a disease of poverty . However , there is surprisingly little direct data that formally quantifies the relationship between trachoma and economic poverty , and none that specifically focuses on trichiasis . We compared 200 people with trachomatous trichiasis ( TT ) to 200 people ( cont...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2015	Trachoma and Relative Poverty: A Case-Control Study
Methods for improving microbial strains for metabolite production remain the subject of constant research . Traditionally , metabolic tuning has been mostly limited to knockouts or overexpression of pathway genes and regulators . In this paper , we establish a new method to control metabolism by inducing optimally tune...	Until recently , engineering of microbial strains has been heavily focused on removing or overexpressing individual genes . Although valuable , these efforts do not take into account the potential benefits of tuning enzymes and , thus , do not exploit the full diversity of available synthetic tools to regulate gene exp...	[ "Abstract", "Introduction", "Results", "Discussion", "Methods" ]	[ "biotechnology", "bioengineering", "biological", "systems", "engineering", "computer", "and", "information", "sciences", "network", "analysis", "engineering", "and", "technology", "synthetic", "biology", "biology", "and", "life", "sciences", "metabolic", "networks", "regu...	2014	Optimizing Metabolite Production Using Periodic Oscillations
Although genetic and non-genetic studies in mouse and human implicate the CD40 pathway in rheumatoid arthritis ( RA ) , there are no approved drugs that inhibit CD40 signaling for clinical care in RA or any other disease . Here , we sought to understand the biological consequences of a CD40 risk variant in RA discovere...	A current challenge in human genetics is to follow-up “hits” from genome-wide association studies ( GWAS ) to guide drug discovery for complex traits . Previously , we identified a common variant in the CD40 locus as associated with risk of rheumatoid arthritis ( RA ) . Here , we fine-map the CD40 signal of association...	[ "Abstract", "Introduction", "Results", "Discussion", "Materials", "and", "Methods" ]	[ "genome-wide", "association", "studies", "medicine", "rheumatoid", "arthritis", "immune", "cells", "genetics", "of", "the", "immune", "system", "b", "cells", "clinical", "immunology", "drug", "research", "and", "development", "drugs", "and", "devices", "genetics", "...	2013	Human Genetics in Rheumatoid Arthritis Guides a High-Throughput Drug Screen of the CD40 Signaling Pathway
Trypanosoma cruzi , the etiological agent of Chagas' disease , presents nutritional requirements for several metabolites . It requires heme for the biosynthesis of several heme-proteins involved in essential metabolic pathways like mitochondrial cytochromes and respiratory complexes , as well as enzymes involved in the...	Trypanosoma cruzi is a protozoan parasite that causes Chagas’ disease , the most common parasitic disease in the Americas , but due to migration movements it has become relevant in non-endemic countries . T . cruzi , as other trypanosomatids responsible for human diseases ( T . brucei and Leishmania spp . ) , lacks the...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[]	2016	The Trypanosoma cruzi Protein TcHTE Is Critical for Heme Uptake
In 2015 , Brazil was faced with the cocirculation of three arboviruses of major public health importance . The emergence of Zika virus ( ZIKV ) presents new challenges to both clinicians and public health authorities . Overlapping clinical features between diseases caused by ZIKV , Dengue ( DENV ) and Chikungunya ( CHI...	Zika virus ( ZIKV ) has been identified in 2015 in Brazil for the first time , causing outbreaks of an illness characterized by skin rash and absent or low grade and short-termed fever . It is difficult to distinguish ZIKV from Dengue ( DENV ) or ( CHIKV ) based on the acute clinical presentation . The virus is closely...	[ "Abstract", "Introduction", "Methods", "Results", "Discussion" ]	[ "medicine", "and", "health", "sciences", "microcephaly", "pathology", "and", "laboratory", "medicine", "togaviruses", "chikungunya", "infection", "pathogens", "geographical", "locations", "microbiology", "tropical", "diseases", "alphaviruses", "viruses", "developmental", "b...	2016	Zika Virus Outbreak in Rio de Janeiro, Brazil: Clinical Characterization, Epidemiological and Virological Aspects

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